figure 5-11 three-dimensional structure of b-dna
DESCRIPTION
Figure 5-12 Watson-Crick base pairs. Figure 5-11 Three-dimensional structure of B-DNA. http://rutchem.rutgers.edu/~xiangjun/3DNA/images/bp_step_hel.gif. Twist varies with sequence. Note: importance of sequence > importance of composition. - PowerPoint PPT PresentationTRANSCRIPT
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Figure 5-11Three-dimensional structure of B-DNA.
Figure 5-12 Watson-Crick base pairs.
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http://rutchem.rutgers.edu/~xiangjun/3DNA/images/bp_step_hel.gif
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Twist varies with sequence.
Note:
importance of sequence > importance of composition.
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Figure 29-7 The conformation of a nucleotide unit is determined by
the seven indicated torsion angles.
Figure 29-9b Sugar ring pucker. (b) The steric strain resulting in
Part a is partially relieved by ring puckering in a half-chair
conformation in which C3 is the out-of-plane atom.
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Table 4.T02: Comparison of Major Features in A-, B-, and Z-Forms of DNA
Adapted from Ussery, D. W. Encyclopedia of Life Sciences. John Wiley & Sons, Ltd., May 2002. [doi: 10.1038/npg.els.0003122].
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Table 29-1 Structural Features of Ideal A-, B-, and Z-DNA.
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Figure 29-10aNucleotide sugar conformations. (a) The C3-endo conformation (on the same side of the sugar ring as C5), which occurs in A-
RNA and RNA-11.
Figure 29-10bNucleotide sugar conformations. (b) The C2-endo conformation,
which occurs in B-DNA.
Greater flexibility of B-DNA allows it to exhibit significant variation in the configuation of its sugar pucker under in vivo conditions. But see: http://www.chem.qmul.ac.uk/iupac/misc/pnuc2.html
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From: http://www.chem.qmul.ac.uk/iupac/misc/pnuc2.html
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Figure 4.05a: Deoxyguanylate in B-DNA in anti conformation
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Figure 4.05b: Deoxyguanylate in Z-DNA in syn conformation
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Figure 29-1a Structure of B-DNA. (a) Ball and stick drawing and corresponding space-filling model viewed perpendicular to the helix
axis.
~10 bp/turn- right handedPitch of 34 AngstromsWide major grooveNarrow minor
grooveStructure adopted byReal DNA deviates from
ideal structure in a
sequence-specific
manner.
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Figure 4.04a: The C2’-endo conformation
Adapted from Voet, D., and Voet, J. G. Biochemistry, Third Edition. John Wiley & Sons, Ltd., 2005.
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Figure 4.04b: The C3’-endo conformation
Adapted from Voet, D., and Voet, J. G. Biochemistry, Third Edition. John Wiley & Sons, Ltd., 2005.
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Figure 29-1b Structure of B-DNA. (b) Ball and stick drawing and corresponding space-
filling model viewed down the helix axis.
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Figure 4.01a: A-DNA
Protein Data Bank ID: 213D. Ramakrishnan, B., and Sundaralingam, M., Biophys. J. 69 (1995): 553-558 (top).
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Figure 29-2a Structure of A-DNA. (a) Ball and stick drawing and corresponding space-filling model viewed perpendicular to the helix
axis.
11.6 bp/turn- right handedPitch of 34 AngstromsDeep major grooveVery shallow minor
grooveStructure adopted byA-RNA (aka. RNA-11)
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Figure 29-2b Structure of A-DNA. (b) Ball and stick drawing and corresponding space-
filling model viewed down the helix axis.
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Figure 4.01b: B-DNA
Protein Data Bank ID: 1BNA. Drew, H. R., et al., Proc. Natl. Acad. Sci. USA 78 (1981): 2179-2183 (middle).
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Figure 29-3a Structure of Z-DNA. (a) Ball and stick drawing and corresponding space-filling model viewed perpendicular to the helix axis.
12 bp/turn- left-handed helixPitch of 44 AngstromsNo major grooveDeep minor grooveStructure adopted byAlternating Purine-
Pyrimidine pairs
(e.g., repeats of 2 bases pairs)Methylation of C favors
formation, as does
high salt conc.Genetic switch?
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Figure 29-3b Structure of Z-DNA. (b) Ball and stick drawing and corresponding space-
filling model viewed down the helix axis.
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Figure 4.01c: Z-DNA
Protein Data Bank ID: 2ZNA. Wang, A. H. J., et al. (bottom).
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Figure 4.02a: Z-DNA with zig-zag sugar phosphate backbone shown in white
Protein Data Bank ID: 2ZNA. Wang, A. H. J., et al.
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Figure 4.02b: The same Z-DNA with the zigzag sugar phosphate backbone shown in space filling display
Protein Data Bank ID: 2ZNA. Wang, A. H. J., et al.
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Figure 29-4 Conversion of B-DNA to Z-DNA.
Base pairs flipped by 180 degrees
Repeat is d(pXpY)
Polyd(GC)-polyd(GC)
Polyd(AC)-polyd(GT)
Anti-C or T
Syn-G or A
May form transiently behind actively transcribing RNA polymerase
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Figure 29-5 X-Ray structure of two ADAR1 Z domains in complex with Z-DNA.
Thought to targeted to Z-DNA upstream of actively transcribing genes
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Figure 4.03: Drosophila (fruit fly) chromosomes with bound antibody to Z-DNA.
Reproduced from Nordheim, A., et al., Nature 294 (1981): 417-422. Photo courtesy of Alexander Rich, Massachusetts Institute of Technology.
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Forces stabilizing nucleic acid structure
BASE PAIRING1) Geometric complementarity2) Electronic complementarity
Book: contribute -2 to -8 kJ/mol of base pairOther sources:A=U/A=T -5 to -9 kJ/mol of bpG=C -13 to -21 kJ/ mol of bpBase pairs replaced by H-bonds to water of nearly equivalent strength when DNA is denatured.Non Watson-Crick H-bonding have little stability
in dsDNAHowever, they do stabilize tertiary structure of tRNAs and have other roles (e.g., wobble base pairing in codon/anti-codon recognition.
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Forces stabilizing nucleic acid structure
BASE STACKING1) Van der Waals radii
of aromatic ring ~1.7 angstroms
2) Adjacent bases 3.4 angstroms apart in helix
3) Contribute -4 kJ/mol
4) Base stacking is responsible for the hyperchromic effect observed when dsDNA is denatured
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Forces stabilizing nucleic acid structure
HYDROPHOBIC FORCES1) Sugar-phosphates
on outside interacting with water.
2) Hydrophobic bases in interior
3) Base stacking is enthalpically driven and entropically opposed
4) Hydrophobic forces poorly understood
5) Increases in ionic strength stabilizes dsDNA and dsRNA.
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Table 4.T01: Sizes of Various DNA Molecules
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Figure 4.08: DNA melting curve.
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Figure 4.09: Effect of G-C content on DNA melting temperature.
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Figure 4.10: Several effects of cooperativity of base-stacking.
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Figure 4.11: The effect of lowering the temperature to 25°C after strand separation has taken place.
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Figure 4.06a: Inverted repeats
Adapted from Bacolla, A., and Wells, R. D., J. Biol. Chem. 279 (2004): 47411-47414.
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Figure 4.06b: Cruciform structure
Adapted from Bacolla, A., and Wells, R. D., J. Biol. Chem. 279 (2004): 47411-47414.
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Figure 4.07: Hairpin RNA.
Adapted from Horton, R. H., et al. Principles of Physical Biochemistry, Second Edition. Prentice Hall, 2006.
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Hyperchromic effect- increase of 1.4xA260 upon denaturation of double-stranded nucleic Acids (dsDNA or dsRNA
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Forces stabilizing nucleic acid structure
IONIC INTERACTIONS1. Electrostatic
repulsion of phosphates destabilize dsDNA structure
2. Effect counteracted or stabilized by cations-Metal ions: Na+, K+,
Mg2+
-polyamines-basic proteins-Mg2+ effect 100-
1000X of Na+ ions.
ENTROPICALLY UNFAVORABLE1) Highly ordered2) Increase temperature= decrease stabilityTm=41.1XG+C + 16.6log[Na+] +81.5