Structures of Biological Macromolecul Structures of Biological Macromolecul Part 2: Nucleic Acids Part 2: Nucleic Acids Jürgen Sühnel Jürgen Sühnel [email protected][email protected]Supplementary Material: www.fli-leibniz.de/www_bioc/3D/ Leibniz Institute for Age Research, Fritz Lipmann Institute, Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena Centre for Bioinformatics Jena Centre for Bioinformatics Jena / Germany Jena / Germany
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3D Structures of Biological Macromolecules Part 2: Nucleic Acids Jürgen Sühnel [email protected] Supplementary Material:
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3D Structures of Biological Macromolecules3D Structures of Biological Macromolecules
Leibniz Institute for Age Research, Fritz Lipmann Institute,Leibniz Institute for Age Research, Fritz Lipmann Institute,Jena Centre for BioinformaticsJena Centre for Bioinformatics
Jena / GermanyJena / Germany
Molecules of LifeMolecules of Life
Nucleic AcidsNucleic Acids
DNAgenomic information (nucleosomes, chromatin)
RNAmessenger RNA, ribosomal RNA, transfer RNA, ribozymes, small RNAs, noncoding RNAs, RNAi (gene silencing),aptamers (alternatives to antibodies)
PNA peptide nucleic acids mimic nucleic acids
New Roles for RNANew Roles for RNA
Couzin J.Breakthrough of the year. Small RNAs make big splash.Science. 2002, 298, 2296-2297.
New Roles for RNANew Roles for RNA
From Gene to ProteinFrom Gene to Protein
History History
HistoryHistory
Nucleic Acid Structure Nucleic Acid Structure
NucleobasesNucleobases
/web.siumed.edu/~bbartholomew/course_material/nucleic_acids.html; no longer active)
Chain Direction in Nucleic AcidsChain Direction in Nucleic Acids
Chain Direction in Nucleic AcidsChain Direction in Nucleic Acids
Ribonucleotides and DeoxyribonucleotidesRibonucleotides and Deoxyribonucleotides
Nucleic Acid Base PairsNucleic Acid Base Pairs
The ten possible purine-pyrimidine base pairs.
Source: Ignacio Tinoco, Jr. in Gesteland, R. F. and Atkins, J. F. (1993) THE RNA WORLD. Cold Spring Harbor Laboratory Press.
The seven possible homo-purinebase pairs.
Source: Ignacio Tinoco, Jr. in Gesteland, R. F. and Atkins, J. F. (1993) THE RNA WORLD. Cold Spring Harbor Laboratory Press.
Nucleic Acid Base PairsNucleic Acid Base Pairs
The four possible hetereo-purine base pairs.
Source: Ignacio Tinoco, Jr. in Gesteland, R. F. and Atkins, J. F. (1993) THE RNA WORLD. Cold Spring Harbor Laboratory Press.
Nucleic Acid Base PairsNucleic Acid Base Pairs
The seven possible pyrimidine-pyrimidine base pairs.
Nucleic Acid Base PairsNucleic Acid Base Pairs
DNA HydrationDNA Hydration
www.lsbu.ac.uk/water/nucleic.html
Nucleic Acid Base Pairs – Water-mediated PairsNucleic Acid Base Pairs – Water-mediated Pairs
Nucleic Acid Base Pairs – Water-mediated PairsNucleic Acid Base Pairs – Water-mediated Pairs
Nucleic Acid Base Pairs – Water-mediated PairsNucleic Acid Base Pairs – Water-mediated Pairs
Nucleic Acid Base Pairs with C-H…O/N InteractionsNucleic Acid Base Pairs with C-H…O/N Interactions
Nucleic Acid Base Pairs with C-H…O/N InteractionsNucleic Acid Base Pairs with C-H…O/N Interactions
Non-Canonical Base Pair DatabaseNon-Canonical Base Pair Database
http://prion.bchs.uh.edu/bp_type/
Selected Base TriplesSelected Base Triples
Base Triples in tRNABase Triples in tRNA
Base triads in the crystal structure of yeast phenylalanine transfer RNA (PDB code: 4tna).
Base Tetrads in a DNA TetraplexBase Tetrads in a DNA Tetraplex
Parallel-stranded DNA tetraplex formed from the Tetrahymena telomeric sequence d(TTGGGGT) solved by NMR spectroscopy (PDB code: 139d).The structure contains four stacked G-tetrads in the center and additional T-tetrads.
Base PolyadsBase Polyads
Base triads and a heptad in the crystal structure of a pseudoknot from beet western yellow virus (BWYV) involved in frameshifting (PDB code: 437d).The heptad is formed from two triads linked by A25.
Base PolyadsBase Polyads
HBexplore – H-bond Analysis in Proteins and Nucleic AcidsHBexplore – H-bond Analysis in Proteins and Nucleic Acids
www.imb-jena.de/www_bioc/hbx/hbx.html
Geometrical ParametersGeometrical Parametersfor Base Pairs infor Base Pairs inNucleic AcidsNucleic Acids
Ideal DNA Conformations and a Real B-DNA Structure Ideal DNA Conformations and a Real B-DNA Structure
Nucleic Acid ConformationsNucleic Acid Conformations• B-DNA is found at low salt concentrations. It is believed to be the native conformation occurring in chromatin.
In the cell nucleus DNA is complexed with about an equivalent mass of protein to form a structure known as chromatin. Chromatin is a periodic structure made up of repeating, regularly spaced subunits, the subunit being the nucleosome. Within the nucleosomes the major part of DNA is wrapped around histones. The remaining DNA joining each nucleosome is known as linker DNA.
• A-DNA In solutions with higher salt concentrations or with alcohol added A-DNA is found. • Z-DNA occurs for alternating poly(dG-dC) sequences in solutions with high salt concentrations or alcohol. • RNA occurs (contrary to DNA) almost exclusively in the A-conformation (or in a related A'-form). • There are further nucleic acid conformations like C-DNA, H-DNA or others which are not discussed
here.
Geometrical features: The distance between two subsequent base pairs along the helical axis is called helical rise (h). The pitch (p) is the length of the helix axis for one complete helix turn. The turn angle per nucleotide or twist angle (t) is given by 360° / number of nucleotides per turn. C2'-endo and C3'-endo are descriptions of sugar conformations. The most frequently occurring nucleic acid model conformations are characterized by the following geometrical parameters :• A-DNA
right-handed helix; sugar pucker: C3'-endo; number of nucleotides per pitch: 11; h: 2.56 Å; t: +32.7°. • B-DNA
right-handed helix; sugar pucker: C2'-endo; number of nucleotides per pitch: 10; h: 3.38 Å; t: +36° . • Z-DNA
left-handed helix; G: syn conformation; sugar pucker: C3'-endo; C: anti conformation, sugar pucker: C2' endo; number of nucleotides per pitch: 6x2; h: 3.7x2 Å; t= -30°x2 (for Z-DNA the repeat unit is the dimer (G-C)2.
H. R. Drew, R. M. Wing, T. Takano, C. Broka, S. Tanaka, K. Itakura, R. E. Dickerson Structure Of A B-/DNA Dodecamer. Conformation And Dynamics Proc. Nat. Acad. Sci. Usa V. 78 2179 1981
First Single-crystal DNA Structure (B-DNA) First Single-crystal DNA Structure (B-DNA)
Drew-Dickerson structure
Diversity of DNA Structures Diversity of DNA Structures
DNA in chromatin is organized in arrays of nucleosomes.Two copies of eachhistone protein, H2A, H2B, H3 and H4,Are assembled into an octamer that has145-147 base pairs of DNA wrappedaround it to form a nucleosome core.
An architectural protein which assists formation of high order protein-DNA complexes such as those found in replication and long distance transcription regulation.
Aptamers are DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules. Aptamers have been selected which bind nucleic acid, proteins, small organic compounds. These novel molecules have many potential uses in medicine and technology.
The Aptamer Database is a comprehensive, annotated repository for information about aptamers and in vitro selection. This resource is provided to collect, organize and distribute all the known information regarding aptamer selection.
http://aptamer.icmb.utexas.edu
AptamersAptamers
Aptamer StructuresAptamer Structures
Nf-Kappa B (P50)2 Complexed To A High-Affinity RNA Aptamer