Research Collection Doctoral Thesis Engineering inorganic nanomaterials for the capturing, storage and release of biomolecules Author(s): Zlateski, Vladimir Publication Date: 2016 Permanent Link: https://doi.org/10.3929/ethz-a-010750035 Rights / License: In Copyright - Non-Commercial Use Permitted This page was generated automatically upon download from the ETH Zurich Research Collection . For more information please consult the Terms of use . ETH Library
99
Embed
Rights / License: Research Collection In Copyright - Non ...49896/...2.2.9 Cobalt leaching experiment 35 ... Das Enzym war im eingeschlossenen ... In the present thesis recent advances
This document is posted to help you gain knowledge. Please leave a comment to let me know what you think about it! Share it to your friends and learn new things together.
Transcript
Research Collection
Doctoral Thesis
Engineering inorganic nanomaterials for the capturing, storageand release of biomolecules
yields. Still, over the range of more than one order of magnitude of initial conditions
(10...300 ng DNA / mg particle) recovery yields of > 50% can be obtained.
Keeping the optimized particles to ssDNA ratio constant (1 mg of particles, 20 pmol of
DNA) we performed a series of up-concentration experiments in which the reaction
volumes were gradually increased, and the DNA concentrations were therefore
decreased (Figure 4.3D). Even when starting with DNA concentrations in the sub
nanomolar region (and a volume of 40 ml) we were able to capture > 30 % of the
specific DNA sequence present and release it into a one thousand times smaller volume
72
(40 µl f
instead
yield of
Figure
ssDNA-
differen
(1 mg);
constan
comple
parame
in the g
To sim
extracti
dissolv
ultrason
The tar
for direct d
d of 1 mg (t
f 80 % was
4.3 A. B
-modified p
nt DNA am
; C. Recov
nt (20 pm
ementary se
eter shown
given exper
mulate a rea
ion and d
ed salmon
nication pr
rget strand
detection).
to increase
s obtained.
inding kin
particles;
mounts wer
very yield o
mol) where
equence wh
in red in t
riment.
alistic scen
etection fr
n sperm
rocessor lo
d (20 pmol
When we
e the statist
netics of th
B. Recove
re used wh
of the com
eas the pa
hen the rea
the boxes o
nario in ter
rom a con
DNA in
ong enough
, 0.14 μg)
repeated t
tics of DNA
he complem
ery yield o
hereas the
mplementar
article mas
action volu
on top of ev
rms of spe
ntaminated
tap water
h to break
was added
this experim
A - particl
mentary se
of the com
amount of
ry sequence
ss varied;
ume was inc
very graph
cificity we
d water sam
r (7 μg/mL
it into sho
d to the sh
ment using
e binding e
equence w
mplementar
f particles
e when its
D. Recov
creased up
is the one
e performe
mple. For
L) and tre
orter fragm
heared DN
g 5 mg of p
events) a r
when added
ry sequenc
was kept c
s amount w
very yield
p to 1000-fo
e that was c
ed a specifi
this purp
eated it w
ments (ca 2
NA solution
particles
ecovery
d to the
ce when
constant
was kept
d of the
fold. The
changed
fic DNA
pose we
with an
200 bp).
n one to
one, res
particle
to recov
the spe
and pur
Scheme
terms o
Standar
Qubit®
The de
target s
min to
hybridi
microti
standar
(estima
(Schem
and eve
h). In a
mixture
using th
sulting in a
es was add
ver 70 % o
cificity of
rifying spe
e 4.2 An ov
of time req
rd laborat
ssDNA As
escribed ex
ssDNA seq
o determin
ization, 5 m
iter plate a
rd laborato
ated time o
me 4.2). To
en then ke
addition, PC
e, thus req
he particle
a 100 fold
ed and the
of the comp
the bindin
cific DNA
verview of
quirement.
tory ssDNA
ssay which
xperimenta
quence, sim
ne DNA
min washin
and measur
ory assay
f analysis
o run a qPC
ep in mind
CR is often
quiring a p
based enri
excess of t
e hybridizat
plementary
g and the p
A sequences
f the ssDNA
The enrich
A detection
requires 1
al procedur
mply by m
presence
ng, 10 min
re the fluo
for ssDNA
is 10 min)
CR instead
d the longe
n affected b
pre-treatme
ichment pro
the salmon
tion reactio
y sequence
potential u
s from envi
A enrichme
hment pro
n method
10 min to p
re allows
magnetic u
and conce
n melting a
orescence).
A detectio
, we would
d one need
er time unt
by some co
ent (an add
ocedure).
n sperm DN
on took pla
added to t
sefulness o
ironmental
ent and det
cedure tak
follows up
erform.
for a fast
up-concentr
entration b
and 5 min t
If we com
on, for ex
d need 50 m
ds to posse
til the resu
omponents
ditional ste
NA by mas
ace. Even t
the mix. Th
of the parti
l samples.1
tection met
kes 40 min
pon enrich
and reliab
ration and
by a fluo
to pipette t
mbine our
x. Qubit®
min for the
ess the exp
ult is out (a
found in th
ep we coul
s (14 μg).
then, we m
his result c
icles for co193
thod from
n until com
hment, for
ble detecti
required
orimeter (2
the sample
procedure
ssDNA as
e whole pr
pensive equ
approxima
he original
ld eliminat
73
1 mg of
managed
confirms
ollecting
DNA in
mpletion.
ex. the
on of a
only 45
25 min
es into a
e with a
ssay kit
ocedure
uipment
tely 2-3
l sample
te when
74
4.4 Conclusion
In summary, we demonstrated a synthesis of a novel magnetic nanomaterial that was
successfully used in DNA enrichment experiments. For this purpose, we combined the
well-known advantages of the silica surfaces in biomolecule attachment with the high
magnetic saturation of the carbon-coated iron nanoparticles used as a starting point in
our synthesis. We managed to stably immobilize ssDNAs of interest on the surface of
our newly produced material. Furthermore, we developed a procedure to enrich (up-
concentrate) a target complementary ssDNA of interest from a mixture of DNAs with
high recovery yield and specificity. No binding of a false DNA sequence could be
monitored. Under the tested conditions, we achieved high recovery yields even when
the complementary DNA sample volume was up-concentrated 1000-fold. Coupled
with a standard laboratory ssDNA detection assay kit we demonstrated a possibility to
PCR-free detect low-concentrated ssDNA in significantly less than an hour, thus
eliminating the need for having a PCR machine and the longer times of detection.
For the future we envision that this proof-of-principle of rapid DNA purification and
up-concentration can be extended and proven useful in the areas of pre-sequencing
DNA enrichment, environmental sample analysis, DNA tracing experiments as well as
point of care diagnostics. It may also be useful in combination with other DNA
detection means (e.g. polyvalent DNA gold nanoparticles, lateral flow devices) in
which the concentration and purity of the natural sample may limit reliable DNA
detection.
75
5 Conclusion and outlook
76
To summarise, biomolecule/inorganic particle hybrids were assembled and some of their
applications were presented in the previous chapters. In other words, we managed to bind
proteins and DNAs to nanomaterials and carry them around in solution. We utilized the
advantages magnetic nanoparticles and silicas have to offer in the field of nanobiotechnology
each of them alone but also combined. Firstly, we successfully constructed promising
enzyme/magnetic particles hybrids which showed high enzyme loadings and activity and most
importantly allowed for a multiliter scale re-use of the biocatalyst. With the idea to improve
enzyme shelf storage at RT (having in mind the fragility of most enzymes) we thought of
sealing high amounts of enzymes in the pores of mesocellular foams and releasing them upon
demand with application in biocatalysis or possibly biosensors. By combining these two
materials and their properties we finally produced magnetic NPs/silica composites which were
stably loaded with single stranded DNAs with which we could selectively enrich a target
DNA strand from a DNA mix.
When it comes to magnetic nanoparticles and their application in biocatalysis, they are
becoming increasingly important and receiving more and more attention. The main reason for
their popularity is the ability to separate them from the reaction medium simply with the aid
of a magnet while the other advantages that nanomaterials offer are preserved, like for
example the high surface area to volume ratio. In the last years, iron oxide nanoparticles
(magnetite or maghemite) have been shown to be a possible platform for enzyme
immobilization. As good as it might sound, the iron oxide nanomaterials show only limited
magnetic saturation which prevents them from use on larger scales, for example in industrial
set-ups. Some iron oxide materials have shown questionable stability which is also very
important when it comes to the enzymatic carrier of choice. The carbon-coated cobalt
nanoparticles utilized in this work not only show high pH, temperature and organic solvent
stability but also could be retracted from the reaction medium in a few seconds (mL scale) or
in a few minutes (L scale) thanks to their high magnetic saturation. In addition, the carbon
surface gave us the possibility to link the enzyme covalently to the surface by reliable organic
chemistries in order to prevent leaching. All three enzyme we bound to the nanomaterials
resulted in high activity and loading and enzyme re-use in 20 L reaction tank was
demonstrated. In terms of applicability of the improved magnetic properties, the rapidly
growing field of chemical biocatalysis can profit from magnetic separation technology, which
is already well established in the fields of analytical immunoprecipitation and cell separation
on the milliliter scale utilizing metal oxide based particles.
77
Silica materials have also been extensively utilized in the field of biocatalysis. The channels
of such pre-fabricated porous inorganic materials proved to be very suitable for enzyme
immobilization. Adsorption is especially attractive due to its simplicity but leaching of the
enzyme is inevitable. With the know-how in pore fine-tuning scientists tried tailoring
mesoporous materials with channel sizes big enough to exactly fit the protein of interest.
However, decreased enzyme activity and substrate diffusion problems were evident. Our
strategy was to completely seal the enzyme inside the porous matrix in order to be able to
stably store it at room temperature for a longer period of time without the need of having a
fridge or a freezer. The silica build-up (sol-gel synthesis) by utilizing silicate precursors is a
well-known reaction and we managed to optimize it to be able cover the pore openings of the
mesocellular foam. The novelty we introduced is the mild fluoride buffer solutions (4 % F-)
needed to completely dissolve the nano-support. Such buffers have a limited use in
biochemistry although we saw no effect on the enzyme stability at the concentrations of
buffer used. For comparison, up to 1.23 wt% fluoride-containing dental products (gels) are
nothing uncommon. In the future, one could pay special attention to sensitive enzymes, which
are very delicate to handle and require low storage temperatures. The multiple freeze-thaw
cycles and the need for a freezer could be eliminated by our approach. In addition, the
possibility to perform field studies (as part of biosensors) in regions where temperature is high
shows a great application potential and is worth further experimentation.
By combining the advantages of both so far utilized nanomaterial classes we aimed at
producing magnetic particles-silica nanocomposites for enrichment applications. Despite the
ease of separation provided by the magnetic core, the silica surface proved to be a good
platform for covalent DNA attachment because of its anti-fouling character and the well-
established silane chemistry. Basically, our ssDNA-loaded beads were thrown into larger
volumes, let hybridize with the complementary strand from a mix of DNAs and the strand
was then released into smaller volumes by heating up the samples. Although here we mainly
showed a proof of concept, the very high specificity achieved opens up a window of
opportunities for future applications. One application would be fast DNA detection from
samples with very low concentrations without the need to do PCR. If we combine our
procedure with a standard laboratory assay for ssDNA detection, for ex. Qubit® ssDNA
Assay kit (estimated time of analysis is 10 min), we would need 50 min for the whole
procedure where 3 h is the estimated time one needs to perform a PCR. The expensive PCR
equipment and the fact that PCR is often affected by some components found in the original
sample mixture makes our approach a faster and cheaper alternative. Other applications could
78
involve targeting certain genomic regions prior to sequencing as another alternative of the
solution-based hybridization approach. Such a platform could be also used for enzyme
applications and possibly biocatalysis. ssDNA-modified enzyme could be obtained with a
sequence complementary to the one attached to the particles surface. A boomerang enzyme
system could be created by controlling the release and immobilization of the enzyme by
changing the temperature.
The thesis shows how the fusion of biomolecules and inorganic materials has not only led to
significant progresses in traditional application fields but has additionally opened up new
opportunities. The combination of these two components in the last years has allowed the
design and manufacturing of hybrid materials with new properties to address different
technological problems. In our work we tried to profit from the advantages some novel
nanomaterials have to offer mainly focussing on applications in the fields of biocatalysis and
DNA enrichment and meeting the industrial needs for a re-usable biocatalyst and long-term
RT storage stability of enzymes. Fast and reliable DNA detection without the need for PCR is
promising in many technological areas.
79
Appendix
80
A.1 Su
Scheme
flow. Fi
80 mL)
(unmod
Afterwa
decante
suspend
upporting
e A1.1 Imm
irst, an enzy
of which th
dified or D
ards the pa
ed and the
ded in dH20
g informat
mobilization
yme solution
he enzymati
DSC-activate
articles wer
e residual
(80 mL) an
ion to Cha
(covalent o
n was prepa
c activity w
ed) were a
re separate
enzymatic
nd were used
apter 2
or adsorptio
ared by diss
was measure
added and
ed with the
activity w
d in the imm
on) of enzy
solving the
ed (total act
the immob
e aid of a
was measur
mobilized en
me on a pa
enzyme in w
tivity). Mag
bilization p
magnet, th
red. The n
nzyme activ
article expe
water (fina
gnetic nanop
proceeded f
he supernat
nanoparticl
vity assays.
erimental
l volume
particles
for 5 h.
tant was
es were
81
Table A1.1 (Upper rows): C, H, N weight gain of the Co/C–enzyme conjugates relative to
their precursors determined by elemental microanalysis measurement (Co/C–C: 6.8 %, H:
0.1 %, N: 0 %). (Lower rows): C, H, N weight gain of the DB–β-Glu compared to the -COOH
functionalized DB
Sample C (%) H (%) N (%)
Co/C–Ph-EtOH + 0.8 + 0 + 0
Co/C–DSC activated + 0.4 + 0.1 + 0.1
Co/C–β-Glu
Co/C–α-CT
+ 1.8
+ 2.3
+ 0.3
+ 0.4
+ 0.8
+ 1
Co/C–CALB + 0.8 + 0.2 + 0.2
DB-COOH 36 3.7 3.9
DB-β-Glu 37.5 3.9 4.4
Table A1.2 Vibrating sample magnetometry (VSM) hysteresis data of magnetic particle–
enzyme conjugates compared to their precursors. The enzyme containing particles show
almost as high magnetic saturation as the unmodified raw products
Sample Ms (emu g-1) Hc (Oe) Mr (emu g-1)
Co/C 143 241 31.1
Co/C–Ph-EtOH 142 158 20.8
Co/C–β-Glu
Co/C–α-CT
133
131
178
170
17.7
21.8
Co/C–CALB 136 175 22.4
DB-COOH 26.2 2.3 0.16
DB-β-Glu 25.1 2.5 0.18
82
Table A
detected
Atomic %
Co/C–Ph
Co/C–DS
Figure
microsc
particle
Figure
(red colu
A1.3 XPS an
d elements
%
h-EtOH
SC activated
A1.1 Scann
copy (SEM)
es coated wi
A1.2 LC/M
umns) β-Glu.
nalysis of th
ning transm
) b) of the
ith a polyme
MS/MS analys
. Actual mas
he Co/C func
C
85.8
82.1
mission elec
enzyme co
eric layer (e
sis of tryptic
s versus sign
ctionalized
O
5.
7.
ctron micro
oated magn
enzyme).
c digests of n
nal intensity
nanopartic
O
4
6
oscopy (STE
netic nanop
native (black
is shown.
les-normali
N
0.0
1.1
EM) a) and
particles dis
k columns) a
ized atomic
Co
8.8
9.2
d scanning
splaying in
and covalent
% of all
electron
ndividual
tly bound
Figure
regions
mass spe
with the
Figure
Co/C) a
placed b
the vials
A1.3 Swiss
indicated: g
ectroscopy a
highest sign
A1.4 The
and the bac
between the
s.
-PdbViewer
green (left)–th
analysis of it
al intensity a
relative tra
ckground pl
e vials; Hol
v4.1 image
he region of
ts tryptic dig
after mass sp
ansmission
lotted again
llow square
of the β-Gl
f the native e
gest and red
pectroscopy a
between th
nst time. So
es-Dynabea
lu monomer
enzyme with
(right)-the r
analysis of it
he particle
olid squares
ads when th
simulation w
the highest
region of the
ts tryptic dig
suspension
s–Co/C wh
he magnet w
with two po
signal inten
e immobilized
gest.
ns (Dynabe
hen the mag
was placed
83
olypeptide
nsity after
d enzyme
eads and
gnet was
between
84
A.2 Su
Figure
(MCF).
extrusio
Figure
extrapo
upporting
A2.1 Cum
Solid circ
on.
A2.2 Size o
lated from t
g informat
mulative me
cles indica
of the pore
the mercury
ion to Cha
ercury intru
te the intr
windows of
y intrusion d
apter 3
usion analy
rusion whe
of the MCF
data.
ysis of the
ereas the e
F cells plotte
siliceous
empty coun
ed against t
mesocellul
nterparts st
the pore vo
ar foam
tand for
olume as
Figure
glucosid
inverted
after fl
immobil
Figure
chymotr
fluoride
A2.3 Influe
dase entrap
d triangles)
luoride buff
lized enzym
A2.4 Influe
rypsin after
e buffer pH
ence of the
pped (black
and β-gluc
ffer suppor
me after diss
ence of fluo
r treatment
4 (1:10 dilu
entrapment
k stars) com
cosidase fre
rt dissoluti
olving its su
ride buffers
of the enzy
uted, sparse
t process an
mpared to th
ee in solutio
ion (dashed
upport coul
s on the enz
ymes with f
e columns) a
nd storage
he β-glucos
on (black sq
d lines). N
ld be observ
zymatic act
fluoride buf
and fluoride
on the enzy
idase immo
quares) befo
No improve
ved.
ivities of β-
ffer at pH
e buffer pH
ymatic activ
obilized onl
ore (solid lin
ed activity
-glucosidase
4 (dense co
5 (black co
85
vity of β-
ly (black
nes) and
y of the
e and α-
olumns),
olumns).
86
References
(1) Feynman, R. P. (2011) There’s plenty of room at the bottom. Resonance 16, 890-905.
(2) Mirkin, C. A. (2005) The beginning of a small revolution. Small 1, 14-16.
(3) Ahn, J. H., Kim, H. S., Lee, K. J., Jeon, S., Kang, S. J., Sun, Y. G., Nuzzo, R. G., and Rogers, J. A. (2006) Heterogeneous three-dimensional electronics by use of printed semiconductor nanomaterials. Science 314, 1754-1757.
(4) Kamyshny, A., and Magdassi, S. (2014) Conductive Nanomaterials for Printed Electronics. Small 10, 3515-3535.
(5) Wang, J. (2005) Nanomaterial-based electrochemical biosensors. Analyst 130, 421-426.
(6) Erdem, A. (2007) Nanomaterial-based electrochemical DNA sensing strategies. Talanta 74, 318-325.
(7) Zhong, C. J., and Maye, M. M. (2001) Core-shell assembled nanoparticles as catalysts. Adv. Mater. 13, 1507-1511.
(8) Salata, O. (2004) Applications of nanoparticles in biology and medicine. J. Nanobiotechnol. 2, 1-6.
(9) Rao, C. N. R., and Cheetham, A. K. (2001) Science and technology of nanomaterials: current status and future prospects. J. Mater. Chem. 11, 2887-2894.
(10) Sapsford, K. E., Tyner, K. M., Dair, B. J., Deschamps, J. R., and Medintz, I. L. (2011) Analyzing Nanomaterial Bioconjugates: A Review of Current and Emerging Purification and Characterization Techniques. Anal. Chem. 83, 4453-4488.
(11) Ball, P. (2002) Natural strategies for the molecular engineer. Nanotechnology 13, R15-R28.
(12) Roco, M. C. (2003) Nanotechnology: convergence with modern biology and medicine. Curr. Opin. Biotechnol. 14, 337-346.
(13) Seeman, N. C. (2010) Structural DNA Nanotechnology: Growing Along with Nano Letters. Nano Lett. 10, 1971-1978.
(14) Pinheiro, A. V., Han, D. R., Shih, W. M., and Yan, H. (2011) Challenges and opportunities for structural DNA nanotechnology. Nat. Nanotechnol. 6, 763-772.
(15) Seeman, N. C. (2003) DNA in a material world. Nature 421, 427-431.
(16) Rothemund, P. W. K. (2006) Folding DNA to create nanoscale shapes and patterns. Nature 440, 297-302.
(17) Winfree, E., Liu, F. R., Wenzler, L. A., and Seeman, N. C. (1998) Design and self-assembly of two-dimensional DNA crystals. Nature 394, 539-544.
87
(18) Ke, Y. G., Ong, L. L., Shih, W. M., and Yin, P. (2012) Three-Dimensional Structures Self-Assembled from DNA Bricks. Science 338, 1177-1183.
(19) Wei, B., Dai, M. J., and Yin, P. (2012) Complex shapes self-assembled from single-stranded DNA tiles. Nature 485, 623-626.
(20) Chworos, A., Severcan, I., Koyfman, A. Y., Weinkam, P., Oroudjev, E., Hansma, H. G., and Jaeger, L. (2004) Building programmable jigsaw puzzles with RNA. Science 306, 2068-2072.
(21) Delebecque, C. J., Lindner, A. B., Silver, P. A., and Aldaye, F. A. (2011) Organization of Intracellular Reactions with Rationally Designed RNA Assemblies. Science 333, 470-474.
(22) Yeates, T. O., and Padilla, J. E. (2002) Designing supramolecular protein assemblies. Curr. Opin. Struc. Biol. 12, 464-470.
(23) Ghadiri, M. R., Granja, J. R., Milligan, R. A., McRee, D. E., and Khazanovich, N. (1993) Self-assembling organic nanotubes based on a cyclic peptide architecture. Nature 366, 324-327.
(24) Hecht, M. H. (1994) De-novo design of beta-sheet proteins. P. Natl. Acad. Sci. USA 91, 8729-8730.
(25) West, M. W., Wang, W. X., Patterson, J., Mancias, J. D., Beasley, J. R., and Hecht, M. H. (1999) De novo amyloid proteins from designed combinatorial libraries. P. Natl. Acad. Sci. USA 96, 11211-11216.
(26) Dotan, N., Arad, D., Frolow, F., and Freeman, A. (1999) Self-assembly of a tetrahedral lectin into predesigned diamondlike protein crystals. Angew. Chem. Int. Edit. 38, 2363-2366.
(27) Patwardhan, S. V., Patwardhan, G., and Perry, C. C. (2007) Interactions of biomolecules with inorganic materials: principles, applications and future prospects. J. Mater. Chem. 17, 2875-2884.
(28) Tirrell, M., Kokkoli, E., and Biesalski, M. (2002) The role of surface science in bioengineered materials. Surf. Sci. 500, 61-83.
(29) Stevens, M. M., and George, J. H. (2005) Exploring and engineering the cell surface interface. Science 310, 1135-1138.
(30) Addadi, L., and Weiner, S. (1985) Interactions between acidic proteins and crystals - stereochemical requirements in biomineralization. P. Natl. Acad. Sci. USA 82, 4110-4114.
(31) Kaplan, D. L. (1998) Mollusc shell structures: novel design strategies for synthetic materials. Curr. Opin. St. M. 3, 232-236.
(32) Faivre, D., and Schuler, D. (2008) Magnetotactic bacteria and magnetosomes. Chem. Rev. 108, 4875-4898.
(33) Matsunaga, T., Okamura, Y., Fukuda, Y., Wahyudi, A. T., Murase, Y., and Takeyama, H. (2005) Complete genome sequence of the facultative anaerobic magnetotactic bacterium Magnetospirillum sp strain AMB-1. DNA Res. 12, 157-166.
88
(34) Arakaki, A., Webb, J., and Matsunaga, T. (2003) A novel protein tightly bound to bacterial magnetic particles in Magnetospirillum magneticum strain AMB-1. J. Biol. Chem. 278, 8745-8750.
(35) Morse, D. E. (1999) Silicon biotechnology: harnessing biological silica production to construct new materials. Trends Biotechnol. 17, 230-232.
(36) Sumper, M., and Kroger, N. (2004) Silica formation in diatoms: the function of long-chain polyamines and silaffins. J. Mater. Chem. 14, 2059-2065.
(37) Kroger, N., Deutzmann, R., and Sumper, M. (1999) Polycationic peptides from diatom biosilica that direct silica nanosphere formation. Science 286, 1129-1132.
(38) Senior, L., Crump, M. P., Williams, C., Booth, P. J., Mann, S., Perriman, A. W., and Curnow, P. (2015) Structure and function of the silicifying peptide R5. J. Mater. Chem. B 3, 2607-2614.
(39) He, Y., Ye, T., Su, M., Zhang, C., Ribbe, A. E., Jiang, W., and Mao, C. D. (2008) Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra. Nature 452, 198-201.
(40) Coffer, J. L., Bigham, S. R., Li, X., Pinizzotto, R. F., Rho, Y. G., Pirtle, R. M., and Pirtle, I. L. (1996) Dictation of the shape of mesoscale semiconductor nanoparticle assemblies by plasmid DNA. Appl. Phys. Lett. 69, 3851-3853.
(41) Hopkins, D. S., Pekker, D., Goldbart, P. M., and Bezryadin, A. (2005) Quantum interference device made by DNA templating of superconducting nanowires. Science 308, 1762-1765.
(42) Becerril, H. A., and Woolley, A. T. (2009) DNA-templated nanofabrication. Chem. Soc. Rev. 38, 329-337.
(43) Braun, E., Eichen, Y., Sivan, U., and Ben-Yoseph, G. (1998) DNA-templated assembly and electrode attachment of a conducting silver wire. Nature 391, 775-778.
(44) Lund, J., Dong, J. C., Deng, Z. X., Mao, C. D., and Parviz, B. A. (2006) Electrical conduction in 7 nm wires constructed on lambda-DNA. Nanotechnology 17, 2752-2757.
(45) Ongaro, A., Griffin, F., Beeeher, P., Nagle, L., Iacopino, D., Quinn, A., Redmond, G., and Fitzmaurice, D. (2005) DNA-templated assembly of conducting gold nanowires between gold electrodes on a silicon oxide substrate. Chem. Mater. 17, 1959-1964.
(46) Monson, C. F., and Woolley, A. T. (2003) DNA-templated construction of copper nanowires. Nano Lett. 3, 359-363.
(47) Mahtab, R., Harden, H. H., and Murphy, C. J. (2000) Temperature- and salt-dependent binding of long DNA to protein-sized quantum dots: Thermodynamics of "inorganic protein"-DNA interactions. J. Am. Chem. Soc. 122, 14-17.
(48) Lakowicz, J. R., Gryczynski, I., Gryczynski, Z., Nowaczyk, K., and Murphy, C. J. (2000) Time-resolved spectral observations of cadmium-enriched cadmium sulfide nanoparticles and the effects of DNA oligomer binding. Anal. Biochem. 280, 128-136.
89
(49) Mahtab, R., Rogers, J. P., Singleton, C. P., and Murphy, C. J. (1996) Preferential adsorption of a ''kinked'' DNA to a neutral curved surface: Comparisons to and implications for nonspecific DNA-protein interactions. J. Am. Chem. Soc. 118, 7028-7032.
(50) Shi, B., Shin, Y. K., Hassanali, A. A., and Singer, S. J. (2015) DNA Binding to the Silica Surface. J. Phys. Chem. B 119, 11030-11040.
(51) Melzak, K. A., Sherwood, C. S., Turner, R. F. B., and Haynes, C. A. (1996) Driving forces for DNA adsorption to silica in perchlorate solutions. J. Colloid Interf. Sci. 181, 635-644.
(52) Gearheart, L. A., Ploehn, H. J., and Murphy, C. J. (2001) Oligonucleotide adsorption to gold nanoparticles: A surface-enhanced raman spectroscopy study of intrinsically bent DNA. J. Phys. Chem. B 105, 12609-12615.
(53) Park, S. J., Lazarides, A. A., Storhoff, J. J., Pesce, L., and Mirkin, C. A. (2004) The structural characterization of oligonucleotide-modified gold nanoparticle networks formed by DNA hybridization. J. Phys. Chem. B 108, 12375-12380.
(54) Patolsky, F., Ranjit, K. T., Lichtenstein, A., and Willner, I. (2000) Dendritic amplification of DNA analysis by oligonucleotide-functionalized Au-nanoparticles. Chem. Commun., 1025-1026.
(55) Bardea, A., Dagan, A., Ben-Dov, I., Amit, B., and Willner, I. (1998) Amplified microgravimetric quartz crystal-microbalance analyses of oligonucleotide complexes: a route to a Tay-Sachs biosensor device. Chem. Commun., 839-840.
(56) Dubertret, B., Calame, M., and Libchaber, A. J. (2001) Single-mismatch detection using gold-quenched fluorescent oligonucleotides. Nat. Biotechnol. 19, 365-370.
(57) Fischler, M., Sologubenko, A., Mayer, J., Clever, G., Burley, G., Gierlich, J., Carell, T., and Simon, U. (2008) Chain-like assembly of gold nanoparticles on artificial DNA templates via 'click chemistry'. Chem. Commun., 169-171.
(58) Cutler, J. I., Zheng, D., Xu, X. Y., Giljohann, D. A., and Mirkin, C. A. (2010) Polyvalent oligonucleotide iron oxide nanoparticle "click" conjugates. Nano Lett. 10, 1477-1480.
(59) Jiang, L., Yang, B. Q., Ma, Y. D., Liu, Y. C., Yang, W. S., Li, T. J., and Sun, C. C. (2003) The binding of phosphorothloate oligonucleotides to CdS nanoparticles. Chem. Phys. Lett. 380, 29-33.
(60) Hilliard, L. R., Zhao, X. J., and Tan, W. H. (2002) Immobilization of oligonucleotides onto silica nanoparticles for DNA hybridization studies. Anal. Chim. Acta 470, 51-56.
(61) Wang, Y. F., Wang, Y., Zheng, X. L., Ducrot, E., Lee, M. G., Yi, G. R., Weck, M., and Pine, D. J. (2015) Synthetic strategies toward DNA-coated colloids that crystallize. J. Am. Chem. Soc. 137, 10760-10766.
(62) Kouassi, G. K., and Irudayaraj, J. (2006) Magnetic and gold-coated magnetic nanoparticles as a DNA sensor. Anal. Chem. 78, 3234-3241.
90
(63) Yang, X. P., Wenzler, L. A., Qi, J., Li, X. J., and Seeman, N. C. (1998) Ligation of DNA triangles containing double crossover molecules. J. Am. Chem. Soc. 120, 9779-9786.
(64) Jeffs, L. B., Palmer, L. R., Ambegia, E. G., Giesbrecht, C., Ewanick, S., and MacLachlan, I. (2005) A scalable, extrusion-free method for efficient liposomal encapsulation of plasmid DNA. Pharmaceut. Res. 22, 362-372.
(65) Lomas, H., Canton, I., MacNeil, S., Du, J., Armes, S. P., Ryan, A. J., Lewis, A. L., and Battaglia, G. (2007) Biomimetic pH sensitive polymersomes for efficient DNA encapsulation and delivery. Adv. Mater. 19, 4238-4243.
(66) Kaneko, T., Okada, T., and Hatakeyama, R. (2007) DNA encapsulation inside carbon nanotubes using micro electrolyte plasmas. Contrib. Plasm. Phys. 47, 57-63.
(67) Shenton, W., Davis, S. A., and Mann, S. (1999) Directed self-assembly of nanoparticles into macroscopic materials using antibody-antigen recognition. Adv. Mater. 11, 449-452.
(68) Ibano, D., Yokota, Y., and Tominaga, T. (2003) Preparation of gold nanoplates protected by an anionic phospholipid. Chem. Lett. 32, 574-575.
(69) Lundqvist, M., Sethson, I., and Jonsson, B. H. (2004) Protein adsorption onto silica nanoparticles: Conformational changes depend on the particles' curvature and the protein stability. Langmuir 20, 10639-10647.
(70) Caruso, F. (2001) Nanoengineering of particle surfaces. Adv. Mater. 13, 11-22.
(71) Caruso, F., and Mohwald, H. (1999) Protein multilayer formation on colloids through a stepwise self-assembly technique. J. Am. Chem. Soc. 121, 6039-6046.
(72) Chen, B., Miller, M. E., and Gross, R. A. (2007) Effects of porous polystyrene resin parameters on Candida antarctica Lipase B adsorption, distribution, and polyester synthesis activity. Langmuir 23, 6467-6474.
(73) Lee, D. G., Ponvel, K. M., Kim, M., Hwang, S., Ahn, I. S., and Lee, C. H. (2009) Immobilization of lipase on hydrophobic nano-sized magnetite particles. J. Mol. Catal. B-Enzym. 57, 62-66.
(74) Katz, E., and Willner, I. (2004) Integrated nanoparticle-biomolecule hybrid systems: Synthesis, properties, and applications. Angew. Chem. Int. Ed. 43, 6042-6108.
(75) Zhang, S. X., Wang, N., Yu, H. J., Niu, Y. M., and Sun, C. Q. (2005) Covalent attachment of glucose oxidase to an Au electrode modified with gold nanoparticles for use as glucose biosensor. Bioelectrochemistry 67, 15-22.
(76) Yang, W. W., Wang, J. X., Zhao, S., Sun, Y. Y., and Sun, C. Q. (2006) Multilayered construction of glucose oxidase and gold nanoparticles on Au electrodes based on layer-by-layer covalent attachment. Electrochem. Commun. 8, 665-672.
(77) Rossi, L. M., Quach, A. D., and Rosenzweig, Z. (2004) Glucose oxidase-magnetite nanoparticle bioconjugate for glucose sensing. Anal. Bioanal. Chem. 380, 606-613.
91
(78) Dyal, A., Loos, K., Noto, M., Chang, S. W., Spagnoli, C., Shafi, K., Ulman, A., Cowman, M., and Gross, R. A. (2003) Activity of Candida rugosa lipase immobilized on -Fe2O3 magnetic nanoparticles. J. Am. Chem. Soc. 125, 1684-1685.
(79) Wang, L., Zhao, W. J., and Tan, W. H. (2008) Bioconjugated silica nanoparticles: development and applications. Nano Res. 1, 99-115.
(80) Santra, S., Zhang, P., Wang, K. M., Tapec, R., and Tan, W. H. (2001) Conjugation of biomolecules with luminophore-doped silica nanoparticles for photostable biomarkers. Anal. Chem. 73, 4988-4993.
(81) Ow, H., Larson, D. R., Srivastava, M., Baird, B. A., Webb, W. W., and Wiesner, U. (2005) Bright and stable core-shell fluorescent silica nanoparticles. Nano Lett. 5, 113-117.
(82) Knopp, D., Tang, D. P., and Niessner, R. (2009) Bioanalytical applications of biomolecule-functionalized nanometer-sized doped silica particles. Anal. Chim. Acta 647, 14-30.
(83) Nemzer, L. R., Schwartz, A., and Epstein, A. J. (2010) Enzyme Entrapment in Reprecipitated Polyaniline Nano- and Microparticles. Macromolecules 43, 4324-4330.
(84) Kouisni, L., and Rochefort, D. (2009) Confocal microscopy study of polymer microcapsules for enzyme immobilisation in paper substrates. J. Appl. Polym. Sci. 111, 1-10.
(85) Luckarift, H. R., Dickerson, M. B., Sandhage, K. H., and Spain, J. C. (2006) Rapid, room-temperature synthesis of antibacterial bionanocomposites of lysozyme with amorphous silica or titania. Small 2, 640-643.
(86) Luckarift, H. R., Balasubramanian, S., Paliwal, S., Johnson, G. R., and Simonian, A. L. (2007) Enzyme-encapsulated silica monolayers for rapid functionalization of a gold surface. Colloid. Surface. B 58, 28-33.
(88) Matsunaga, T., and Kamiya, S. (1987) Use of magnetic particles isolated from magnetotactic bacteria for enzyme immobilization. Appl. Microbiol. Biot. 26, 328-332.
(89) Crumbliss, A. L., Perine, S. C., Stonehuerner, J., Tubergen, K. R., Zhao, J. G., and Henkens, R. W. (1992) Colloidal gold as a biocompatible immobilization matrix suitable for the fabrication of enzyme electrodes by electrodeposition. Biotechnol. Bioeng. 40, 483-490.
(90) Besteman, K., Lee, J. O., Wiertz, F. G. M., Heering, H. A., and Dekker, C. (2003) Enzyme-coated carbon nanotubes as single-molecule biosensors. Nano Lett. 3, 727-730.
(91) Takahashi, H., Li, B., Sasaki, T., Miyazaki, C., Kajino, T., and Inagaki, S. (2000) Catalytic activity in organic solvents and stability of immobilized enzymes depend on the pore size and surface characteristics of mesoporous silica. Chem. Mater. 12, 3301-3305.
(92) Xie, W. L., and Ma, N. (2009) Immobilized lipase on Fe3O4 nanoparticles as biocatalyst for biodiesel production. Energ. Fuel. 23, 1347-1353.
(93) Lee, J., Lee, Y., Youn, J. K., Bin Na, H., Yu, T., Kim, H., Lee, S. M., Koo, Y. M., Kwak, J. H., Park, H. G., Chang, H. N., Hwang, M., Park, J. G., Kim, J., and Hyeon, T.
92
(2008) Simple synthesis of functionalized superparamagnetic magnetite/silica core/shell nanoparticles and their application as magnetically separable high-performance biocatalysts. Small 4, 143-152.
(94) Koneracka, M., Kopcansky, P., Timko, M., Ramchand, C. N., de Sequeira, A., and Trevan, M. (2002) Direct binding procedure of proteins and enzymes to fine magnetic particles. J. Mol. Catal. B: Enzym. 18, 13-18.
(95) Wang, P., Dai, S., Waezsada, S. D., Tsao, A. Y., and Davison, B. H. (2001) Enzyme stabilization by covalent binding in nanoporous sol-gel glass for nonaqueous biocatalysis. Biotechnol. Bioeng. 74, 249-255.
(96) Shendure, J., and Ji, H. L. (2008) Next-generation DNA sequencing. Nat. Biotechnol. 26, 1135-1145.
(97) Cheung, V. G., Morley, M., Aguilar, F., Massimi, A., Kucherlapati, R., and Childs, G. (1999) Making and reading microarrays. Nat. Genet. 21, 15-19.
(98) Lipshutz, R. J., Fodor, S. P. A., Gingeras, T. R., and Lockhart, D. J. (1999) High density synthetic oligonucleotide arrays. Nat. Genet. 21, 20-24.
(99) Mertes, F., ElSharawy, A., Sauer, S., van Helvoort, J., van der Zaag, P. J., Franke, A., Nilsson, M., Lehrach, H., and Brookes, A. J. (2011) Targeted enrichment of genomic DNA regions for next-generation sequencing. Brief. Funct. Genom. 10, 374-386.
(100) Kneuer, C., Sameti, M., Haltner, E. G., Schiestel, T., Schirra, H., Schmidt, H., and Lehr, C. M. (2000) Silica nanoparticles modified with aminosilanes as carriers for plasmid DNA. Int. J. Pharm. 196, 257-261.
(101) He, X. X., Wang, K. M., Li, D., Tan, W. H., He, C. M., Huang, S. S., Liu, B., Lin, X., and Chen, X. H. (2003) A novel DNA-enrichment technology based on amino-modified functionalized silica nanoparticles. J. Disper. Sci. Technol. 24, 633-640.
(102) Song, Z. L., Zhao, X. H., Liu, W. N., Ding, D., Bian, X., Liang, H., Zhang, X. B., Chen, Z., and Tan, W. H. (2013) Magnetic Graphitic Nanocapsules for Programmed DNA Fishing and Detection. Small 9, 951-957.
(103) Gnirke, A., Melnikov, A., Maguire, J., Rogov, P., LeProust, E. M., Brockman, W., Fennell, T., Giannoukos, G., Fisher, S., Russ, C., Gabriel, S., Jaffe, D. B., Lander, E. S., and Nusbaum, C. (2009) Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat. Biotechnol. 27, 182-189.
(104) Sheldon, R. A. (2007) Enzyme immobilization: The quest for optimum performance. Adv. Synth. Catal. 349, 1289-1307.
(105) Bornscheuer, U. T. (2003) Immobilizing enzymes: How to create more suitable biocatalysts. Angew. Chem. Int. Ed. 42, 3336-3337.
(106) Lu, A. H., Salabas, E. L., and Schuth, F. (2007) Magnetic nanoparticles: Synthesis, protection, functionalization, and application. Angew. Chem. Int. Ed. 46, 1222-1244.
(107) Chen, D. H., and Liao, M. H. (2002) Preparation and characterization of YADH-bound magnetic nanoparticles. J. Mol. Catal. B: Enzym. 16, 283-291.
93
(108) Gao, X., Yu, K. M. K., Tam, K. Y., and Tsang, S. C. (2003) Colloidal stable silica encapsulated nano-magnetic composite as a novel bio-catalyst carrier. Chem. Commun., 2998-2999.
(109) Park, H. J., McConnell, J. T., Boddohi, S., Kipper, M. J., and Johnson, P. A. (2011) Synthesis and characterization of enzyme-magnetic nanoparticle complexes: effect of size on activity and recovery. Colloid. Surf. B 83, 198-203.
(110) Saiyed, Z. M., Sharma, S., Godawat, R., Telang, S. D., and Ramchand, C. N. (2007) Activity and stability of alkaline phosphatase (ALP) immobilized onto magnetic nanoparticles (Fe3O4). J. Biotechnol. 131, 240-244.
(111) Wu, Y., Wang, Y. J., Luo, G. S., and Dai, Y. Y. (2009) In situ preparation of magnetic Fe3O4-chitosan nanoparticles for lipase immobilization by cross-linking and oxidation in aqueous solution. Bioresource Technol. 100, 3459-3464.
(112) Mavré, F., Bontemps, M., Ammar-Merah, S., Marchal, D., and Limoges, B. (2007) Electrode surface confinement of self-assembled enzyme aggregates using magnetic nanoparticles and its application in bioelectrocatalysis. Anal. Chem. 79, 187-194.
(113) Schumacher, C. M., Herrmann, I. K., Bubenhofer, S. B., Gschwind, S., Hirt, A.-M., Beck-Schimmer, B., Günther, D., and Stark, W. J. (2013) Quantitative recovery of magnetic nanoparticles from flowing blood: Trace analysis and the role of magnetization. Adv. Funct. Mater., 4888-4896.
(114) Yavuz, C. T., Mayo, J. T., Yu, W. W., Prakash, A., Falkner, J. C., Yean, S., Cong, L. L., Shipley, H. J., Kan, A., Tomson, M., Natelson, D., and Colvin, V. L. (2006) Low-field magnetic separation of monodisperse Fe3O4 nanocrystals. Science 314, 964-967.
(115) Schaetz, A., Zeltner, M., Michl, T. D., Rossier, M., Fuhrer, R., and Stark, W. J. (2011) Magnetic silyl scaffold enables efficient recycling of protecting groups. Chem. Eur. J. 17, 10566-10573.
(116) Matei, E., Predescu, C., Berbecaru, A., Predescu, A., and Trusca, R. (2011) Leaching tests for synthesized magnetite nanoparticles used as adsorbent for metal ions from liquid solutions. Dig. J. Nanomater. Bios. 6, 1701-1708.
(117) Grass, R. N., Athanassiou, E. K., and Stark, W. J. (2007) Covalently functionalized cobalt nanoparticles as a platform for magnetic separations in organic synthesis. Angew. Chem. Int. Ed. 46, 4909-4912.
(118) Schatz, A., Reiser, O., and Stark, W. J. (2010) Nanoparticles as semi-heterogeneous catalyst supports. Chem. Eur. J. 16, 8950-8967.
(119) Schatz, A., Grass, R. N., Kainz, Q., Stark, W. J., and Reiser, O. (2010) Cu(II)-azabis(oxazoline) complexes immobilized on magnetic Co/C nanoparticles: kinetic resolution of 1,2-diphenylethane-1,2-diol under batch and continuous-flow conditions. Chem. Mater. 22, 305-310.
(120) Rossier, M., Schaetz, A., Athanassiou, E. K., Grass, R. N., and Stark, W. J. (2011) Reversible As(V) adsorption on magnetic nanoparticles and pH dependent desorption concentrates dilute solutions and realizes true moving bed reactor systems. Chem. Eng. J. 175, 244-250.
94
(121) Herrmann, I. K., Grass, R. N., and Stark, W. J. (2009) High-strength metal nanomagnets for diagnostics and medicine: carbon shells allow long-term stability and reliable linker chemistry. Nanomedicine 4, 787-798.
(122) Avrameas, S., and Ternynck, T. (1998) Enzyme-Linked Immunosorbent Assay (ELISA), in Encyclopedia of Immunology (Delves, P. J., and Roitt, I. M., Eds.) pp 816-819, Elsevier, Oxford.
(123) Calvaresi, M., and Zerbetto, F. (2013) The devil and holy water: protein and carbon nanotube hybrids. Accounts Chem. Res. 46, 2454-2463.
(124) Gao, Y., and Kyratzis, I. (2008) Covalent immobilization of proteins on carbon nanotubes using the cross-linker 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide—a critical assessment. Bioconjugate Chem. 19, 1945-1950.
(125) Hirsh, S. L., Bilek, M. M. M., Nosworthy, N. J., Kondyurin, A., dos Remedios, C. G., and McKenzie, D. R. (2010) A comparison of covalent immobilization and physical adsorption of a cellulase enzyme mixture. Langmuir 26, 14380-14388.
(126) Felhofer, J. L., Caranto, J. D., and Garcia, C. D. (2010) Adsorption kinetics of catalase to thin films of carbon nanotubes. Langmuir 26, 17178-17183.
(127) Frey, B. L., and Corn, R. M. (1996) Covalent attachment and derivatization of poly(L-lysine) monolayers on gold surfaces as characterized by polarization-modulation FT-IR spectroscopy. Anal. Chem. 68, 3187-3193.
(128) Barth, A. (2007) Infrared spectroscopy of proteins. BBA-Bioenergetics 1767, 1073-1101.
(129) Rossier, M., Schreier, M., Krebs, U., Aeschlimann, B., Fuhrer, R., Zeltner, M., Grass, R. N., Günther, D., and Stark, W. J. (2012) Scaling up magnetic filtration and extraction to the ton per hour scale using carbon coated metal nanoparticles. Sep. Purif.Technol. 96, 68-74.
(130) Paustenbach, D. J., Tvermoes, B. E., Unice, K. M., Finley, B. L., and Kerger, B. D. (2013) A review of the health hazards posed by cobalt. Crit. Rev. Toxicol. 43, 316-362.
(131) Donaldson, J. D. a. B., D. 2005. (2005) in Ullmann`s encyclopedia of industrial chemistry.
(132) Wirnt, R., and Bergmeyer, H. U. (1974) Chymotrypsin, in Methods of enzymatic analysis pp 1009-1012, New York.
(133) Talbert, J. N., and Goddard, J. M. (2012) Enzymes on material surfaces. Colloids Surf. B 93, 8-19.
(134) Alcalde, M., Ferrer, M., Plou, F. J., and Ballesteros, A. (2006) Environmental biocatalysis: from remediation with enzymes to novel green processes. Trends Biotechnol. 24, 281-7.
(135) Garcia-Galan, C., Berenguer-Murcia, Á., Fernandez-Lafuente, R., and Rodrigues, R. C. (2011) Potential of different enzyme immobilization strategies to improve enzyme performance. Adv. Synth. Catal. 353, 2885-2904.
95
(136) Kim, J., Jia, H., and Wang, P. (2006) Challenges in biocatalysis for enzyme-based biofuel cells. Biotechnol. Adv. 24, 296-308.
(137) Hartmann, M., and Jung, D. (2010) Biocatalysis with enzymes immobilized on mesoporous hosts: the status quo and future trends. J. Mater. Chem. 20, 844-857.
(138) Cao, L. (2006) Introduction: Immobilized Enzymes: Past, Present and Prospects, in Carrier-bound Immobilized Enzymes pp 1-52, Wiley.
(139) Hudson, S., Magner, E., Cooney, J., and Hodnett, B. K. (2005) Methodology for the immobilization of enzymes onto mesoporous materials. J. Phys. Chem. B 109, 19496-19506.
(140) Hudson, S., Cooney, J., and Magner, E. (2008) Proteins in mesoporous silicates. Angew. Chem. Int. Ed. 47, 8582-8594.
(141) Ispas, C., Sokolov, I., and Andreescu, S. (2009) Enzyme-functionalized mesoporous silica for bioanalytical applications. Anal. Bioanal. Chem. 393, 543-554.
(142) Zhou, Z., and Hartmann, M. (2013) Progress in enzyme immobilization in ordered mesoporous materials and related applications. Chem. Soc. Rev. 42, 3894-3912.
(143) Fadnavis, N. W., Bhaskar, V., Kantam, M. L., and Choudary, B. M. (2003) Highly efficient “tight fit” immobilization of α-chymotrypsin in mesoporous MCM-41: A novel approach using precursor immobilization and activation. Biotechnol. Prog. 19, 346-351.
(144) Aburto, J., Ayala, M., Bustos-Jaimes, I., Montiel, C., Terrés, E., Domínguez, J. M., and Torres, E. (2005) Stability and catalytic properties of chloroperoxidase immobilized on SBA-16 mesoporous materials. Microporous Mesoporous Mater. 83, 193-200.
(145) Yiu, H. H. P., Wright, P. A., and Botting, N. P. (2001) Enzyme immobilisation using siliceous mesoporous molecular sieves. Microporous Mesoporous Mater. 44–45, 763-768.
(146) He, J., Song, Z., Ma, H., Yang, L., and Guo, C. (2006) Formation of a mesoporous bioreactor based on SBA-15 and porcine pancreatic lipase by chemical modification following the uptake of enzymes. J. Mater. Chem. 16, 4307-4315.
(147) Ma, H., He, J., Evans, D. G., and Duan, X. (2004) Immobilization of lipase in a mesoporous reactor based on MCM-41. J. Mol. Catal. B: Enzym. 30, 209-217.
(148) Paunescu, D., Puddu, M., Soellner, J. O. B., Stoessel, P. R., and Grass, R. N. (2013) Reversible DNA encapsulation in silica to produce ROS-resistant and heat-resistant synthetic DNA 'fossils'. Nat. Protoc. 8, 2440-2448.
(149) Puddu, M., Stark, W. J., and Grass, R. N. (2015) Silica microcapsules for long-term, robust, and reliable room temperature rna preservation. Adv. Healthcare Mater. 4, 1332-8.
(150) Liu, B., Cao, Y. Y., Huang, Z. H., Duan, Y. Y., and Che, S. N. (2015) Silica biomineralization via the self-assembly of helical biomolecules. Adv. Mater. 27, 479-497.
(151) Liu, B., Han, L., and Che, S. A. (2013) Silica mineralisation of DNA chiral packing: helicity control and formation mechanism of impeller-like DNA-silica helical architectures. J. Mater. Chem. B 1, 2843-2850.
96
(152) Matsuura, S.-i., Baba, T., Chiba, M., and Tsunoda, T. (2014) Nanoporous scaffold for DNA polymerase: pore-size optimisation of mesoporous silica for DNA amplification. RSC Adv. 4, 25920-25923.
(153) Fan, J., Yu, C., Gao, F., Lei, J., Tian, B., Wang, L., Luo, Q., Tu, B., Zhou, W., and Zhao, D. (2003) Cubic mesoporous silica with large controllable entrance sizes and advanced adsorption properties. Angew. Chem. Int. Ed. 115, 3254-3258.
(154) Schmidt-Winkel, P., Lukens, W. W., Zhao, D., Yang, P., Chmelka, B. F., and Stucky, G. D. (1999) Mesocellular siliceous foams with uniformly sized cells and windows. J. Am. Chem. Soc. 121, 254-255.
(155) Han, Y., Lee, S. S., and Ying, J. Y. (2006) Pressure-driven enzyme entrapment in siliceous mesocellular foam. Chem. Mater. 18, 643-649.
(156) Zhao, D., Feng, J., Huo, Q., Melosh, N., Fredrickson, G. H., Chmelka, B. F., and Stucky, G. D. (1998) Triblock copolymer syntheses of mesoporous silica with periodic 50 to 300 angstrom pores. Science 279, 548-552.
(157) Nguyen, T. P. B., Lee, J.-W., Shim, W. G., and Moon, H. (2008) Synthesis of functionalized SBA-15 with ordered large pore size and its adsorption properties of BSA. Microporous Mesoporous Mater. 110, 560-569.
(158) Lettow, J. S., Han, Y. J., Schmidt-Winkel, P., Yang, P., Zhao, D., Stucky, G. D., and Ying, J. Y. (2000) Hexagonal to mesocellular foam phase transition in polymer-templated mesoporous silicas. Langmuir 16, 8291-8295.
(159) Ryoo, R., Joo, S. H., and Jun, S. (1999) Synthesis of highly ordered carbon molecular sieves via template-mediated structural transformation. J. Phys. Chem. B 103, 7743-7746.
(160) Miyahara, M., Vinu, A., Hossain, K. Z., Nakanishi, T., and Ariga, K. (2006) Adsorption study of heme proteins on SBA-15 mesoporous silica with pore-filling models. Thin Solid Films 499, 13-18.
(161) Bechtold, M. F., Vest, R. D., and Plambeck, L. (1968) Silicic acid from tetraethyl silicate hydrolysis. Polymerization and properties. J. Am. Chem. Soc. 90, 4590-4598.
(162) Paunescu, D., Fuhrer, R., and Grass, R. N. (2013) Protection and deprotection of DNA—high-temperature stability of nucleic acid barcodes for polymer labeling. Angew. Chem. Int. Ed. 52, 4269-4272.
(163) Groen, J. C., Peffer, L. A. A., and Pérez-Ramı́rez, J. (2003) Pore size determination in modified micro- and mesoporous materials. Pitfalls and limitations in gas adsorption data analysis. Microporous Mesoporous Mater. 60, 1-17.
(164) Morishige, K., Tateishi, M., Hirose, F., and Aramaki, K. (2006) Change in desorption mechanism from pore blocking to cavitation with temperature for nitrogen in ordered silica with cagelike pores. Langmuir 22, 9220-9224.
(165) Voelkerding, K. V., Dames, S. A., and Durtschi, J. D. (2009) Next-Generation sequencing: From basic research to diagnostics. Clin. Chem. 55, 641-658.
97
(166) Beaudet, A. L., and Belmont, J. W. (2008) Array-based DNA diagnostics: Let the revolution begin, in Annu. Rev. Med. pp 113-129.
(167) Vo-Dinh, T., and Cullum, B. (2000) Biosensors and biochips: advances in biological and medical diagnostics. Fresenius J. Anal. Chem. 366, 540-551.
(168) Albert, T. J., Molla, M. N., Muzny, D. M., Nazareth, L., Wheeler, D., Song, X. Z., Richmond, T. A., Middle, C. M., Rodesch, M. J., Packard, C. J., Weinstock, G. M., and Gibbs, R. A. (2007) Direct selection of human genomic loci by microarray hybridization. Nat. Methods 4, 903-905.
(169) Hodges, E., Rooks, M., Xuan, Z. Y., Bhattacharjee, A., Gordon, D. B., Brizuela, L., McCombie, W. R., and Hannon, G. J. (2009) Hybrid selection of discrete genomic intervals on custom-designed microarrays for massively parallel sequencing. Nat. Protoc. 4, 960-974.
(170) Chou, L. S., Liu, C. S. J., Boese, B., Zhang, X. M., and Mao, R. (2010) DNA sequence capture and enrichment by microarray followed by next-generation sequencing for targeted resequencing: Neurofibromatosis Type 1 gene as a model. Clin. Chem. 56, 62-72.
(171) Lockhart, D. J., and Winzeler, E. A. (2000) Genomics, gene expression and DNA arrays. Nature 405, 827-836.
(172) Sassolas, A., Leca-Bouvier, B. D., and Blum, L. J. (2008) DNA biosensors and microarrays. Chem. Rev. 108, 109-139.
(173) Khrapko, K. R., Lysov, Y. P., Khorlin, A. A., Ivanov, I. B., Yershov, G. M., Vasilenko, S. K., Florentiev, T. V. L., and Mirzabekov, A. D. (1991) A method for DNA sequencing by hybridization with oligonucleotide matrix. DNA Sequence 1, 375-388.
(174) Phaner-Goutorbe, M., Dugas, V., Chevolot, Y., and Souteyrand, E. (2011) Silanization of silica and glass slides for DNA microarrays by impregnation and gas phase protocols: A comparative study. Mat. Sci. Eng. C-Bio. S. 31, 384-390.
(175) Beier, M., and Hoheisel, J. D. (1999) Versatile derivatisation of solid support media for covalent bonding on DNA-microchips. Nucleic Acids Res. 27, 1970-1977.
(176) Schuler, T., Nykytenko, A., Csaki, A., Moller, R., Fritzsche, W., and Popp, J. (2009) UV cross-linking of unmodified DNA on glass surfaces. Anal. Bioanal. Chem. 395, 1097-1105.
(177) Mamanova, L., Coffey, A. J., Scott, C. E., Kozarewa, I., Turner, E. H., Kumar, A., Howard, E., Shendure, J., and Turner, D. J. (2010) Target-enrichment strategies for next-generation sequencing. Nat. Methods 7, 111-118.
(178) Wang, C., Yang, G., Luo, Z., and Ding, H. (2009) In vitro selection of high-affinity DNA aptamers for streptavidin. Acta. Bioch. Bioph. Sin. 41, 335-340.
(179) Nam, J. M., Stoeva, S. I., and Mirkin, C. A. (2004) Bio-bar-code-based DNA detection with PCR-like sensitivity. J. Am. Chem. Soc. 126, 5932-5933.
(180) Hawkins, T. L., O'Connor-Morin, T., Roy, A., and Santillan, C. (1994) DNA purification and isolation using a solid-phase. Nucleic Acids Res. 22, 4543.
98
(181) Alderton, R. P., Eccleston, L. M., Howe, R. P., Read, C. A., Reeve, M. A., and Beck, S. (1992) Magnetic bead purification of M13 DNA sequencing templates. Anal. Biochem. 201, 166-169.
(182) Shalon, D., Smith, S. J., and Brown, P. O. (1996) A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res. 6, 639-645.
(183) Blalock, E. M. (2003) A beginner’s guide to microarrays, Springer Science & Business Media.
(184) Schaetz, A., Zeltner, M., Michl, T. D., Rossier, M., Fuhrer, R., and Stark, W. J. (2011) Magnetic silyl scaffold enables efficient recycling of protecting groups. Chem-Eur. J. 17, 10566-10573.
(185) Herrmann, I. K., Grass, R. N., Mazunin, D., and Stark, W. J. (2009) Synthesis and covalent surface functionalization of nonoxidic iron core− shell nanomagnets. Chem. Mater. 21, 3275-3281.
(186) Star, A., Tu, E., Niemann, J., Gabriel, J. C. P., Joiner, C. S., and Valcke, C. (2006) Label-free detection of DNA hybridization using carbon nanotube network field-effect transistors. P. Natl. Acad. Sci. USA 103, 921-926.
(187) Tang, X. W., Bansaruntip, S., Nakayama, N., Yenilmez, E., Chang, Y. L., and Wang, Q. (2006) Carbon nanotube DNA sensor and sensing mechanism. Nano Lett. 6, 1632-1636.
(188) Pretsch, E., Bühlmann, P., and Badertscher, M. (2010) Spektroskopische Daten zur Strukturaufklärung organischer Verbindungen, Springer-Verlag.
(189) Brinker, C. J. (1988) Hydrolysis and condensation of silicates - effects on structure. J. Non-Cryst. Solids 100, 31-50.
(190) Qin, M., Hou, S., Wang, L. K., Feng, X. Z., Wang, R., Yang, Y. B., Wang, C., Yu, L., Shao, B., and Qiao, M. Q. (2007) Two methods for glass surface modification and their application in protein immobilization. Colloid. Surface. B. 60, 243-249.
(191) Lamture, J. B., LBeattie, K., Burke, B. E., Eggers, M. D., Ehrlich, D. J., Fowler, R., Hollis, M. A., Kosicki, B. B., Reich, R. K., and Smith, S. R. (1994) Direct detection of nucleic acid hybridization on the surface of a charge coupled device. Nucleic Acids Res. 22, 2121-2125.
(192) Huang, E., Zhou, F., and Deng, L. (2000) Studies of surface coverage and orientation of DNA molecules immobilized onto preformed alkanethiol self-assembled monolayers. Langmuir 16, 3272-3280.
(193) Turner, C. R., Uy, K. L., and Everhart, R. C. (2015) Fish environmental DNA is more concentrated in aquatic sediments than surface water. Biol. Conserv. 183, 93-102.