Folie 1 - PowerPoint PPT Presentation

Loading...

PPT – Folie 1 PowerPoint presentation | free to download - id: 56fb63-OTBjO



Loading


The Adobe Flash plugin is needed to view this content

Get the plugin now

View by Category
About This Presentation
Title:

Folie 1

Description:

Title: Folie 1 Author: J rgen S hnel Last modified by: jsuehnel Created Date: 5/15/2005 4:33:10 AM Document presentation format: Bildschirmpr sentation (4:3) – PowerPoint PPT presentation

Number of Views:56
Avg rating:3.0/5.0
Slides: 80
Provided by: J408
Learn more at: http://www.fli-leibniz.de
Category:
Tags: database | folie

less

Write a Comment
User Comments (0)
Transcript and Presenter's Notes

Title: Folie 1


1
- 2010 - 3D Structures of Biological
Macromolecules Part 3 Nucleic Acids
Jürgen Sühnel jsuehnel_at_fli-leibniz.de
Leibniz Institute for Age Research, Fritz Lipmann
Institute, Jena Centre for Bioinformatics Jena /
Germany
Supplementary Material www.fli-leibniz.de/www_bio
c/3D/
2
Molecules of Life
3
Nucleic Acids
DNA genomic information (nucleosomes,
chromatin) 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, 2296-2297.
6
(No Transcript)
7
(No Transcript)
8
From Gene to Protein
9
History
10
History
11
Nucleic Acid Structure
12
(No Transcript)
13
Nucleobases
14
Chain Direction in Nucleic Acids
/web.siumed.edu/bbartholomew/course_material/nucl
eic_acids.html no longer active)
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
www.lsbu.ac.uk/water/nucleic.html
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-HO/N Interactions
28
Nucleic Acid Base Pairs with C-HO/N Interactions
29
Non-Canonical Base Pair Database
http//prion.bchs.uh.edu/bp_type/
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
www.imb-jena.de/www_bioc/hbx/hbx.html
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/vorl
esung1/kapitel1e.html?/chemie/bioorganic/vorlesung
1/k1e-20.html
42
DNA Conformations
B
A
Z
www.rcsb.org/pdb/molecules/pdb23_3.html
43
Ideal DNA Conformations and a Real B-DNA
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

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
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
First Single-crystal DNA Structure (B-DNA)
Drew-Dickerson structure
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
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 145-147 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
www.ibpc.fr/UPR9080/Curonline.html
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) Global 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
Analysis
Coordinate system and helical axis
61
Integration Host Factor (1ihf) Globale Bending
Analysis
Coordinate system and helical axis
62
Integration Host Factor (1ihf) Global Bending
Analysis
63
Integration Host Factor (1ihf) Global Bending
Analysis
64
Nucleic Acid Structure - Bending
65
Cover Images for all 2003-2011 Issues of the
Journal RNA
66
Large Ribosomal Subunit (1jj2) - 2001
67
Jena Structures 5S rRNA E-loop/L25 complex
(1d6k)
IMB/FLI 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. http//aptamer.icmb.utexas.edu
69
Aptamers
70
Aptamer Structures
Nf-Kappa B (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
www.mpibpc.gwdg.de/inform/MpiNews/cientif/jahrg6/2
.00/fig4.html
73
Aptamer Structures
RNA aptamer complex with tobramycin
PDB code 1tob
74
Aptamer Structures
RNA aptamer complex with tobramycin
PDB code 1tob
75
Cloverleaf Structure of tRNA
www.mona.uwi.edu/biochem/courses/
dd120/documents/
76
t-RNA (4tna) - 1978
77
Pseudoknots
78
Chemical Structures of DNA and PNA
http//www.bentham.org/coc-sample/ganesh/ganesh.ht
m
79
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. 265
777 1994
PDB code 176d
About PowerShow.com