1X2S

NMR solution structures of a DNA dodecamer containing a tandem GT mismatches using NOE and residual dipolar couplings

Summary for 1X2S

• Entry DOI: 10.2210/pdb1x2s/pdb
• Related: 1X2O 1X2U 1X2V 1X2X 1X2Y 1X2Z 1X30
• Descriptor: 5'-D(*GP*AP*CP*TP*GP*TP*AP*CP*AP*GP*TP*C)-3' (1 entity in total)
• Functional Keywords: rdc, deoxyribonucleic acid, liquid crystal, dna
• Total number of polymer chains: 2
• Total formula weight: 7324.81

Authors

Alvarez-Salgado, F.,Desvaux, H.,Boulard, Y. (deposition date: 2005-04-26, release date: 2006-08-01, Last modification date: 2024-05-29)

Primary citation

Alvarez-Salgado, F.,Desvaux, H.,Boulard, Y.
NMR assessment of the global shape of a non-labelled DNA dodecamer containing a tandem of G--T mismatches
Magn.Reson.Chem., 44:1081-1089, 2006

PubMed Abstract: We have carried out a solution study of two non-labelled self-complementary DNA dodecamers d(GACTGTACAGTC)2 and d(GACTGTGCAGTC)2 by NMR, the second sequence composed of two G-T mismatches. Structures were determined using distances extracted from NOE effects alone or using both NOE and RDC constraints, measured in three different liquid crystalline media. We ensured that our data on the influence of the mesogen on the DNA structures, and the way in which the RDCs were incorporated as constraints in the protocol refinement, were consistent. We also tested the influence of different sets of RDCs and the best means of optimizing the calculation of D(a) and R. Resolution and accuracy of the ten best energy final structures were compared. The addition of a small set of RDC constraints significantly improves the final determined structures. We took advantage of the specificity of the RDC, i.e. it contains orientational information, and explored the global shape of the DNA duplexes; it was found that the duplexes do not have a large curvature. For the G-T base pair, we observed, in this particular sequence (tandem of G-T mismatches), a new pattern of base pairing, which involved the formation of a bifurcated hydrogen bond.

PubMed: 16972306
DOI: 10.1002/mrc.1902

Experimental method

SOLUTION NMR