Quantitative gamma-HCNCH: determination of the glycosidic torsion angle chi in RNA oligonucleotides from the analysis of CH dipolar cross-correlated relaxation by solution NMR spectroscopy.
A novel NMR pulse sequence is introduced to determine the glycosidic torsion angle chi in (13)C,(15)N-labeled oligonucleotides. The quantitative Gamma-HCNCH measures the dipolar cross-correlated relaxation rates Gamma(DD,DD)(C8H8,C1'H1') (pyrimidines) and Gamma(DD,DD)(C6H6,C1'H1') (purines). Cross-correlated relaxation rates of a (13)C,(15)N-labeled RNA 14mer containing a cUUCGg tetraloop were determined and yielded chi-angles that agreed remarkably well with data derived from the X-ray structure of the tetraloop. In addition, the method was applied to the larger stemloop D (SLD) subdomain of the Coxsackievirus B3 cloverleaf 30mer RNA and the effect of anisotropic rotational motion was examined for this molecule. It could be shown that the chi-angle determination especially for nucleotides in the anti conformation was very accurate and the method was ideally suited to distinguish between the syn and the anti-conformation of all four types of nucleotides.
Rinnenthal
Jörg
J
Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 7, 60438 Frankfurt/Main, Germany.
Richter
Christian
C
Ferner
Jan
J
Duchardt
Elke
E
Schwalbe
Harald
H
D000241:Adenosine / Q000737:chemistry; D001483:Base Sequence; D006027:Glycosides / Q000737:chemistry*; D008969:Molecular Sequence Data; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D009690:Nucleic Acid Conformation; D009843:Oligoribonucleotides / Q000737:chemistry* / Q000235:genetics; D011743:Pyrimidines / Q000737:chemistry; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics; D012399:Rotation; D012996:Solutions
D006027:Glycosides; D009843:Oligoribonucleotides; D011743:Pyrimidines; D012367:RNA, Viral; D012996:Solutions; D000241:Adenosine