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3D Structures of Biological Macromolecules3D Structures of Biological Macromolecules
Part 2: Nucleic AcidsPart 2: Nucleic Acids
Jürgen SühnelJürgen Sü[email protected]@fli-leibniz.de
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 BioinformaticsJena Centre for Bioinformatics
Jena / GermanyJena / Germany
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Molecules of LifeMolecules of Life
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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
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New Roles for RNANew Roles for RNA
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Couzin J.Breakthrough of the year. Small RNAs make big splash.Science. 2002, 298, 2296-2297.
New Roles for RNANew Roles for RNA
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From Gene to ProteinFrom Gene to Protein
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History History
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HistoryHistory
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Nucleic Acid Structure Nucleic Acid Structure
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NucleobasesNucleobases
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/web.siumed.edu/~bbartholomew/course_material/nucleic_acids.html; no longer active)
Chain Direction in Nucleic AcidsChain Direction in Nucleic Acids
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Chain Direction in Nucleic AcidsChain Direction in Nucleic Acids
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Nucleic Acid BackboneNucleic Acid Backbone
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Nucleic Acid Backbone Torsion AnglesNucleic Acid Backbone Torsion Angles
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Ribonucleotides and DeoxyribonucleotidesRibonucleotides and Deoxyribonucleotides
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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.
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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
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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
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The seven possible pyrimidine-pyrimidine base pairs.
Nucleic Acid Base PairsNucleic Acid Base Pairs
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DNA HydrationDNA Hydration
www.lsbu.ac.uk/water/nucleic.html
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Nucleic Acid Base Pairs – Water-mediated PairsNucleic Acid Base Pairs – Water-mediated Pairs
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Nucleic Acid Base Pairs – Water-mediated PairsNucleic Acid Base Pairs – Water-mediated Pairs
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Nucleic Acid Base Pairs – Water-mediated PairsNucleic Acid Base Pairs – Water-mediated Pairs
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Nucleic Acid Base Pairs with C-H…O/N InteractionsNucleic Acid Base Pairs with C-H…O/N Interactions
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Nucleic Acid Base Pairs with C-H…O/N InteractionsNucleic Acid Base Pairs with C-H…O/N Interactions
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Non-Canonical Base Pair DatabaseNon-Canonical Base Pair Database
http://prion.bchs.uh.edu/bp_type/
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Selected Base TriplesSelected Base Triples
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Base Triples in tRNABase Triples in tRNA
Base triads in the crystal structure of yeast phenylalanine transfer RNA (PDB code: 4tna).
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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.
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Base PolyadsBase Polyads
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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
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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
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Geometrical ParametersGeometrical Parametersfor Base Pairs infor Base Pairs inNucleic AcidsNucleic Acids
ndbserver.rutgers.edu/archives/report/tsukuba_sup/bp_step_hel.html
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Nucleic Acid StructureNucleic Acid Structure
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Nucleic Acid Structure – Sugar ConformationNucleic Acid Structure – Sugar Conformation
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Nucleic Acid Structure – Sugar ConformationNucleic Acid Structure – Sugar Conformation
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Nucleic Acid Structure – Sugar ConformationNucleic Acid Structure – Sugar Conformation
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Nucleic Acid StructureNucleic Acid Structure
P: P is the pitch of the helix corresponding to the distance between a base and the base obtained after walking along the DNA one full turn of 360°.
n: n is the number on nucleotides within one pitch.h: distance between base planes.
online-media.uni-marburg.de/chemie/bioorganic/vorlesung1/kapitel1e.html?/chemie/bioorganic/vorlesung1/k1e-20.html
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DNA ConformationsDNA Conformations
www.rcsb.org/pdb/molecules/pdb23_3.html
BA Z
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Ideal DNA Conformations and a Real B-DNA Structure Ideal DNA Conformations and a Real B-DNA Structure
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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.
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Nucleic Acid ConformationsNucleic Acid Conformations
Groove width
Groove depth
major minor major minor
A-DNA 2.7 Å 11.0 Å 13.5 Å 2.8 Å
B-DNA 11.7 Å 5.7 Å 8.5 Å 7.5 Å
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Nucleic Acid Conformations - B-DNANucleic Acid Conformations - B-DNA
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Nucleic Acid Conformations - B-DNANucleic Acid Conformations - B-DNA
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Nucleic Acid Conformations – B-DNANucleic Acid Conformations – B-DNA
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Nucleic Acid Conformations – B-DNANucleic Acid Conformations – B-DNA
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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
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Diversity of DNA Structures Diversity of DNA Structures
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Nucleosome Core Particle (1aoi)Nucleosome Core Particle (1aoi)
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.
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Integration Host Factor (1ihf)Integration Host Factor (1ihf)
An architectural protein which assists formation of high order protein-DNA complexes such as those found in replication and long distance transcription regulation.
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CURVESCURVES
www.ibpc.fr/UPR9080/Curindex.html
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Integration Host Factor (1ihf) – CURVES OutputIntegration Host Factor (1ihf) – CURVES Output
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Integration Host Factor (1ihf) – CURVES Output:Integration Host Factor (1ihf) – CURVES Output:Local Bending AnalysisLocal Bending Analysis
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Integration Host Factor (1ihf): Local Bending Analysis Integration Host Factor (1ihf): Local Bending Analysis
Dinucleotide steps with unusual large valuesof the roll and tilt angleare indicated in red.
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Integration Host Factor (1ihf): Global Bending Analysis Integration Host Factor (1ihf): Global Bending Analysis
Coordinate systemandhelical axis
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Integration Host Factor (1ihf): Global Bending Analysis Integration Host Factor (1ihf): Global Bending Analysis
Coordinate systemandhelical axis
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Integration Host Factor (1ihf): Global Bending AnalysisIntegration Host Factor (1ihf): Global Bending Analysis
Coordinate systemandhelical axis
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Integration Host Factor (1ihf): Globale Bending Analysis Integration Host Factor (1ihf): Globale Bending Analysis
Coordinate systemandhelical axis
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Integration Host Factor (1ihf): Global Bending Analysis Integration Host Factor (1ihf): Global Bending Analysis
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Integration Host Factor (1ihf): Global Bending Analysis Integration Host Factor (1ihf): Global Bending Analysis
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Nucleic Acid Structure - BendingNucleic Acid Structure - Bending
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Cover Images for all 2003/2004/2005/2006 Issues of the Journal RNA Cover Images for all 2003/2004/2005/2006 Issues of the Journal RNA
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Large Ribosomal Subunit (1jj2) - 2001Large Ribosomal Subunit (1jj2) - 2001
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Jena Structures: 5S rRNA E-loop/L25 complex (1d6k)Jena Structures: 5S rRNA E-loop/L25 complex (1d6k)
IMB/FLI: Molecular Biophysics/NMR Spectroscopy (M. Görlach)
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AptamersAptamers
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
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AptamersAptamers
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Aptamer StructuresAptamer Structures
Nf-Kappa B (P50)2 Complexed To A High-Affinity RNA Aptamer
PDB code: 1ooa
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Aptamer StructuresAptamer Structures
PDB code: 1koc
RNA aptamer complex with arginine
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Aptamer StructuresAptamer Structures
www.mpibpc.gwdg.de/inform/MpiNews/cientif/jahrg6/2.00/fig4.html
RNA aptamer complex with tobramycin
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Aptamer StructuresAptamer Structures
PDB code: 1tob
RNA aptamer complex with tobramycin
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Aptamer StructuresAptamer Structures
PDB code: 1tob
RNA aptamer complex with tobramycin
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Cloverleaf Structure of tRNACloverleaf Structure of tRNA
www.mona.uwi.edu/biochem/courses/ dd120/documents/
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t-RNA (4tna) - 1978
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Pseudoknots
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Chemical Structures of DNA and PNAChemical Structures of DNA and PNA
http://www.bentham.org/coc-sample/ganesh/ganesh.htm
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RNA/PNA ComplexRNA/PNA Complex
S. C. Brown, S. A. Thomson, J. M. Veal, D. G. Davis NMR Solution Structure Of A Peptide Nucleic Acid Complexed With RNA Science V. 265 777 1994
PDB code: 176d