1bjd
From Proteopedia
(New page: 200px<br /><applet load="1bjd" size="450" color="white" frame="true" align="right" spinBox="true" caption="1bjd" /> '''SOLUTION STRUCTURE OF A DNA DODECAMER CONTAI...) |
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'''SOLUTION STRUCTURE OF A DNA DODECAMER CONTAINING SINGLE G*T MISMATCHES USING RELAXATION MATRIX ANALYSIS AND RESTRAINED MOLECULAR DYNAMICS, NMR, 1 STRUCTURE'''<br /> | '''SOLUTION STRUCTURE OF A DNA DODECAMER CONTAINING SINGLE G*T MISMATCHES USING RELAXATION MATRIX ANALYSIS AND RESTRAINED MOLECULAR DYNAMICS, NMR, 1 STRUCTURE'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The three-dimensional solution structure of the self-complementary DNA | + | The three-dimensional solution structure of the self-complementary DNA dodecamer (CGT_GACGT_TACG above GCAT_TGCAG_TGC] which contains the thermodynamically destabilizing [TG_A above AT_T] motif was determined using two-dimensional NMR spectroscopy and simulated annealing protocols. Relaxation matrix analysis methods were used to yield accurate NOE derived distance restraints. Scalar coupling constants for the sugar protons were determined by quantitative simulations of DQF-COSY cross-peaks and used to determine sugar pucker populations. Twenty refined structures starting from random geometries converged to an average pairwise root mean square deviation of 0.49 A. Back calculated NOEs give Rc and Rx factors of 0.38 and 0.088, respectively. The final structure shows that each of the single G@T mismatches form a wobble pair with two hydrogen bonds where the guanine projects into the minor groove and the thymine projects into the major groove. The incorporation of the destabilizing [TG_A above AT_T] motif has little effect on the backbone torsion angles and helical parameters compared to standard B-form duplexes, which may explain why G.T mismatches are among the most commonly observed in DNA. The structure shows that perturbations caused by a G.T mismatch extend only to its neighboring Watson-Crick base pair, thus providing a structural basis for the applicability of the nearest-neighbor model to the thermodynamics of internal G.T mismatches. |
==About this Structure== | ==About this Structure== | ||
| - | 1BJD is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http:// | + | 1BJD is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BJD OCA]. |
==Reference== | ==Reference== | ||
NMR solution structure of a DNA dodecamer containing single G.T mismatches., Allawi HT, SantaLucia J Jr, Nucleic Acids Res. 1998 Nov 1;26(21):4925-34. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9776755 9776755] | NMR solution structure of a DNA dodecamer containing single G.T mismatches., Allawi HT, SantaLucia J Jr, Nucleic Acids Res. 1998 Nov 1;26(21):4925-34. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9776755 9776755] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Allawi, H | + | [[Category: Allawi, H T.]] |
| - | [[Category: Junior, J | + | [[Category: Junior, J Santalucia.]] |
[[Category: deoxyribonucleic acid]] | [[Category: deoxyribonucleic acid]] | ||
[[Category: dna]] | [[Category: dna]] | ||
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[[Category: nmr]] | [[Category: nmr]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:55:56 2008'' |
Revision as of 09:55, 21 February 2008
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SOLUTION STRUCTURE OF A DNA DODECAMER CONTAINING SINGLE G*T MISMATCHES USING RELAXATION MATRIX ANALYSIS AND RESTRAINED MOLECULAR DYNAMICS, NMR, 1 STRUCTURE
Overview
The three-dimensional solution structure of the self-complementary DNA dodecamer (CGT_GACGT_TACG above GCAT_TGCAG_TGC] which contains the thermodynamically destabilizing [TG_A above AT_T] motif was determined using two-dimensional NMR spectroscopy and simulated annealing protocols. Relaxation matrix analysis methods were used to yield accurate NOE derived distance restraints. Scalar coupling constants for the sugar protons were determined by quantitative simulations of DQF-COSY cross-peaks and used to determine sugar pucker populations. Twenty refined structures starting from random geometries converged to an average pairwise root mean square deviation of 0.49 A. Back calculated NOEs give Rc and Rx factors of 0.38 and 0.088, respectively. The final structure shows that each of the single G@T mismatches form a wobble pair with two hydrogen bonds where the guanine projects into the minor groove and the thymine projects into the major groove. The incorporation of the destabilizing [TG_A above AT_T] motif has little effect on the backbone torsion angles and helical parameters compared to standard B-form duplexes, which may explain why G.T mismatches are among the most commonly observed in DNA. The structure shows that perturbations caused by a G.T mismatch extend only to its neighboring Watson-Crick base pair, thus providing a structural basis for the applicability of the nearest-neighbor model to the thermodynamics of internal G.T mismatches.
About this Structure
1BJD is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
NMR solution structure of a DNA dodecamer containing single G.T mismatches., Allawi HT, SantaLucia J Jr, Nucleic Acids Res. 1998 Nov 1;26(21):4925-34. PMID:9776755
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