Literature DB >> 9109652

Solution structure of (rGGCAGGCC)2 by two-dimensional NMR and the iterative relaxation matrix approach.

M Wu1, J SantaLucia, D H Turner.   

Abstract

The three-dimensional solution structure of the RNA self-complementary duplex [formula in text] was derived from two-dimensional NMR and the iterative relaxation matrix approach. Each GA mismatch forms two hydrogen bonds: A-NH6 to G-O6 and A-N1 to G-NH1 (imino). This GA structure differs from the sheared tandem GA structure in [formula in text] which also has two hydrogen bonds: A-N7 to G-NH2 and A-NH6 to G-N3 [SantaLucia, J., Jr & Turner, D. H. (1993) Biochemistry 32, 12612-12623], although the only difference between the two sequences is the order of the two GA mismatches. Inspection of three-dimensional structures indicates that substituting [formula in text] for [formula in text] makes GA mismatches unable to have stable sheared conformations. This may explain why the [formula in text] motif is rarely observed in nature, whereas [formula in text] common.

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Year:  1997        PMID： 9109652     DOI： 10.1021/bi9625915

Source DB:  PubMed          Journal:  Biochemistry        ISSN： 0006-2960            Impact factor:   3.162


  21 in total

1.  Prediction of proton chemical shifts in RNA. Their use in structure refinement and validation.

Authors:  J A Cromsigt; C W Hilbers; S S Wijmenga
Journal:  J Biomol NMR       Date:  2001-09       Impact factor: 2.835

2.  Rearrangement of a 1,3-trans-[Pt(NH3)2[(GXG)-N7G,N7G]] intrastrand cross-link into interstrand cross-links within RNA duplexes.

Authors:  Marine Escaffre; Jean-Claude Chottard; Sophie Bombard
Journal:  Nucleic Acids Res       Date:  2002-12-01       Impact factor: 16.971

3.  Molecular dynamics reveals the stabilizing role of loop closing residues in kissing interactions: comparison between TAR-TAR* and TAR-aptamer.

Authors:  François Beaurain; Carmelo Di Primo; Jean Jacques Toulmé; Michel Laguerre
Journal:  Nucleic Acids Res       Date:  2003-07-15       Impact factor: 16.971

4.  Heat capacity changes in RNA folding: application of perturbation theory to hammerhead ribozyme cold denaturation.

Authors:  Peter J Mikulecky; Andrew L Feig
Journal:  Nucleic Acids Res       Date:  2004-07-28       Impact factor: 16.971

5.  An alternating sheared AA pair and elements of stability for a single sheared purine-purine pair flanked by sheared GA pairs in RNA.

Authors:  Gang Chen; Scott D Kennedy; Jing Qiao; Thomas R Krugh; Douglas H Turner
Journal:  Biochemistry       Date:  2006-06-06       Impact factor: 3.162

6.  Consecutive GA pairs stabilize medium-size RNA internal loops.

Authors:  Gang Chen; Douglas H Turner
Journal:  Biochemistry       Date:  2006-03-28       Impact factor: 3.162

7.  Stacking effects on local structure in RNA: changes in the structure of tandem GA pairs when flanking GC pairs are replaced by isoG-isoC pairs.

Authors:  Gang Chen; Ryszard Kierzek; Ilyas Yildirim; Thomas R Krugh; Douglas H Turner; Scott D Kennedy
Journal:  J Phys Chem B       Date:  2007-04-06       Impact factor: 2.991

8.  NMR structures of (rGCUGAGGCU)2 and (rGCGGAUGCU)2: probing the structural features that shape the thermodynamic stability of GA pairs.

Authors:  Blanton S Tolbert; Scott D Kennedy; Susan J Schroeder; Thomas R Krugh; Douglas H Turner
Journal:  Biochemistry       Date:  2007-01-20       Impact factor: 3.162

9.  Direct identification of NH...N hydrogen bonds in non-canonical base pairs of RNA by NMR spectroscopy.

Authors:  J Wöhnert; A J Dingley; M Stoldt; M Görlach; S Grzesiek; L R Brown
Journal:  Nucleic Acids Res       Date:  1999-08-01       Impact factor: 16.971

10.  Molecular basis of double-stranded RNA-protein interactions: structure of a dsRNA-binding domain complexed with dsRNA.

Authors:  J M Ryter; S C Schultz
Journal:  EMBO J       Date:  1998-12-15       Impact factor: 11.598
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