dnab - Principles of nucleic acid structure Biophysical...

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Unformatted text preview: Principles of nucleic acid structure Biophysical Chemistry 1, Fall 2010 Reading assignment: Chap. 3 Web assignment: http://w3dna.rutgers.edu Nucleic acids: phosphates, sugars, bases eotide i is joined to the 5´-oxygen of nucleo ( i ) ( I +1) The sugar-phosphate backbone Basics of Nucleic Acid Structure Chain direction nucleotide unit O3’ O5’ O4’ O3’ P Base 1’ 2’ 3’ 4’ 5’ O O P α β δ ε ζ χ ζ α = O3’ i-1 —P—O5’—C5’ β = P—O5’—C5’—C4’ γ = O5’—C5’—C4’-C3’ δ = C5’—C4’—C3’—C2’ ε = C4’—C3’—O3’—P i+1 ζ = C3’—O3’—P i+1-O3’ i+1 γ P OP2 OP1 O5’ C5’ C3’ O3’ Residue i Residue i-1 Sugar puckering Basics of Nucleic Acid Structure 63 C5’ 2’ 3’ O4’ B C5’ 2’ 3’ O4’ B C5’ 2’ 3’ O4’ B C5’ 2’ 3’ B C5’ 2’ O4’ B C5’ 3’ O4’ B 2 E 2 T 3 E 3 3 E 3 T 2 E 2 Sugar puckering ctural Biology 0˚ 72˚ 108˚ 252˚ 288˚ 324˚ 36˚ C4’-exo C4’-endo C1’-exo C4’-endo O4’-exo C1’-endo C2’-exo C3’-endo N T E 3 T 3 4 E 4 4 E T 1 E 1 T 2 1 2 2 T 4 3 E 4 T 4 E T 1 E 1 T 1 2 E 2 T 3 2 purines and pyrimidines n. Conformational angles of P are divided into two categories, north (N) and so N N NH N NH 2 N NH NH N NH 2 O NH NH O O NH NH O O N NH NH 2 O Adenine Guanine Uracil Thymine Cytosine 5 6 1 2 3 4 5 6 7 8 9 1 2 3 4 5 6 7 8 9 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 The glycosidic torsion parameter Basics of Nucleic Acid Structure 65 Watson-Crick base pairing f Structural Biology N N O N H H N N H H O major groove major groove A and B-form helices Base pairs displaced from A-DNA helical axis. A-DNA minor groove wider and more shallow, major groove narrower and more deep cf . B DNA A-DNA B-DNA- +salt and/or +alcohol . +H 2 O base pairs inclined with respect to helical axis and untwisted cf . B DNA. . B transition: first known change of DNA double-helical state. 10 bp/turn n A and B-form helices urn. One full turn measures 3.4 nm in the axial direction Base stacking cessive base pairs depends on duplex form. Concentrate on the basepair structures Basics of Nucleic Acid Structure 73 x x x x x x x x x x y y y y y y y y z z z z z z z z z z z z Propeller Buckle Shear Stretch Shift Slide Roll Tilt Getting DNA to bend ••••• ••••• ••••• ••••• C . C deformations tighten the bending of DNA: Global bend: 360°/75 bp left-handed superhelix A The nucleosome core particle f Structural Biology DNA binding to the histone core proteins Comparison to elastic rod models Bending rigidity: A = M ( 2 πν n ) 2 LP 4 n ; a = A / ( k B T ) Twisting rigidity: C = I ( 2 L ν n ) 2 n 2 Stretching rigidity: Y = ML ( 2 ν n ) 2 n 2 Lord Rayleigh, The Theory of Sound , 1894 Bending rigidity for linear duplex DNA Stretching rigidity for linear duplex DNA Stretching motions d(GACT) 60 base pairs n GB frequencies Analytical frequencies 1 0.664 0.619 2 1.289 1.237 3 1.807 1.846 Y = 1502 pN Salt dependence of bending and stretching are not the same...
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dnab - Principles of nucleic acid structure Biophysical...

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