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==Structure and dynamics of a DNA GNRA hairpin solved vy high-sensitivity NMR with two independent converging methods, simulated annealing (DYANA) and mesoscopic molecular modelling (BCE/AMBER)==
<StructureSection load='2k71' size='340' side='right'caption='[[2k71]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2k71]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2K71 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2K71 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2k71 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2k71 OCA], [https://pdbe.org/2k71 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2k71 RCSB], [https://www.ebi.ac.uk/pdbsum/2k71 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2k71 ProSAT]</span></td></tr>
</table>
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== Publication Abstract from PubMed ==
Determination of DNA solution structure is a difficult task even with the high-sensitivity method used here based on simulated annealing with 35 restraints/residue (Cryoprobe 750 MHz NMR). The conformations of both the phosphodiester linkages and the dinucleotide segment encompassing the sharp turn in single-stranded DNA are often underdetermined. To obtain higher quality structures of a DNA GNRA loop, 5'-d(GCGAAAGC)-3', we have used a mesoscopic molecular modeling approach, called Biopolymer Chain Elasticity (BCE), to provide reference conformations. By construction, these models are the least deformed hairpin loop conformation derived from canonical B-DNA at the nucleotide level. We have further explored this molecular conformation at the torsion angle level with AMBER molecular mechanics using different possible (epsilon,zeta) constraints to interpret the 31P NMR data. This combined approach yields a more accurate molecular conformation, compatible with all the NMR data, than each method taken separately, NMR/DYANA or BCE/AMBER. In agreement with the principle of minimal deformation of the backbone, the hairpin motif is stabilized by maximal base-stacking interactions on both the 5'- and 3'-sides and by a sheared G.A mismatch base pair between the first and last loop nucleotides. The sharp turn is located between the third and fourth loop nucleotides, and only two torsion angles beta6 and gamma6 deviate strongly with respect to canonical B-DNA structure. Two other torsion angle pairs epsilon3,zeta3 and epsilon5,zeta5 exhibit the newly recognized stable conformation BIIzeta+ (-70 degrees, 140 degrees). This combined approach has proven to be useful for the interpretation of an unusual 31P chemical shift in the 5'-d(GCGAAAGC)-3' hairpin.

Nucleic acid folding determined by mesoscale modeling and NMR spectroscopy: solution structure of d(GCGAAAGC).,Santini GP, Cognet JA, Xu D, Singarapu KK, Herve du Penhoat C J Phys Chem B. 2009 May 14;113(19):6881-93. PMID:19374420<ref>PMID:19374420</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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== References ==
<references/>
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</StructureSection>
[[Category: Large Structures]]
[[Category: Cognet JAH]]
[[Category: Herve du Penhoat CLM]]
[[Category: Santini GPH]]
[[Category: Singarapu KK]]
[[Category: Xu D]]