1YFV

STRUCTURE OF (5'-R(GP*GP*CP*GP*AP*GP*CP*C)-3')2 BY 2-D NMR, 1 STRUCTURE

Summary for 1YFV

• Entry DOI: 10.2210/pdb1yfv/pdb
• Descriptor: RNA (5'-R(GP*GP*CP*GP*AP*GP*CP*C)-3') (1 entity in total)
• Functional Keywords: ribonucleic acid, g:a mismatch, 2-d nmr, anti-parallel rna duplex, rna
• Biological source: synthetic construct
• Total number of polymer chains: 2
• Total formula weight: 5161.23

Authors

Santalucia Junior, J.,Turner, D.H. (deposition date: 1997-05-17, release date: 1997-10-15, Last modification date: 2024-05-22)

Primary citation

SantaLucia Jr., J.,Turner, D.H.
Structure of (rGGCGAGCC)2 in solution from NMR and restrained molecular dynamics.
Biochemistry, 32:12612-12623, 1993

PubMed Abstract: The duplex (rGGCGAGCC)2 contains tandem G x A mismatches--a common motif in the secondary structures of biological RNAs. The three-dimensional structure of (rGGCGAGCC)2 was derived using molecular dynamics and energy minimization with NMR-derived restraints for 78 interproton distances (per strand), 18 hydrogen bonds for the six Watson-Crick G x C pairs, and 26 dihedral angles (per strand). The G x A mismatch structures are similar to those observed in a DNA duplex [Li, Y., Zon, G., & Wilson, W. D. (1991) Proc. Natl. Acad. Sci. U.S.A. 80, 26-30] and an RNA hairpin [Heus, H. A., & Pardi, A. (1991) Science 253, 191-193], with hydrogen bonds from guanine 2-amino and N3 to adenine N7 and 6-amino, respectively. The other G 2-amino and A 6-amino protons are within hydrogen-bonding distance of a phosphate oxygen and 2'-oxygen, respectively. Strong interstrand A-A and G-G stacking is observed between the G x A mismatches. This contrasts with the poor stacking observed between the G x A mismatches and closing G x C base pairs. The stems are basically A-form with all bases in the anti conformation and all nonterminal sugars in the C3'-endo conformation. The structure rationalizes previous thermodynamic, circular dichroism, and imino proton NMR results and suggests tandem G x A mismatches in RNA may provide a contact site for tertiary interactions.

PubMed: 8251479
DOI: 10.1021/bi00210a009

Experimental method

SOLUTION NMR