References - Shodhgangashodhganga.inflibnet.ac.in/bitstream/10603/13272/12/12_references.… · Amado, RG., Mitsuyasu, RT., Symonds, G. (1999) A phase I trial of autologous CD34p

I References

References

Abounader, R, Montgomery, R, Dietz, H., Laterra, J. (2004) Design and

expression of chimeric U1/ribozyme transgenes. Methods Molecular Biology,

252 :209-219.

Adaichi, A., Glendelman, H.E., Koenig, S., Folks, T., Willey, R, Rabsom, A.,

and Martin, M. (1986). Production of acquired immunodeficiency syndrome

associated retrovirus in human and nonhuman cells transfected with an

infectious molecular clone. Journal of Virology, 59: 284-291.

Akkina, R, Banerjea, A., Bai, J., Anderson, J., Li, M. J. & Rossi, J. J. (2003) Si­

RNAs, ribozymes, and RNA decoys in modeling stem cell based gene

therapy for HIV/AIDS. Anticancer Research, 23:1997-2005.

Amado, RG., Mitsuyasu, RT., Symonds, G. (1999) A phase I trial of

autologous CD34p hematopoietic progenitor cells transduced with an anti­

HIV ribozyme. Human Gene Therapy,10 :2255- 2270.

Andersen, A.A. and Collins,RA. (2000) Rearrangement of a stable RNA

secondary structure during VS ribozyme catalysis. Molecular Cell, 5: 469-478.

Andersen, J.L., DeHart, J.L., Zimmerman, E.S., Ardon, 0., Kim, B., Jacquot, G.

(2006) HIV-1 Vpr-Induced Apoptosis Is Cell Cycle Dependent and Requires

Bax but Not ANT. PLoS Pathogens, 2(12): e127.

Andersen, J.L., Le Rouzic, E., Planelles, V. (2008) HIV-1 Vpr: Mechanisms of

G2 arrest and apoptosis. Experimental and Molecular Pathology, 85: 2-10.

Anderson, J. and Akkina, R (2005). HIV-1 resistance conferred by siRNA

cosuppression of CXCR4 and CCR5 coreceptors by a bi-specific lentiviral

vector. AIDS Research Therapy, 2: 1-12.

149 I P age

I References

Anderson J, Banerjea A, Akkina R(2003a) Bispecific short hairpin siRNA

constructs targeted to CD4, CXCR4, and CCR5 confer HIV -1 resistance.

Oligonucleotides, 13(5):303-312.

Anderson, J., Banerjea, A., and Akkina, R (2003b). Suppression of HIV-l

infection by a stem loop structured anti-CXCR4 siRNA. AIDS Research and

Human Retroviruses, 19: 699-706.

Angers, S. (2006). Molecular architecture and assembly of the DDBI-CUL4A

ubiquitin ligase machinery. Nature, 443: 590-593.

Appaiahgari, M.B., Vrati, S. (2007) DNAzyme-mediated inhibition of Japanese

encephalitis virus replication in mouse brain. Molecular Therapy,15(9):1593-

1599.

Arunagiri, c., Macreadie, I., Hewish, D. and Azad, A. (1997) A C-terminal

domain of HIV-l accessory protein Vpr is involved in penetration,

mitochondrial dysfunction and apoptosis of human CD4+ lymphocytes.

Apoptosis, 2: 69-76.

Bahner, I., Kearns, K., Haq, Q.-L., Smogorzewska, E. M., and Kohn, D. B.

(1996). Transduction of human CD34+ hematopoetic progenitor cells by a

retroviral vector expressing an RRE decoy inhibits human immunodeficiency

virus type I replication in myelomonocytic cells produced in long term

culture. Journal of Virology, 70: 4352-4360.

Bai, J., Gorantala, S., Banda, N., Cagnon, L., Rossi, J., and Akkina R (2002).

Characterisation of anti-CCR5 ribozyme transduced CD34+ hematopoetic

progenitor cells in vitro and in a SCID-hu mouse model in vivo. Molecular

Therapy, 1: 244-254.

150 I P age

I References

Bai, J., Rossi, J., and Akkina, R(200l). Multivalent anti CCR5 ribozymes for

stem cell based HIV type I gene therapy. AIDS Research and Human

Retroviruses, 17: 385-399.

Banerjea, A.C. (2008) Host genes that affect AIDS/HIV progression in India

and novel gene therapeutic approaches against HIV. Indian Journal of

Biochemistry and Biophysics, 45: 141-148.

Banerjea, A.C., Chakraborti, S., Unwalla, H., Goila, R, Shrabani, B., Dash,

B.c., Sriram, B., Paramasivam, N., and Vishwanathan, S. (2005). Potential

therapeutic application of DNA enzymes and siRNAs against viral and

cellular genes. In: Synthetic Nucleic Acids as Inhibitors of Gene Expression:

Mechanisms, Applications, and Therapeutic Implications. L.M. Khachigian,

ed. (CRC Press, Boca Raton, FL), pp. 115-134.

Bano, AS., Gupta, N., Sood, V., Banerjea, A.C. (2007) Vpr from HIV-1

subtypes Band C exhibit significant differences in their ability to transactivate

LTR-mediated gene expression and also in their ability to promote apoptotic

DNA ladder formation. AIDS, 21: 1832-1834.

Bao, P., Wu, Q-J., Yin, P., Jiang, Y., Wang, X., Xie, M-H., Sun, T., Huang, L.,

Mo, D.D., Zhang, Y. (2008) Coordination of two sequential ester-transfer

reactions: exogenous guanosine binding promotes the subsequent G binding

to a group I intron. Nucleic Acids Research, 36(21):6934-6943.

Barre-Sinoussi, F., Chermann, J. c., Rey, F., Nugeyre, M. T., Chamaret, S.,

Gruest, J. (1983). Isolation of a T-lymphotropic retrovirus from a patient at

risk for acquired immune deficiency syndrome (AIDS). Science, 220: 868-871.

Bartz, S.R, Rogel, M.E., Emerman, M. (1996) Human immunodeficiency virus

type 1 cell cycle control: Vpr is cytostatic and mediates G2 accumulation by a

151 I P age

I References

mechanism which differs from DNA damage checkpoint control. Journal of

Virology, 70(4) :2324-2331.

Basu, S., Sriram, S., Goila, Rand Banerjea, A. C. (2000).Targeted cleavage of

HIV-1 coreceptor - CXCR-4 by RNA cleaving DNA-enzyme: Inhibition of

coreceptor function. Antiviral Research, 46: 125-134.

Baum, D.A. and Silverman, S.K(2008) Deoxyribozymes: useful DNA catalysts

in vitro and in vivo. Cellular and Molecular Life Science, 65: 2156 - 2174.

Beigelman, L., McSwiggen,J.A., Draper,KG., Gonzalez,C., Jensen,K,

Karpeisky,A.M., Modak,A.5., Matulic-AdamicJ., DiRenzo, A. B., Haeberli, P.,

Sweedler,D., Tracz, D., Grimm,S., Wincott,F.E.,Thackray,V.G. and Usman,N.

(1995)Chemical Modification of Hammerhead Ribozymes. Journal of

biological chemistry,270( 43): 25702-25708.

Belzile, J.P. (2007). HIV-1 Vpr-mediated G2 arrest involves the DDB1-CUL4A

(VPRBP) E3 ubiquitin ligase. PLoS Pathogen, 3(7): 882-894.

Berger, E. A., Murphy, P. M. and Farber, J. M. (1999) Chemokine receptorsas

HIV -1 coreceptor: Roles in viral entry, tropism, and disease. Annual Review

of Immunology, 17: 657-700.

Berson, J.F., Long, D., Doranz, B.J., Rucker, L Jirik, F.R, Doms, RW. (1996) A

seven-transmembrane domain receptor involved in fusion and entry of T -cell­

tropic human immunodeficiency virus type 1 strains. Journal of Virology, 70:

6288-95.

Bhanja, P., Sengupta, S., Banerjee, B., Sarkar, K, Jana, S., Chakrabarti, S.

(2007) Detection of intersubtype recombinants with respect to env and nef

genes of HIV-1 among female sex workers in Calcutta, India. Virus Research,

130: 310-314.

152 I P age

I References

Bhindi, R, Fahmy, RG., Lowe, H.C, Chesterman, CN., Dass, CR, Cairns,

M.J., Saravolac, E.G., Sun, L.Q. and Khachigian, L.M. (2007) Brothers in Arms

DNA Enzymes, Short Interfering RNA, and the Emerging Wave of Small­

Molecule Nucleic Acid-Based Gene-Silencing Strategies. The American

Journal of Pathology,l71 (4): 1079-1089.

Bikandou, B., Takehisa, J., et aI., (2000) Genetic Subtypes of HIV Type 1 in

Republic of Congo. AIDS Research and Human Retroviruses, 16(7): 613-619.

Blackard, J.T., Renjifo, B., Fawzi, W., Hertzmark, E., Msamanga, G.,

Mwakagile, D., et aI., (2001) HIV-l LTR subtype and perinatal transmission.

Virology, 287 : 261-265.

Bleul, CC, Farzan, M., Choe, H., Parolin, C, Clark-Lewis, I., Sodroski, J.

(1996) The lymphocyte chemoattractant SDF-l is a ligand for LESTR/ fusin

and blocks HIV-l entry. Nature, 382: 829-833.

Bobkov, A.F., Kazennova, E.V., Sukhanova, A.L., Bobkova, M.R, Pokrovsky,

V.V., Zeman, V.V., Kovtunenko, N.G., Erasilova, LB. (2004) An HIV type 1

subtype A outbreak among injecting drug users in Kazakhstan.AIDS Research

and Human Retroviruses, 20(10):1134-1136.

Bogerd, H.P., Wiegand, H.L., Hulme, A.E., Garcia-Perez, J.L., O'Shea, K.S.,

Moran, J.V., Cullen, B.R(2006). Cellular inhibitors of long interspersed

element 1 and Alu retrotransposition. Proceedings of National Academy of

Sciences U. S. A,103: 8780-8785.

BouHamdan, M. (2001) Inhibition of HIV -1 infection by down-regulation of

the CXCR4 co-receptor using an intracellular single chain variable fragment

against CXCR4. Gene Therapy, 8: 408-418.

153 I P age

I References

Bourbigot, S. (2005). The C-terminal domain of the HIV-1 regulatory protein

VPR adopts an anti parallel dime ric structure in solution via its leu cine-zip per­

like domain. Biochemical Journal, 387: 333-341.

Breaker, RR and Joyce, G.F. (1994) A DNA enzyme that cleaves RNA.

Chemical Biology, 1(4): 223-229.

Bukrinsky, M.I., Haffar, O.K.(1998) HIV-1 nuclear import: matrix protein is

back on center stage, this time together with Vpr. Molecular Medicine, 4:138-

143.

Cairns, M.J., Hopkins, T.M., Witherington, c., Wang, L., and Sun, L.Q. (1999).

Target site selection for an RNA-cleaving catalytic DNA. Nature

Biotechnology, 17: 480-486.

Campbell, T. B., McDonald, C. K. and Hagen, M.(1997a) The effect of

structure in a large target RNA on ribozyme cleavage efficiency, Nucleic

Acids Research, 25 (24), 4985.

Campbell, T.B., McDonald, c.K. and Hagen, M. (1997b) The effect of structure

in a large target RNA on ribozyme cleavage efficiency, Nucleic Acids

Research, 25 (24): 4985-4993.

Cassol, S., Weniger, B.G., Babu, P.G., Salminen, M.O., Zheng, X., Htoon, M.T.,

Delaney, A., O'Shaughnessy, M. and Ou, c.y. (1996) Detection of HIV type 1

env subtypes A, B, C, and E in Asia using dried blood spots: a new

surveillance tool for molecular epidemiology. AIDS Research and Human

Retroviruses, 12: 1435-1441.

Carl Woese, 1967 The Genetic Code. New York: Harper and Row

Carmi, N. and Breaker, RR (2001) Characterization of a DNA-cleaving

deoxyribozyme. Bioorganic Medicinal Chemistry, 9: 2589-2600.

154 I P age

- --- - - -----------------------

I References

Cech, T.R (1993) The efficiency and versatility of catalytic RNA: implications

for an RNA world. Gene, 135: 33-36.

Cech, T.R, Zaug, A.J. and Grabowski, P.J. (1981) In vitro splicing of the

ribosomal RNA precursor of tetrahymena :involvement of a guanosine

nucleotide in the excision of the intervening sequence. Cell 27: 487-496.

Chakraborti, S. and Banerjea, A.C (2003a). Identification of cleavage sites in

the HIV-l TAR RNA by 10- 23 and 8-17 catalytic motif containing DNA­

enzymes. Biomacromolecules, 4: 568-571.

Chakraborti, S. and Banerjea, A.C (2003b). Inhibition of HIV -1 replication by

10-23 catalytic motif containing DNA-enzymes targeted against HIV-l TAR

element: potential effectiveness against all HIV -1 isolates. Molecular Therapy,

7: 817-826.

Chan, D.C, Fass, D., Berger, J.M., Kim, P.s.(1997) Core structure of gp41 from

the HIV envelope glycoprotein. Cell, 89(2):263-273.

Chaudhry, A., Verghese, D.A., Das, S.R, Jameel, S., George, A., Bal, V.,

Mayor, S., Rath, S. (2009). HIV-l Nef Promotes Endocytosis of Cell Surface

MHC Class II Molecules via a Constitutive Pathway. Journal of Immunology,

183(4): 2415-2424.

Chen, J., Dang, Q., Unutmaz, D., Pathak, V.K., Maldarelli, F., Powell, D. (2005)

Mechanisms of nonrandom human immunodeficiency virus type 1 infection

and double infection: preference in virus entry is important but is not the sole

factor. Journal of Virology, 79: 4140-4149.

Chiu, Y.L., Rana, T.M.(2003) siRNA function in RNAi: a chemical

modification analysis. RNA, 9:1034-1048.

155 I P age

I References

Chun, T.W., Fauci, A.s.(1999) Latent reservoirs of HIV: obstacles to the

eradication of virus. Proceedings of National Academy of Sciences USA, 96:

10958-10961.

Clavel, F., Guetard, D., Brun-Vezinet, F., Chamaret, S., Rey, M.A., Santos­

Ferreira, M.O., Laurent, A.G., Dauguet, C, Katlama, C, Rouzioux, C(1986)

Isolation of a new Human retrovirus from West African patients with AIDS.

Science, 233:343-346.

Coburn, G.A. and Cullen, B.R(2002) Potent and specific inhibition of human

immunodeficiency virus type 1 replication by RNA interference. Journal of

Virology, 76: 9225-9231.

Cocchi, F., DeVico, A.L., Garzino-Demo, A., Arya, S.K., Gallo, RC, Lusso, P.

(1995) Identification of RANTES, MIP-1a, and MIP-1b as the major HIV

suppressive factors produced by CD8+ T cells. Science, 270:1811-1815.

Cocchi, F., DeVico, A.L., Garzino-Demo, A., Cara, A., Gallo, RC, Lusso, P.

(1996) The V3 domain of the HIV-1 gp120 envelope glycoprotein is critical for

chemokine-mediated blockade of infection. Nature Medicine, 2: 1244-1247.

Cochrane, J.C, Lipchock, S.V. and Strobe, S.A. (2007) Structural Investigation

of the GlmS Ribozyme Bound to Its Catalytic Cofactor. Chemistry & Biology,

14(1): 97-105.

Coffin, J., Haase, A., Levy, J.A, Montagnier, L., Oroszlan, S., Teich, N.(1986)

Human immunodeficiency viruses [letter]. Science, 232: 697.

Cohen, E.A., Dehni, G., Sodroski, J.G., Haseltine, W.A.(1990) Human

immunodeficiency virus vpr product is a virion-associated regulatory protein.

Journal of Virology, 64: 3097-3099.

156 I P age

I References

Combadiere, c., Ahuja, S.K., Tiffany, H.L., Murphy, P.M.(1996) Cloning and

functional expression of CC CKR5, a human monocyte CC chemokine

receptor selective for MIP-1(alpha), MIP-1(beta), and RANTES. Journal of

Leukocyte Biology, 60:147-152.

Cruz, RP.G., Withers, J.B., Li, Y. (2004) Dinucleotide junction cleavage

versatility of 8-17 deoxyribozyme. Chemical. Biology, 11: 57-67.

Cullen, B.R (1995). Regulation of HIV gene expression. AIDS, 9: 19-32.

Cullen, B.R (2006). Role and mechanism of action of the APOBEC3 family of

antiretroviral resistance factors. Journal of Virology, 80: 1067-1076.

Dalgleish, A.G., Beverley, P.c., Clapham, P.R, Crawford, D.H., Greaves, M.F.,

Weiss, RA.(1984) The CD4 (T4) antigen is an essential component of the

receptor for the AIDS retrovirus. Nature, 312: 763-767.

Danial, N.N., Korsmeyer, S.J. (2004). Cell death: critical control points. Cell,

116: 205-219.

Dash, B. C. and Banerjea, A. C. (2004) Sequence specific cleavage activities of

DNA-enzymes targeted against HIV-1 Gag and Nef regions.

Oligonucleotides, 14: 41-47.

Davidson, A., Leeper, T.C., Athanassiou, Z., Patora-Komisarska, K., Karn, J.,

Robinson, J.A., Varani, G. (2009) Simultaneous recognition of HIV-1 TAR

RNA bulge and loop sequences by cyclic peptide mimics of Tat protein.

Proceedings of National Academy of Sciences USA, 106(29):11931-11936.

de Noronha, C.M. (2001). Dynamic disruptions in nuclear envelope

architecture and integrity induced by HIV-1 Vpr. Science, 294: 1105-1108.

Deniaud, A., Brenner, c., Kroemer, G. (2004) Mitochondrial membrane

permeabilisation by HIV-1 Vpr. Mitochondrion, 4: 223-233.

157 I P age

I References

Deshpande A, Pinson PR, Deshmukh R, Faure M, Jauvin V, Garrigue I, et al.

Molecular characterization of HIV type 1 isolates from untreated patients of

Mumbai (Bombay), India, and detection of rare resistance mutations. AIDS

Res Hum Retroviruses 2004; 20:1032-1035.

Deshpande, A., Jauvin, V., Pinson, P., Jeannot, A.C. and Fleury, H.J. (2009)

Phylogenetic analysis of HIV -1 reverse transcriptase sequences from 382

patients recruited in JJ Hospital of Mumbai, India, between 2002 and 2008.

AIDS Research and Human Retroviruses, 25: 633-635

Doms, R.W.(2000) Beyond receptor expression: the influence of receptor

conformation, density, and affinity in HIV -1 infection. Virology, 276: 229-237.

Donze,G., and Picard, D. (2002). RNA interference in mammalian cells using

siRNAs synthesized with T7 RNA polymerase. Nucleic Acids Research,

30(10): e46.

Doranz, B.J., Berson, J.F., Rucker, J., Doms, R.W. (1997)Chemokine receptors

as fusion cofactors for human immunodeficiency virus type 1 (HIV-l).

Immunological Research,16: 15-28.

Dragic, T., Charneau, P., Clavel, F., Alizon, M.(1992) Complementation of

murine cells for human immunodeficiency virus envelope/CD4- mediated

fusion in human/murine heterokaryons. Journal of Virology, 66: 4794-4802.

Egelhofer, M. (2004) Inhibition of human immunodeficiency virus type 1

entry in cells expressing gp41-derived peptides. Journal of Virology, 78: 568-

575.

Evans, D., Marquez, S.M. and Pace, N.R. (2006) RNase P: an interface of RNA

and Protein world. TRENDS in Biochemical Sciences, 31(6): 333-341.

158 I P age

I References

Fahmy, RG., Dass, CR, Sun, L.Q., Chesterman, CN., Khachigian, L.M. (2003)

Transcription factor Egr-1 supports FGF-dependent angiogenesis during

neovascularization and tumor growth. Nature Medicine, 9:1026-1032.

Fahmy, R, Waldman, A., Zhang, G., Mitchell, A., Tedla, N., Cai, H.,

Chesterman, CN., Geczy, CR, Perry, M.A., Khachigian, L.M. (2006)

Suppression of vascular permeability and inflammation by targeting of the

transcription factor c-Jun. Nature Biotechnology, 24: 856-863.

Fan, J., Negroni, M., Robertson, D.L. (2007) The distribution of HIV-1

recombination breakpoints. Infection, Genetics and Evolution, 7: 717-723.

Fedor, M. J. (1999) Tertiary Structure Stabilization Promotes Hairpin

Ribozyme Ligation. Biochemistry, 38: 11040-11050.

Fedor,M.J.(2009)Comparative Enzymology and Structural Biology of RNA

Self-Cleavage, Annual Review of Biophysics, 38: 271-299.

Fedoruk-Wyszomirska, A., Giel-Pietraszuk, M., Wyszko, E., Szymanski, M.

Ciesiolka, J., Barciszewska, M.Z., Barciszewski, J.(2008)The mechanism of

acidic hydrolysis of esters explains the HDV ribozyme activity, Molecular

Biology Reports, 36(7):1647-1650.

Fedoruk-Wyszomirska, A., Szymanski, M., Wyszko, E., Barciszewska, M.Z.,

Barciszewski, J. (2009) Highly active low magnesium hammerhead ribozyme.

J Biochem.145(4):451-459.

Feng, Y., Broder, CC, Kennedy, P.E., Berger, E.A. (1996) HIV-1 entry cofactor:

functional cDNA cloning of a seven-transmembrane, G proteincoupled

receptor. Science, 272:872-877.

Feng, Y., Leavitt, M., Tritz, R, Duarte E., Kang, D., Mamounas, M., Gilles, P.,

Wong-Staal, F., Kennedy, S., Merson, J., Yu, M., and Barber, J. R (2000).

159 I P age

I References

Inhibition of CCR5 dependent HIV -1 infection by hairpin ribozyme gene

therapy against CC-chemokine receptor 5. Virology, 276: 271-278.

Ferre-D'Amare, A.R (2004) The hairpin ribozyme. Biopolymers, 73: 71-78.

Ferre-D'Amare, A.R, Zhou, K, Doudna, J.A. (1998) Crystal structure of

Hepatitis delta virus, Nature, 395 (6702): 567-574.

Fire, A., Xu,S., Montgomery, M., Kostas,S., Driver,S., Mello, C (1998) Potent

and specific genetic interference by double-stranded RNA in Caenorhabditis

elegans. Nature, 391(6669): 806-811.

Forster, A. C, and Altman, S. (1990) External guide sequences for an RNA

enzyme. Science, 249: 783-786.

Forster, A.C and Symons, RH. ,(1987) self cleaving of virusoid RNA is

performed by the proposed 55- nucleotide active site, cell, 50: 9-16

Fukushima, A., Fukuda, N., Lai, Y., Ueno, T., Moriyama, M., Taguchi, F.,

Iguchi, A., Shimizu, K, Kuroda, K(2009) Development of a chimeric DNA­

RNA hammerhead ribozyme targeting SARS virus.lntervirology. 52(2):92-99.

Gadkari, D.A., Moore, D., Sheppard, H.W., Kulkarni, 5.5., Mehendale, S.M.

and Bollinger, RG. (1998) Transmission of genetically diverse strains of HIV-1

in Pune, India. Indian Journal of Medical Research, 107: 1-9.

Gallo, RC, Salahuddin, S.Z., Popovic, M., Shearer, G.M., Kaplan, M., Haynes,

B.F.(1984). Frequent detection and isolation of cytopathic retroviruses (HTLV­

III) from patient with AIDS and at a risk for AIDS. Science, 224: 500-503.

Ganeshan, 5., Dickover, R E., Korber, B. T., Bryson, V. J. & Wolinsky, S. M.

(1997). Human immunodeficiency virus type 1 genetic evolution in children

with different rates of development of disease. Journal of Virology, 71: 663-

677.

160 I P age

I References

Garzino-Demo, A., DeVico, A.L., Cocchi, F., Gallo, RC ~-chemokines and

protection from HIV type 1 disease. AIDS Research and Human Retroviruses,

14:S177-184.

Gibbs, J.S., Lackner, A.A., Lang, S.M., Simon, M.A.,Sehgal, P.K., Daniel, M.D.,

and Desrosiers, RC(1995). Progression to AIDS in the absence of a gene for

Vpr or Vpx. Journal of Virology, 69: 2378-2383.

Goh, W.C, Rogel, M.E., Kinsey, CM., Michael, S.F., Fultz, P.N., Nowak, M.A.,

Hahn, B.H., Emerman, M.(1998) HIV-1 Vpr increases viral expression by

manipulation of the cell cycle: a mechanism for selection of Vpr in vivo.

Nature Medicine, 4(1): 65-71.

Goila, R, Banerjea, A. C (1998) Sequence specific cleavage of the HIV-1

coreceptor CCR5 gene by a hammer-head ribozyme and a DNA-enzyme:

inhibition of the coreceptor function by DNA-enzyme. FEBBS Letter, 436

(2):233-238.

Goila, Rand Banerjea, A.C (2001) Inhibition of hepatitis B virus X gene

expression by novel DNA enzymes. Biochemical Journal, 353 (3): 701-708.

Goila-Gaur, R and Strebel, K.(2008) HIV-1 Vif, APOBEC, and Intrinsic

Immunity. Retrovirology, 5: 51-66.

Goodchild, J. (1992) Enhancement of ribozyme catalytic activity by a

contiguous oligonucleotide (facilitator) and by 2' -O-methylation. Nucleic

Acids Research, 20: 4607-4612.

Gupta, N., Bano, AS., Sharma, Y., Banerjea, A.C (2008) Potent knockdown of

the X RNA of hepatitis B by a novel chimeric siRNA-ribozyme construct and

modulation of intracellular target RNA by selectively disabled

mutants. Oligonucleotides. 18(3 ) :225-233.

161 I P age

I References

Gupta, N., Bano,A.S., Sharma, Y.,Sood, V. and Banerjea, A.C(2007). Potent

intracellular knock down of hepatitis B virus X RNA by catalytic hammerhead

ribozymes or DNA-enzymes with antisense DNA-oligonucleotides or 10-23

DNA-enzymes that powerfully augment in vitro sequence specific cleavage

activities. The Open Biotechnology Journal, 1: 81-92.

Haase, A.T.(1986) pathogenesis of lentivirus infections. Nature, 322:131-136.

Hampel, A. and Tritz, R (1989) RNA catalytic properties of the minimum (-) s

TRSV sequence. Biochemistry, 28: 4929-4933.

He, Z., Zhang, W., Chen, G., Xu, Rand Yu, X. F. (2008). Characterization of

Conserved Motifs in HIV-1 Vif Required for APOBEC3G and APOBEC3F

Interaction. Journal of Molecular Biology, 381:1000-1011.

Hendry, P., Mc Call, M.J., Santiago, F.5. and Jennings, P.A. (1995) In vitro

activity of minimized hammerhead ribozymes. Nucleic acid research, 23:

3922-3927.

Herring, B.L., Ge, Y.C, Wang, B., Ratnamohan, M., Zheng, F., Cunningham,

A.L., Saksena, N.K. and Dwyer, D.E. (2003) Segregation of Human

Immunodeficiency Virus Type 1 Subtypes by Risk Factor in Australia. Journal

of Clinical Microbiology, 41(10): 4600-4604.

Higa, L. A. and Zhang, H. (2007) Stealing the spotlight: CUL4-DDB1

ubiquitin ligase docks WD40-repeat proteins to destroy. Cell Division, 2: 5-14.

Hirsch, V.M., Sharkey, M.E., Brown,CR, Brichacek, B., Goldstein, S.,

Wakefield, J., Byrum, R, Elkins, W.R, Hahn, B.H., Lifson, J.D., and Stevenson,

M. (1998). Vpx is required for dissemination and pathogenesis of SIV (SM):

evidence of macrophage-dependent viral amplification. Nature Medicine, 4:

1401-1408.

162 I P age

I References

Hiscott, J., Kwon, H., Genin, P. (2001). "Hostile takeovers: viral appropriation Ii)

of the NF-kappaB pathway". Journal of Clinical Investigation, 107 (2): 143-

151.

Hogan, T.H., Nonnemacher, M.R, Krebs, F.C, Henderson, A., Wigdahl,

B.(2003) HIV-1 Vpr binding to HIV-1 LTR C/EBP cis-acting elements and

adjacent regions is sequence-specific. Biomedical Pharmacotherapy, 57: 41-48.

Horn, S., Schwenzer, B.(1999) Oligonucleotide facilitators enhance the

catalytic activity of RNA-cleaving DNA enzymes. Antisense Nucleic Acid

Drug Development, 9: 465-472.

Hornung, V., Guenthner-Biller, M., Bourquin, C, Ablasser, A., Schlee, M.,

Vematsu, S., Noronha,A., Manoharan, M., Akira, S., de Fougerolles, A.,

Endres, S.,Hartmann, G.(200S) Sequence-specific potent induction of IFN­

alpha by short interfering RNA in plasmacytoid dendritic cells through TLR7.

Nature Medicine, 11: 263-270.

Huang, Y., Paxton, W.A., Wolinsky, S.M., Neumann, A.V., Zhang, 1., He, T.,

Kang, S., Ceradini, D., Jin, Z., Yazdanbakhsh, K., Kunstman, K., Erickson, D.,

Dragon, E., Landau, N.R, Phair, J., Ho, D.D., Koup, RA.(1996) The role of a

mutant CCRS allele in HIV -1 transmission and disease progression. Nature

Medicine, 2(11):1240-1243.

Husain S, Goila R, Shahi Sand Banerjea AC(1998) First report of a healthy

Indian heterozygous for D32 mutant of HIV -1 coreceptor-CCRS gene. Gene,

207: 141-147.

Isaka, Y., Nakamura, H., Mizui, M., Takabatake, Y., Horio, M., Kawachi, H.,

Shimizu, F., Imai, E., Hori, M. (2004) DNAzyme for TGF-~ suppressed

extracellular matrix accumulation in experimental glomerulonephritis.

Kidney International, 66:586-590.

163 I P age

I References

Iversen, P.O., Nicolaysen, G., Sioud, M. (2001) DNA enzyme targeting

TNFalpha mRNA improves hemodynamic performance in rats with

postinfarctionheart failure. American Journal of Physiology, 281: H2211-

H2217.

Jacotot, E., Ravagnan, L., Loeffler, M., Ferri, KF., Vieira, H.L., Zamzami, N.

(2000) The HIV -1 viral protein R induces apoptosis via a direct effect on the

mitochondrial permeability transition pore.

Medicine, 191: 33-46.

Journal of Experimental

Jacque, J.M., Triques, K, Stevenson, M.(2002) Modulation of HIV-1 replication

by RNA interference. Nature, 418: 435-438.

Jameel, 5., Zafrulla, M., Ahmad, M., Kapoor, G.P. and Sehgal, S. (1995) A

genetic analysis of HIV -1 from Punjab, India reveals the presence of multiple

variants. AIDS, 9: 685-690.

Jankowsky, E.B., Schwenzer, B. (1996) Oligonucleotide facilitators may inhibit

or activate a hammerhead ribozyme. Nucleic Acids Research, 24: 423-429.

Jensen, M.A., 't Wout, A.B.(2003) Predicting HIV-1 coreceptor usage with

sequence analysis. AIDS Review, 5:104-112.

Jere, A., Tripathy, 5., Agnihotri, K, Jadhav, 5., Paranjape, R. (2004) Genetic

analysis of Indian HIV -1 nef subtyping, variability and implications. Microbes

and Infection, 6: 279-289.

Jian, H., and Zhao, L.J. (2003). Pro-apoptotic activity of HIV-1 auxillary

regulatory protein Vpr is subtype-dependent and potentially enhanced by

nonconservative changes of the leucine residue at position 64. Journal of

Biological Chemistry, 278: 44326-44330.

164 I P age

I References

Joyce, G.F. (2004) Directed evolution of nucleic acid enzymes. Annual Review

of Biochemistry, 73: 791-836.

Karni, 0., Friedler, A., Zakai, N., Gilon, c., Loyter, A.(1998) A peptide derived

from the N-terminal region of HIV-1 Vpr promotes nuclear import in

permeabilized cells: elucidation of the NLS region of the Vpr. FEBS Letter,

429:421-425.

Khachigian, L.M., Fahmy, R.G., Zhang, G., Bobryshev, Y.V., Kaniaros, A.

(2002) c-Jun regulates vascular smooth muscle cell growth and neointima

formation after arterial injury: inhibition by a novel DNAzyme targeting c­

Jun. Journal of Biological Chemistry, 277: 22985-22991.

Kim, D. H. and Rossi, J. J. (2007). Strategies for silencing human disease using

RNA interference. Nature review Genetics, 8: 173-184

Kino, T., Gragerov, A., Slobodskaya, 0., Tsopanomichalou, M., Chrousos,

G.P., Pavlakis, G.N.(2002) Human immunodeficiency virus type 1 (HIV-1)

accessory protein Vpr induces transcription of the HIV-1 and glucocorticoid­

responsive promoters by binding directly to p300/CBP coactivators. Journal of

Virology, 76(19): 9724-9734.

Klatzmann, D., Champagne, E., Chamaret, S., Gruest, l, Guetard, D.,

Hercend, T.(1984)T-lymphocyte T4 molecule behaves as the receptor for

human retrovirus LA V. Nature, 312:767-768.

Konopka K, Diizgiine~ N, Rossi J, Lee NS.(1998) Receptor ligand-facilitated

cationic liposome delivery of anti-HIV -1 Rev-binding aptamer and ribozyme

DNAs.J Drug Target.5(4):247-259.

Kostrikis, L.G., Huang, Y., Moore, J.P., Wolinsky, S.M., Zhang, L.Q., Guo, Y.,

Deutsch, L., Phair, J., Neumann, A.D., Ho, D.D. (1998). A chemokine receptor

165 I P age

I References

CCR2 allele delays HIV -1 disease progression and is associated with a CCR5

promoter mutation. Nature Medicine, 4:350-353.

Kraus, G., Geffin, R, Spruill, G., Young, A.K., Seivright, R, Cardona, D.,

Burzawa, I., Hnatyszyn, H.J. (2002) Cross-clade inhibition of HIV-1 replication

and cytopathology by using RNase P-associated external guide sequences.

Proceedings of National Academy of Sciences, USA., 99: 3406-3411.

Kruger, K., Grabowski, P.J., Zaug, A.I., Sands, I., Gottschling, D.E., Cech, T.R

(1982) Self-splicing RNA: autoexcision and autocyclization of the ribosomal

RNA intervening sequence of Tetrahymena.Cell, 31(1):147-157.

Kumar, M., Jain, S.K., Pasha, S.T., Chattopadhaya, D., Lal, S. and Rai, A.

(2006) Genomic diversity in the regulatory nef gene sequences in Indian

isolates of HIV type 1: emergence of a distinct subclade and predicted

implications. AIDS Research and Human Retroviruses, 22: 1206-1219.

Kurle, S., Tripathy, S., Jadhav, S., Agnihotri, K. and Paranjape, R (2004) Full­

length gag sequences of HIV type 1 subtype C recent seroconverters from

Pune, India. AIDS Research and Human Retroviruses, 20: 1113-1118.

Kurreck, J. (2003). Antisense technologies: Improvement through novel

chemical modifications. European Journal of Biochemistry, 270: 1628-1644.

Kurreck, J., Bieber, B., Jahnel, R and Erdmann, V.A. (2002) Comparative

Study of DNA Enzymes and Ribozymes against the Same Full-length

Messenger RNA of the Vanilloid Receptor Subtype I. Journal of Biological

Chemistry, 277(9): 7099-7107.

Lafontaine, D.A., Norman, D.G. and Lilley, D.M.J. (2002) The global structure

of the VS ribozyme, Embo Journal, 21(10): 2461-2471.

166 I P age

I References

Lakhashe, S., Thakar, M., Godbole, S., Tripathy, S. and Paranjape, R. (2008)

HIV infection in India: epidemiology, molecular epidemiology and

pathogenesis. Journal of Biosciences, 33: 515-525.

Lambowitz, A.M. and Zimmerly, S. (2004) Mobile group II introns. Annual

Review of Genetics, 38: 1-35

Le Gall, S., Heard, J.M., Schwartz, 0.(1997).Analysis of Nef induced MHC-I

endocytosis. Research Virology, 148: 43-47.

Le Rouzic, E. (2007). HIVI Vpr arrests the cell cycle by recruiting

DCAFINprBP, a receptor of the Cul4-DDBI ubiquitin ligase. Cell Cycle,

6:182-188.

Le Rouzic, E., Benichou, S. (2005) The Vpr protein from HIV-l: distinct roles

along the viral life cycle. Retrovirology, 2:11-25.

Levine, B.L. (2006) Gene transfer in humans using a conditionally replicating

lentiviral vector. Proceedings of National Academy of Sciences USA, 103:

17372-17377.

Levy, D.N., Aldrovandi, G.M., Kutsch, 0., Shaw, G.M. (2004) Dynamics of

HIV-l recombination in its natural target cells. Proceedings of National

Academy of Sciences, USA, 101: 4204-4209.

Li, M.J. (2005)Long-term inhibition of HIV-l infection in primary

hematopoietic cells by lentiviral vector delivery of a triple combination of

anti-HIV shRNA, anti-CCR5 ribozyme, and a nucleolar-localizing TAR decoy.

Molecular Therapy 12, 900-909.

Li, Y., Li, X., Stremlau, M., Lee, M. and Sodroski, J. (2006) Removal of arginine

332 allows human TRIM5a to bind human immunodeficiency virus capsids

and to restrict infection. Journal of Virology, 80: 6738-6744.

167 I P age

I References

Li, Y., Liu, Y. and Breaker, RR (2000) Capping DNA with DNA.

Biochemistry, 39: 3106-3114.

Liang, Z., Wei, S., Guan, J., Luo, Y., Gao, J., Zhu, H., Wu, S., Liu, T. (2005)

DNAzyme mediated cleavage of survivin mRNA and inhibition of the growth

of P ANC-1 cells. Journal of Gastroenterology and Hepatology,20 :1595-1602.

Liu, S., Bokinsky, G., Walter, N.G., Zhuang, X.(2007) Dissecting the multistep

reaction pathway of an RNA enzyme by single molecule kinetic

"fingerprinting". Proceedings of National Academy of Sciences USA, 104:

12634-12639.

Lole, KS., Bollinger, RC, Paranjape, RS., Gadkari, D., Kulkarni, S.S., Novak,

N.G. (1999) Full-length human immunodeficiency virus type 1 genomes from

subtype C-infected seroconverters in India, with evidence of intersubtype

recombination. Journal of Virology, 73: 152-160.

Lorsch, J.R, Szostak, J.W. (1994) In vitro evolution of new ribozymes with

polynucleotide kinase activity. Nature, 371: 31-36.

Lumm, J.J., Cohen, Ol, Nie, Z., Weaver, J.G., Gomez, T.s., Yao, X.J., Lynch,

D., Pilon, A.A., Hawley, N, Kim, J.E.(2003). Vpr R77Q is associated with long

term nonprogressive HIV infection and impaired induction of apoptosis.

Journal of Clinical Investigations, 111: 1547-1554.

Lyngstadaas, S.P., Risnes, S., Sproat, B.s., Thrane, p.s. and Prydz, H.P. (1995)

TI A synthetic, chemically modified ribozyme eliminates amelogenin,

the major translation product in developing mouse enamel in vivo. EMBO

Journal, 14(21),5224-5229.

Macejak, D.G., Jensen, KL., Jamison, S.F., Domenico, K, Roberts, E.C,

Chaudhary, N., von Carlowitz, I., Bellon, L., Tong,M.J., Conrad, A., Pavco,

P.A. and Blatt, L.M. (2000) Inhibition of hepatitis C virus (HCV)-RNA-

168 I P age

I References

dependent translation and replication of a chimeric HCV poliovirus using

synthetic stabilized ribozymes. Hepatology, 31(3): 769-776.

Maddon, P.J., Dalgleish, A.G., McDougal, J.5., Clapham, P.R, Weiss, RA.,

Axel, R (1986) The T4 gene encodes the AIDS virus receptor and is expressed

in the immune system and the brain. Cell, 47: 333-348.

Maitra, A., Singh, B., Banu, S., Deshpande, A., Robbins, K, Kalish, M.L.,

Broor, S., Seth, P. (1999) Subtypes of HIV type 1 circulating in India: Partial

envelope sequences. AIDS Research and Human Retroviruses, 15: 941-944.

Malim, M.H., Hauber, J., Le, S.-Y., Maizel, J.V., and Cullen, B.R (1989). The

HIV-l rev trans-activator acts through a structured target sequence to activate

nuclear export of unspliced viral mRNA. Nature, 338: 254-257.

MandaI, D., Jana, S., Bhattacharya, S.K and Chakrabarti, S. (2002) HIV type 1

subtypes circulating in eastern and northeastern regions of India. AIDS

Research and Human Retroviruses, 18: 1219-1227.

Mangasarian, A. and Trono, D. (1997).The multifaceted role of HIV Nef.

Research Virology, 148:30-33.

Marasco, W.A., LaVecchio, J .. and Winkler, A. (1999) Human anti-HIV-l tat

sFv intrabodies for gene therapy of advanced HIV-l-infection and AIDS.

Journal of Immunological Methods, 231: 223-238.

Margottin, F., Bour, S.P., Durand, H., Selig, L., Benichou, S., Richard, V.,

Thomas, D., Strebel, K, Benarous, R(1998) A novel human WD protein, h­

beta TrCP, that interacts with HIV-l Vpu connects CD4 to the ER degradation

pathway through an F- box motif. Molecular Cell,l: 565- 574.

Martick, M. and Scott, W.G.(2006) Tertiary Contacts Distant from the Active

Site Prime a Ribozyme for Catalysis, cell,126:309-320.

.169 I P age

I References

Martinez, M.A., Gutierrez, A., Armand-U gon, M., Blanco, J., Parera, M.,

Gomez, J., Clotet, B., Este, J.A.(2002) Suppression of chemokine receptor

expression by RNA interference allows for inhibition of HIV-l replication.

AIDS, 16: 2385-2390.

McCaffrey, A.P., Nakai, H., Pandey, K., Huang, Z., Salazar, F.H., Xu, H.,

Wieland, S.F., Marion,P.L., Kay, M.A.(2003) Inhibition of hepatitis B virus in

mice by RNA interference. Nature Biotechnology, 21: 639-644.

McCutchan, F.E. (2000) Understanding the genetic diversity of HIV-l. AIDS,

14 (SuppI3): S31-44.

McDermott, D.H., Zimmerman, P.A., Guignard, F., Kleeberger, CA., Leitman,

S.F., Murphy, P.M. (1998). CCR5 promoter polymorphism and HIV-l disease

progression. Lancet 352:866-870.

Meister, G., Landthaler,M., Patkaniowska, A., Dorsett, Y., Teng, G., Tuschl, T.

(2004) Human Argonaute2 mediates RNA cleavage targeted by miRNAs and

siRNAs. Molecular Cell,15: 185-197.

Meli, M., Vergne, J., Maurel, M.C (2003) In vitro selection of adenine

dependent hairpin ribozymes. Journal of Biological Chemistry, 278: 9835-9842 .

. Michael, N.L., Nelson, J.A., KewalRamani, V.N., Chang, G., O'Brien, SJ,

Mascola, J.R, Volsky, B., Louder, M., White, G.C, Littman, D.R, Swanstrom,

R, O'Brien, T.R(1998) Exclusive and persistent use of the entry coreceptor

CXCR4 by human immunodeficiency virus type 1 from a subject homozygous

for CCR5 delta32. Journal of Virology, 72(7): 6040-6047.

Michel, F., Jacquier, A. and Dujon, B. (1982) Comparison of fungal

mitochondrial introns reveals extensive homologies in RNA secondary

structure. Biochemie, 64: 867-81

170 I P age

--------------------

I References

Miedema, F., Meyaard, L., Koot, M., Klein, M.R, Roos, M.T., Groenink, M.

(1994) Changing virus-host interactions in the course of HIV-1 infection.

Immunology Review, 140: 35-72.

Miller, J.W. (2008). Preliminary Results of Gene Therapy for Retinal

Degeneration.The New England journal of Medicine

Millow, KH., Greenough, T.C., Bretttler, D.B., Schindler, M., Wildum, S.,

Sullivan, J.L. (2003) Alterations in HIV-1 LTR promoter activity during AIDS

progression. Virology, 317: 109-118.

Mishra, M., Vetrivel, S., Siddappa, N.B., Ranga, V., Seth, P. (2008) Clade-

specific differences in neurotoxicity of human immunodeficiency virus-1 B

and C Tat of human neurons: significance of dicysteine C30C31 motif. Annual

Neurology, 63(3): 366-376.

Mitchell, A., Dass, C.R, Sun, L-Q., Khachigian, L.M. (2004) Inhibition of

human breast carcinoma proliferation, migration, chemoinvasion and solid

tumor growth by DNAzymes targeting the zinc finger transcription factor

EGR-l. Nucleic Acids Research, 32:3065-3069.

Morellet, N. (2003). NMR structure of the HIV-1 regulatory protein VPR

Journal of Molecular Biology, 327: 215-227.

Morgan, RA. (2005) Preferential survival of CD4+ T lymphocytes engineered

with anti-human immunodeficiency virus (HIV) genes in HIV -infected

individuals. Human Gene Therapy, 16: 1065-1074.

Murrell, M., Khachigian, L., Ward, M.R (2007) The role of c-jun in PDTC-

sensitive flow-dependent restenosis after angioplasty and stenting.

Atherosclerosis, 194(2): 364-71.

171 I P age

I References

Muthumani, K. (2002). HIV-1 Vpr induces apoptosis through caspase 9 in T

cells and peripheral blood mononuclear cells. Journal of Biological Chemistry,

277: 37820-37831.

Neil, S.J., Zang, T., Bieniasz, P.D.(2008) Tetherin inhibits retrovirus release

and is antagonized by HIV -1 Vpu. Nature, 451:425-430.

Neogi, V., Sood, V., Banerjee,S., Ghosh, N., Verma,S., Samrat, 5., Sharma, Y.,

Saxena, A., Husain,S., Ramachandran, V.G., Das, 5., Sreedhar, K.V., Goel, N.,

Wanchu, A. and Banerjea A.C. (2009) Global HIV -1 molecular epidemiology

with special reference to genetic analysis of HIV -1 subtypes circulating in

North India: functional and pathogenic implications of genetic variation.

Indian Journal of Experimental Biology, 47: 424-431.

Neogi, V., Sood, V., Goel, N., Wanchu, A., Banerjea, A.C. (2008) Novel HIV-1

Long Terminal Repeat (LTR) sequences of Subtype B and mosaic intersubtype

BIC Recombinants in North India. Archives of Virology, 153(10): 1961-1966.

Neville, M., Stutz, F., Lee, L., Davis, L.I., and Rosbash, M. (1997).The

importin-beta family member Crm1 p bridges the interaction between Rev and

the nuclear pore complex during nuclear export. Current Biology, 7: 767-775.

Nunamaker, E.A., Zhang, H.Y., Shirasawa, Y., Benoit, J.N., Dean, D.A. (2003)

Electroporation- mediated delivery of catalytic oligodeoxynucleotides for

manipulation of vascular gene expression. American Journal of Physiology,

285:H2240-H2247

Okumura, A., Lu, G., Pitha-Rowe, I., Pitha, P.M.(2006) Innate antiviral

response targets HIV -1 release by the induction of ubiquitin like protein

ISG15. Proceedings of National Academy of Sciences V.s.A. ,103: 1440-1445.

172 I P age

I References

Pan, W.H., Clawson, G.A. (2006) Identifying accessible sites in RNA: the first

step in designing antisense reagents. Current Medicinal Chemistry,13(25):

3083-103.

Pan, W.H., Xin, P., Morrey, J.D. and Clawson, G.A. (2004) A self-processing

ribozyme cassette: utility against human papillomavirus 11 E6/E7 mRNA and

hepatitis B virus. Molecular therapy, 9(4): 596-606.

Paul, M. and Jabbar, M.A.(1997) Phosphorylation of both phospho acceptor

sites in the HIV-1 Vpu cytoplasmic domain is essential for Vpu mediated ER

degradation of CD4. Virology, 232: 207-216.

Peeters, M. (2000) Recombinant HIV sequences: Their role in the global

epidemic. In "Human Retroviruses and AIDS: A Compilation and Analysis of

Nucleic Acid and Amino Acid Sequences" (C Kuiken, B. Foley, B. Hahn, B.

Korber, F. McCutchan, P. Marx, J. Mellors, J. Mullins, J. Sidroski, and J.

Wolinsky, Eds.), 54-72. Los Alamos National Laboratory, Los Alamos, New

Mexico.

Perriman, R, Delves, A. and Gerlach, W.L. (1992) Extended target site

specificity for a hammerhead ribozyme, Gene 113, 157-163.

Pfister, E.L., Kennington, L., Straubhaar, J., Wagh, S., Liu, W., DiFiglia, M.,

Landwehrmeyer, B., Vonsattel, J.P., Zamore, P.D., Aronin, N. (2009) Five

siRNAs targeting three SNPs may provide therapy for three-quarters of

Huntington's disease patients. Current Biology, 19(9):774-8.

Piller, S. C, Ewart, G. D., Jans, D. A., Gage, P. W. and Cox, G. B. (1999).The

amino-terminal region of Vpr from human immunodeficiency virus type 1

forms ion channels and kills neurons. Journal of Virology, 73: 4230- 4238.

Platz, J., Grassi, M., Kuhn, A., Kandolf, R, Racchi, G., Farra, R, Dapas, B.,

Pascotto, A., Giansante, C, Fiotti, N., Guarnieri, G., Grassi, G.(2007) Effects of

173 I P age

I References

various promoter derived sequences on the cleavage kinetic of an

hammerhead ribozyme directed against cyclin E1 mRNA.Drug Metab

Lett.1(3):218-225.

Pley, H.W., Flaherty, KM., McKay, D.B. (1994) Three-dimensional structure of

a hammerhead ribozyme. Nature, 372(6501):68-74.

Poller, W., Fechner, H., Kurreck, J., Pauschinger, M., Kiihl, U., Erdmann, V.A.,

Lamers, J.M.J. and Schultheiss, H.-P. (2004) Nucleic acid-based modulation of

cardiac gene expression for the treatment of cardiac diseases. Z. Kard. 93(3),

171-193.

Poon, B., Chang, M.A. and Chen, I.S.Y. (2007). Vpr is required for efficient Nef

expression from unintegrated HIV-1 DNA. Journal of Virology, 81:10515-

10523.

Prody, G.A., Bakos, J.T., Buzayan, J.M., Schneider, I.R, Breuning, G. (1986)

Autolytic processing of dimeric plant virus satellite RNA. Science 231: 1577-

1580.

Purtha, W.E., Coppins, RL., Smalley, M.K and Silverman, S.K (2005) General

deoxyribozyme- catalyzed synthesis of native 3'-5' RNA linkages. Journal of

American Chemical Society, 127: 13124-13125.

Qin, X. F., An, D. S., Chen, I. S. and Baltimore, D. (2003) Inhibiting HIV-1

infection in human T cells by lentiviral-mediated delivery of small interfering

RNA against CCR5. Proceedings of National Academy of Sciences USA, 100:

183-188.

Ramezani, A., Ma, X.Z., Ameli, M., Arora, A., Joshi, S.(2006) Assessment of an

anti-HIV-1 combination gene therapy strategy using the antisense RNA and

multimeric hammerhead ribozymes. Frontier Bioscience,l1: 2940-2948.

174 I P age

I References

Rhodes, T., Wargo, H., Hu, W.5. (2003) High rates of human

immunodeficiency virus type 1 recombination: near-random segregation of

markers one kilobase apart in one round of viral replication. Journal of Virol

2003; 77, 11193-200.

Rodriguez MA,Shen C, Ratner D, Paranjape RS, Kulkarni 55, Chatterjee R.

(2007) Genetic and Functional Characterization of the L TR of HIV -1 Subtypes

A and C circulating in India. AIDS Research and Human Retroviruses, 23:

1428-1433.

Romani, B., Engelbrecht, S. (2009) Human immunodeficiency virus type 1

Vpr: functions and molecular interactions. Journal of General Virology, 90(8):

1795-1805.

Roshal, M. (2001). Apoptosis in AIDS. Apoptosis, 6: 103-116.

Roshal, M., Kim, B., Zhu, Y., Nghiem, P., Planelles, V. (2003) Activation of the

ATR-mediated DNA damage response by the HIV-1 viral protein R. Journal

of Biological Chemistry, 278(28):25879-25886.

Rossi, J. J. (1999). The application of ribozymes to HIV infection. Current

opinion molecular therapy, 1: 316-322.

Rossi, J.J., June, C.H. and Kohn, D.B. (2007) Genetic therapies against HIV.

Nature Biotechnology, 25(12): 1444-1454.

Roth, A., Nahvi,A., Lee,M.(2006) Characteristics of the glmS ribozyme suggest

only structural roles for divalent metal ions. RNA,12: 607-619.

Roumier,T., Vieira, H. L., Castedo, M., Ferri, K. F., Boya, P., Andreau, K.,

Druillennec, 5., Joza, N., Penninger, J. M. (2002). The C-terminal moiety of

HIV -1 Vpr induces cell death via a caspaseindependent mitochondrial

pathway. Cell Death and Differentiation, 9:1212-1219.

175 I P age

I References

Rousseau, C.M., Learn, G.H., Bhattacharya, T., Nickle, D.C., Heckerman, D.,

Chetty, c., Brander, c., Goulder, P.J.R., Walker, B.D., Kiepiela, P., Korber,

B.T., and Mullins, J.I. (2007). Extensive intra subtype recombination in South

African human immunodeficiency virus type 1 subtype C infections. Journal

of Virology, 81: 4492-4500.

Rouzic, E.L., and Benichou, S. (2005). The Vpr protein from HIV-1: distinct

roles along the viral life cycle. Retrovirology, 2: 11.

Rupert, P. B. and Ferre-D'Amare, A. R. (2001) Crystal structure of a hairpin

ribozyme-inhibitor complex with implications for catalysis Nature, 410: 780-

786.

Sahni, A.K., Prasad, V.V. and Seth, P. (2002) Genomic diversity of human

immunodeficiency virus type-1 in India. International Journal of SID.AIDS,

13: 115-118.

Sakai, S., Dimas, J., and Lenardo, J.M. (2006). The Vif and Vpr accessory

proteins independently cause HIV -1 induced T cell cytopathocity and cell

cycle arrest. Proceedings of National Academy of Sciences USA, 103: 3369-

3374.

Salminen MO, Carr JK, Robertson DL, Hegerich P, Gotte D, Koch C. (1997)

Evolution and probable transmission of intersubtype recombinant human

immunodeficiency virus type 1 in a Zambian couple. Journal of Vir'ology, 71:

2647-2655.

Salminen, M. 0., ~arr, J. K., Burke, D. S. & McCutchan, F. E. (1995).

Identification of breakpoints in intergenotypic recombinants of HIV type 1 by

bootscanning. AIDS Research and Human Retroviruses, 11: 1423-1425.

Samson, M., Libert, F., Doranz, B.J., Rucker,J., Liesnard, c., Farber, C.M.,

Saragosti, S., Lapoumeroulie, c., Cognaux, J., Forceille, c., Muyldermans, G.,

176 I P age

I References

Verhofstede, c., Burtonboy, G., Georges, M., Imai, T., Rana, S., Yi, Y.J., Smyth,

RJ., Collman, RG., Doms, RW., Vassart, G., Parmentier, M. (1996). Resistance

to HIV -1 infection in Caucasian individuals bearing mutant alleles of the

CCR-5 chemokine receptor gene. Nature, 382:722-725

Santoro, S.W. and Joyce, G.F. (1997) A general purpose RNA-cleaving DNA

enzyme. Proceedings of National Academy of Sciences USA. 94(9): 4262-

4266.

Sawaya, B.E., Khalili, K., Gordon, J., Taube, R, Amini, S.(2000) Cooperative

interaction between HIV-l regulatory proteins Tat and Vpr modulates

transcription of the viral genome. Journal of Biological Chemistry, 275(45):

35209-35214.

Schlosser, K., Gu, J., Lam, J.c., Li, Y. (2008) In vitro selection of small RNA-

cleaving deoxyribozymes that cleave pyrimidine-pyrimidine

junctions. Nucleic Acids Research, 36(14):4768-77.

Schroers, R, Davis, C.M., Wagner, H.J. and Chen, S.Y. (2002)Lentiviral

transduction of human T-Iymphocytes with a RANTES intrakine inhibits

human immunodeficiency virus type 1 infection. Gene Therapy, 9: 889-897.

Schubert, S. and Kurreck, J. (2004) Ribozyme- and Deoxyribozyme-Strategies

for Medical Applications. Current Drug Targets, 5: 667-681.

Schubert, S., Furste, J. P., Werk, D., Grunert, H. P., Zeichhardt, H., Erdmann,

V. A. and Kurreck, J. (2004) Gaining target access for deoxyribozymes.

Journal of Molecular Biology, 339: 355-363.

Schwartz, S.(1991). Expression of human immunodeficiency virus type 1 vif

and vpr mRNAs is Rev-dependent and regulated by splicing. Virology, 183:

677-686.

177 I P age

I References

Sengupta, S., Jana, S., Roy, P., Sarkar, K, Bhattacharya, S.K, Chakrabarti,

S.(2005a) Phylogenetic analysis of the p24-p7 region of the human

immunodeficiency virus type 1 gag gene to determine subtype distribution

among female sex workers in Calcutta. Indian Journal of Clinical

Microbiology, 43: 5787-5791.

Sengupta, S., Khetawat, D., Jana, S., Sarkar, K, Bhattacharya, S.K.,

Chakrabarti, S. (2005b) Polymorphism of HIV-l gag (pI7) gene from female

sex workers in Calcutta, India. Archives of Virology, 150: 2117-2124.

Shankarappa, R, Chatterjee, R, Learn, G.H., Neogi, D., Ding, M., Roy, P.

(2002) Human immunodeficiency virus type 1 env sequences from Calcutta in

eastern India: identification of features that distinguish subtype C sequences

in India from other subtype C sequences. Journal of Virology, 75: 10479-

10487.

Sheehy, A.M., Gaddis, N.C., Choi, J.D., Malim, M.H.(2002) Isolation of a

human gene that inhibits HIV -1 infection and is suppressed by the viral Vif

protein. Nature, 418 (6898): 646-650.

Sherman, M.P., de Noronha, C.M., Pearce, D., Greene, W.C.(2000) Human

immunodeficiency virus type 1 vpr contains two leucine-rich helices that

mediate glucocorticoid receptor coactivation independently of its effects on

G(2) cell cycle arrest. Journal of Virology, 74: 8159-8165.

Shimayama, T., Nishikawa, S. and Taira, K (1995) Generality of the NUX

Rule: Kinetic Analysis of the Results of Systematic Mutations in the

Trinucleotide at the Cleavage Site of Hammerhead Ribozymes, Biochemistry

34: 3649-3654.

178 I P age

I References

Shiota, M., Sano, M., Miyagishi, M. and Taira, K (2004) Ribozymes:

Applications to Functional Analysis and Gene Discovery J. Biochem. 136, 133-

147.

Shriner, D., Rodrigo, A.G., Nickle, D.C., Mullins, J.I.(2004) Pervasive genomic

recombination of HIV -1 in vivo. Genetics, 167: 1573-1583.

Shrivastava, N., Srivastava, A. (2008) RNA interference: an emerging

generation of biologicals. Biotechnol Journal, 3(3):339-353.

Siddappa, N.B., Dash, P.K, Mahadevan, A., Jayasuryan, N., Hu, F., Dice, B.,

Keefe, R, Satish, KS., Satish, B., Sreekanthan, K, Chatterjee, R, Venu, K,

Satishchandra, P., Ravi, V., Shankar, S.K, Shankarappa, Rand Ranga, U.

(2004) Identification of subtype C human immunodeficiency virus type 1 by

subtype-specific PCR and its use in the characterization of viruses circulating

in the southern parts of India. Journal of Clinical Microbiology, 42: 2742-2751.

Siddappa, N.B., Venkatramanan, M., Venkatesh, P., Janki, M.V., Jayasuryan,

N., Desai, A., Ravi, V., Ranga, U.(2006) Transactivation and signaling

functions of Tat are not correlated: biological and immunological

characterization of HIV -1 subtype-C Tat protein. Retrovirology, 3: 53.

Silverman, S.K (2005) In vitro selection, characterization, and application of

deoxyribozymes that cleave RNA. Nucleic Acids Research, 33(19): 6151-6163.

Simoes, E.A., Babu, P.G., John, T.J., Nirmala, S., Solomon, S.,

Lakshminarayana, C.S. and Quinn, T.C. (1987) Evidence for HTLV-III

infection in prostitutes in Tamil Nadu (India). Indian Journal of Medical

Research, 85: 335-338.

Simon-Loriere, E., Galetto, R, Hamoudi, M., Archer, J., Lefeuvre, P. (2009)

Molecular Mechanisms of Recombination Restriction in the Envelope Gene of

the Human Immunodeficiency Virus. PLoS Pathogens, 5(5)

179 I P age

I References

Singh, H.K, Gupta, A., Siberry, G.K, Gupte, N., Sastry, J., Kinikar, A., Shah,

1., Gangakhedkar, RR, Bollinger, RC and Kulkarni, V. (2008)The Indian

pediatric HIV epidemic: a systematic review. Current HIV Research, 6, 419-

432.

Sioud, M., and Leirdal, M. (2002). Gene silencing in mammalian cells by

performed RNA duplexes. Biochemical Biophysical Research

Communications, 295: 744-748.

Slim, G. and Gait, M.J. (1991) Configurationally defined phosphothioate

containing oligoribonucleotide in the study of the mechanism of cleavage of

hammerhead ribozymes. Nucleic Acid Research,19: 1183-1188.

Song, E., Zhu, P., Lee, S.K, Chowdhury, D., Kussman, S., Dykxhoorn, D.M.,

Feng, Y., Palliser, D., Weiner, D.B., Shankar, P., Marasco, W.A., Lieberman,

J.(2005) Antibody mediated in vivo delivery of small interfering RNAs via cell­

surface receptors. Nature biotechnology, 23: 709-717.

Sood, V., Gupta, N., Bano, A. S. and Banerjea, A.C (2007)DNA-Enzyme­

Mediated Cleavage of Human Immunodeficiency Virus Type 1 Gag RNA Is

Significantly Augmented by Antisense-DNA Molecules Targeted to

Hybridize Close to the Cleavage Site. Oligonucleotides, 17(1) : 113-121.

Sood, V., Ranjan, R, Banerjea, A.C (2008) Functional analysis of HIV-1

subtypes Band C HIV -1 Tat exons and RGD/QGD motifs with respect to Tat­

mediated transactivation and apoptosis. AIDS, 22(13): 1683-1685.

Soutschek, J., Akinc, A., Bramlage, B., Charisse, K, Constien, R, Donoghue,

M., Elbashir, S., Geick, A., Hadwiger, P., Harborth, J., John, M., Kesavan, V.,

Lavine, G., Pandey, RK, Racie, T., Rajeev, KG. (2004) Therapeutic silencing

of an endogenous gene by systemic administration of modified siRNAs.

Nature, 432: 173-178.

180 I P age

I References

Spina, CA., Kwoh, T.J., Chowers, M.Y., Guatelli, J.C, and Richman, D.D.

(1994). The importance of nef in the induction of human immunodeficiency

virus type 1 replication from primary quiescent CD4 lymphocytes. Journal of

Experimental Medicine, 179: 115-123.

Sreedhara, A., Li,Y. and Breaker,RR (2004) Ligating DNA with DNA. Journal

of American Chemical Society, 126: 3454-3460.

Srinivasan, A., Ayyavoo, V., Mahalingam, S., Kannan, A., Boyd, A., Datta, D.,

Kalyanaraman, V. S., Cristillo, A., Collman, R G. (2008). A comprehensive

analysis of the naturally occurring polymorphisms in HIV -1 Vpr: potential

impact on CTL epitopes. Virology Journal, 5: 99-116.

Stark, B. C, Kole, R, Bowman, E. J., and Altman, S. (1978) Ribonuclease P: an

Enzyme with an Essential RNA Component. Proceedings of National

Academy of Sciences, U. S. A. 75: 3717-3721.

Strebel, K., Klimkait, T., Martin, M.A. (1988) A novel gene of HIV-l, vpu, and

its 16 KDa product. Science, 241:1221-1223.

Sun, L-Q., Cairns, M.J., Gerlach, W.L., Witherington, C, Wang, L., King, A.

(1999) Suppression of smooth muscle cell proliferation by a c-myc RNA

cleaving deoxyribozyme. Journal of Biological Chemistry, 274: 17236-17241.

Surabhi, RM. and Gaynor, RB.(2002) RNA interference directed against viral

and cellular targets inhibits human immunodeficiency Virus Type 1

replication. Journal of Virology, 76: 12963-12973.

Suryavanshi, G.W., Dixit, N.M. (2007) Emergence of recombinant forms of

HIV: dynamics and scaling. PLoS Computational Biology, 3: e205.

Suzuki, T., Yamamoto, N., Nonaka, M., Hashimoto, Y., Matsuda, G.,

Takeshima, S. N., Matsuyama, M., Igarashi, T., Miura, T. (2009). Inhibition of

----_._ ..... 181 I P age

I References

human immunodeficiency virus type 1 (HIV-1) nuclear import via Vpr­

importin a interactions as a novel HIV-1 therapy. Biochemical Biophysical

Research Communications, 380: 838-843.

Talini, G., Gallori, E., Maurel, M.C(2009) Natural and unnatural ribozymes:

back to the primordial RNA world. Research in microbiology,160 (7): 457-465.

Taylor, N.R, Kaplan, B.E., Swiderski, P., Li,H., Rossi, J.J.(1992) Chimeric

DNA-RNA hammerhead ribozymes have enhanced in vitro catalytic efficiency

and increased stability in vivo.Nucleic Acids Res.20(17):4559-65.

Templeton, A.R, Kramer, M.G., Jarvis, J., Kowalski, J., Gange, S., Michael F

Schneider, M.F. Shao, Q., Zhang, G.W., Yeh, M.F., Tsai, H.L., Zhang, H.and

Markham, RB. (2009) Multiple-infection and recombination in HIV -1 within a

longitudinal cohort of women. Retrovirology, 6:54

Thotala, D., Schafer, E.A., Majumder, B., Janket, M.L., Wagner, M., Srinivasan,

A. (2004) Structure-functional analysis of human immunodeficiency virus

type 1 (HIV-1) Vpr: role of leucine residues on Vpr-mediated transactivation

and virus replication. Virology, 328: 89-100.

Tripathy, S.P., Kulkarni, S.5., Jadhav, S.D., Agnihotri, KD., Jere, A.J., Kurle,

S.N., Bhattacharya, S.K, Singh, K, Tripathy, S.P. and Paranjape, RS. (2005)

Subtype B and Subtype C HIV Type 1 Recombinants in the Northeastern State

of Manipur, India. AIDS Research and Human Retroviruses, 21, 152-157.

Tristem, M.(1998). Complex evolutionary history of primate lentiviral vpr

genes. Virology, 240: 232-237.

Trkola, A., Dragic, T., Arthos, J., Binley, J.M., Olson, W.C, Allaway, G.P.

(1996) CD4-dependent, antibody-sensitive interactions between HIV-1 and its

co-receptor CCR-S. Nature, 384:184-187.

182 I P age

I References

Tungaturthi, P.K. (2003). Role of HIV-1 Vpr in AIDS pathogenesis: relevance

and implications of intravirion, intracellular and free Vpr. Biomedical

Pharmacotherapy, 57: 20-24.

Uhlenbeck, O.C (1987) A small catalytic oligoribonudeotide. Nature,. 328:

596-600.

UNAIDS Report of the global AIDS epidemic. 2008. http://www.unaids.org

len IKnowledgecentre/HIVData/GlobaIReport/2008/2008_Global_report. asp.

accessed in September 2008

Unwalla, H., Banerjea, A.C (2001) Novel mono- and di-DNA-enzymes

targeted to cleave TAT or TAT-REV RNA inhibit HIV-1 gene

expression. Antiviral Research, 51:127-139.

Unwalla, H.J., Li, H., Li, S.Y., Abad, D., Rossi, J.J .. (2008) Use of a U16

snoRNA-containing ribozyme library to identify ribozyme targets in HIV-

l.Mol Ther. 16(6):1113-1119.

Usman, N. and Blatt, L.M. (2000) Nuclease-resistant synthetic ribozymes:

developing a new class of therapeutics Journal of Clinical Investigation,

106(10): 1197-1202.

Vanitharani, R., Mahalingam, 5., Rafaeli, Y., Singh, S.P., Srinivasan, A.,

Weiner, D.B., Ayyavoo, V.(2001) HIV-1 Vpr transactivates LTR-directed

expression through sequences present within -278 to -176 and increases virus

replication in vitro. Virology, 289: 334-342.

Vodicka, M. A., Goh, W. C, Li,W., Rogel, M. E., Bartz, S. R., Schweickart, V.

L., Raport, C J., and Emerman, M. (1997) Indicator cell lines for detection of

primary strains of human and simian immunodeficiency viruses. Virology,

233: 193-198.

183 I P age

-----------------

I References

Wang, D.Y., Sen, D. (2001) A novel mode of regulation of an RNA-cleaving

DNAzyme by effectors that bind to both enzyme and substrate. Journal of

Molecular Biology, 310: 723-34.

Wang, L., Mukherjee, S., Jia, F., Narayan, O. & Zhao, L. J. (1995). Interaction of

virion protein Vpr of human immunodeficiency virus type 1 with cellular

transcription factor Sp 1 and trans-activation of viral long terminal repeat.

Journal of Biological Chemistry, 270: 25564-25569.

Wang, W., Billen, L.P. and Li, Y. (2002) Sequence diversity, metal specificity,

and catalytic proficiency of metal-dependent phosphorylating DNA enzymes.

Chemical Biology, 9: 507-517.

Weiss, R, Teich, N., Varmus, H. And Coffin, J., eds (1984) RNA tumor

viruses. Vol.1 & 2. Cold spring Harbour: Cold spring harbour lab.1292 pp.,

2344 pp 2nd edition.

Weiss, RA.(200l) Gulliver's travel in HIVland. Nature, 410: 963-967.

Weissenhoni., W., Dessen, A., Harrison, S.C, Skehel, J.J., Wiley, D.C (1997)

Atomic structure of the ectodomain from HIV-1 gp41. Nature, 387:426-430.

Win, M.N., Smolke, CD. (2007) A modular and extensible RNA-based gene­

regulatory platform for engineering cellular function.Proc Natl Acad Sci USA

104:14283-14288.

Winkler, C, Modi, W., Smith, M.W., Nelson, G.W., Wu, X., Carrington, M.,

Dean, M., Honjo, T., Tashiro, K., Yabe, D., Buchbinder, S., Vittinghoff, E.,

Goedert, J.J., O'Brien, T.R, Jacobson, L.P., Detels, R, Donfield, S., Willoughby,

A., Gomperts, E., Vlahov, D., Phair, J., O'Brien, S.J. (1998). Genetic restriction

of AIDS pathogenesis by an SDF-1 chemokine gene variant. Science, 279: 389-

393.

184 I P age

I References

Woffendin, c., Ranga, V., Yang, Z., Xu, L. and Nabel, G.J. (1996) Expression of

a protective gene-prolongs survival of T cells in human immunodeficiency

virus-infected patients. Proceedings of National Academy of Sciences, VSA,

93: 2889-2894.

Wong-Staal, F., Poeschla, E.M. and Looney, D.J.(1998) A controlled, phase 1

clinical trial to evaluate the safety and effects in HIV -1 infected humans of

autologous lymphocytes transduced with a ribozyme that cleaves HIV-l

RNA. Human Gene Therapy, 9: 2407-2425.

Wu, Y., McMahon, R, Rossi, J.J., Forman, S.J., Snyder, D.5. (1999) Inhibition of

bcr-abl oncogene by novel deoxyribozymes (DNAzymes). Human Gene

Therapy, 10:2847 -2857.

Xiang, G., Seki, T., Schuster, M.D., Witkowski, P., Boyle, Al, See, F., Martens,

T.P., Kocher, A., Sondermeijer, H., Krum, H., Itescu, S. (2005) Catalytic

degradation of vitamin D up-regulated protein 1 mRNA enhances

cardiomyocyte survival and prevents left ventricular remodeling after

myocardial ischemia. Journal of Biological Chemistry, 280: 39394-39402.

Yamamoto, K., Morishita, R, Tomita, N., Shimozato, T., Nakagami, H.,

Kikuchi, A., Aoki, M., Higaki, J., Kaneda, Y. and Ogihara, T. (2000) Ribozyme

oligonucleotide against transforming growth factor B inhibited neonatal

formation after vascular injury in rat model: potential application of

Ribozyme strategy to treat cardiovascular disease. Circulation, 102(11), 1308-

1314.

Young, K.J., Gill, F. and Grasby, J.A. (1997) Metal ions playa passive role in

the hairpin ribozyme catalysed reaction, Nucliec Acid research, 25(19): 3760-

3766.

185 I P age

I References

Yu, X., Yu, Y., Liu, B., Luo, K., Kong,W., Mao, P. & Yu, X. F. (2003). Induction

of APOBEC3G ubiquitination and degradation by an HIV -1 Vif-CuI5-SCF

complex. Science, 302: 1056-1060.

Zander, K. (2003). Cyclophilin A interacts with HIV-1 Vpr and is required for

its functional expression. Journal of Biological Chemistry, 278: 43202-43213.

Zhang, G., Dass, C.R, Sumithran, E., Di Girolimo, N.R, Sun, L-Q.,

Khachigian, L.M. (2004) Effect of deoxyribozymes targeting c-Jun on solid

tumor growth and angiogenesis in rodents. Journal of National Cancer

Institute, 96: 683-696.

Zhang, G., Luo, X., Sumithran, E., Pua, V.S.c., Barnetson, RS., Halliday, G.M.,

Khachigian, L.M.(2006) Squamous cell carcinoma growth in mice and in

culture is regulated by c-Jun and its control of matrix metalloproteinase- 2

and -9 expression. Oncogene, 25: 7260-7266.

Zhang, H., Kolb, F.A., Jaskiewicz, L., Westhof, E., Filipowicz, W. (2004) Single

processing center models for human Dicer and bacterial RNase III. Cell, 118:

57-68.

Zhang, L., Gasper, W.J., Stass, S.A., Ioffe, O.B., Davis, M.A., Mixson, A.J.

(2002) Angiogenic inhibition mediated by a DNAzyme that targets vascular

endothelial growth factor receptor 2. Cancer Research, 62: 5463-5469.

Zheng,Y.H., Lovsin, N. and Peterlin, B. M. (2005). "Newly identified host

factors modulate HIV replication". Immunology Letter, 97 (2): 225-234.

Zhou, B.B., Elledge, S.J.(2000). The DNA damage response: putting

checkpoints in perspective. Nature, 408: 433-439.

186 I P age

I References

Zhou, J., Li, H., Li, 5., Zaia, J., Rossi, J.J. (2008) Novel dual inhibitory function

aptamer-siRNA delivery system for HIV-1 therapy. Molecular

Therapy,16(8):1481-1489.

Zimmerman, B.S., Chen, J., Andersen, J.L., Ardon, 0., Dehart, J.L., Blackett, J.,

Choudhary, S.K., Camerini, D., Nghiem, P., Planelles, V.(2004) Human

immunodeficiency virus type 1 Vpr-mediated G2 arrest requires Rad17 and

Hus1 and induces nuclear BRCA1 and gamma-H2AX focus formation.

Molecular Cell Biology, 24(21): 9286-9294.

Zinnen, S.P., Domenico, K., Wilson, M., Dickinson, B.A., Beaudry, A., Mokler,

v., Daniher, A.T., Burgin, A. and Beigelman, L. (2002) Selection, design, and

characterization of a new potentially therapeutic ribozyme.RNA, 8(2): 214-228.

187 I P age