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1 3D Structures of Biological Macromolecules Part 2 Nucleic Acid Structures Jürgen Sühnel jsuehnel@imb-jena.de jena.de Institute of Molecular Biotechnology,, Jena Centre for Bioinformatics Jena / Germany Supplementary Material:
2 Molecules of Life
3 Nucleic Acids DNA genomic information RNA messenger RNA, ribosomal RNA, transfer RNA, ribozymes, small RNAs, noncoding RNAs, RNAi (gene silencing), aptamers (alternatives to antibodies) PNA peptide nucleic acids mimic nucleic acids
4 New Roles for RNA
5 New Roles for RNA Couzin J. Breakthrough of the year. Small RNAs make big splash. Science. 2002, 298,
6
7
8 From Gene to Protein
9 History
10 History
11 Nucleic Acid Structure
12
13 Nucleobases
14 Chain Direction in Nucleic Acids /web.siumed.edu/~bbartholomew/course_material/nucleic_acids.html
15 Chain Direction in Nucleic Acids
16 Nucleic Acid Backbone
17 Nucleic Acid Backbone Torsion Angles
18 Ribonucleotides and Deoxyribonucleotides
19 Nucleic 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.
20 Nucleic Acid Base Pairs The seven possible homo-purine base pairs. Source: Ignacio Tinoco, Jr. in Gesteland, R. F. and Atkins, J. F. (1993) THE RNA WORLD. Cold Spring Harbor Laboratory Press.
21 Nucleic 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.
22 Nucleic Acid Base Pairs The seven possible pyrimidine-pyrimidine base pairs.
23 DNA Hydration
24 Nucleic Acid Base Pairs Water-mediated Pairs
25 Nucleic Acid Base Pairs Water-mediated Pairs
26 Nucleic Acid Base Pairs Water-mediated Pairs
27 Nucleic Acid Base Pairs with C-H O/N C Interactions
28 Nucleic Acid Base Pairs with C-H O/N C Interactions
29 Non-Canonical Base Pair Database
30 Selected Base Triples
31 Base Triples in trna Base triads in the crystal structure of yeast phenylalanine transfer RNA (PDB code: 4tna).
32 Base 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.
33 Base Polyads
34 Base 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.
35 HBexplore H-bond Analysis in Proteins and Nucleic Acids
36 Geometrical Parameters for Base Pairs in Nucleic Acids ndbserver.rutgers.edu/archives/report/tsukuba_sup/bp_step_hel.html
37 Nucleic Acid Structure
38 Nucleic Acid Structure Sugar Conformation
39 Nucleic Acid Structure Sugar Conformation
40 Nucleic Acid Structure Sugar Conformation
41 Nucleic 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
42 DNA Conformations A B Z
43 Ideal DNA Conformations and a Real B-DNA B Structure
44 Nucleic 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: 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.
45 Nucleic 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
46 Nucleic Acid Conformations - B-DNA
47 Nucleic Acid Conformations - B-DNA
48 Nucleic Acid Conformations B-DNA
49 Nucleic Acid Conformations B-DNA
50 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 First Single-crystal DNA Structure (B-DNA) Drew-Dickerson structure
51 Diversity of DNA Structures
52 Nucleosome Core Particle (1aoi) DNA in chromatin is organized in arrays of nucleosomes.two copies of each histone protein, H2A, H2B, H3 and H4, Are assembled into an octamer that has base pairs of DNA wrapped around it to form a nucleosome core.
53 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.
54 CURVES
55 Integration Host Factor (1ihf) CURVES Output
56 Integration Host Factor (1ihf) CURVES Output: Local Bending Analysis
57 Integration Host Factor (1ihf): Local Bending Analysis Dinucleotide steps with unusual large values of the roll and tilt angle are indicated in red.
58 Integration Host Factor (1ihf): Globale Bending Analysis Coordinate system and helical axis
59 Integration Host Factor (1ihf): Global Bending Analysis Coordinate system and helical axis
60 Integration Host Factor (1ihf): Global Bending Abnalysis Coordinate system and helical axis
61 Integration Host Factor (1ihf): Globale Bending Analysis Coordinate system and helical axis
62 Integration Host Factor (1ihf): Globale Bending Analysis Coordinate system and helical axis
63 Integration Host Factor (1ihf): Globale Bending Analysis
64 Nucleic Acid Structure - Bending
65 Cover Images for all 2003/2004/2005 Issues of the Journal RNA
66 Large Ribosomal Subunit (1jj2)
67 Jena Structures: : 5S rrna E-loop/L25 complex (1d6k) IMB: Molecular Biophysics/NMR Spectroscopy (M. Görlach)
68 Aptamers 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.
69 Aptamers
70 Aptamer Structures Nf-Kappab (P50)2 Complexed To A High-Affinity RNA Aptamer PDB code: 1ooa
71 Aptamer Structures RNA aptamer complex with arginine PDB code: 1koc
72 Aptamer Structures RNA aptamer complex with tobramycin
73 Aptamer Structures RNA aptamer complex with tobramycin PDB code: 1tob
74 Aptamer Structures RNA aptamer complex with tobramycin PDB code: 1tob
75 Aptamer Structures RNA aptamer complex with tobramycin PDB code: 1tob
76 Cloverleaf Structure of trna dd120/documents/
77 t-rna (4tna)
78 Pseudoknots
79 Chemical Structures of DNA and PNA
80 RNA/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 PDB code: 176d
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