Identification of Ribose-Base Sequential NOEs According to Base Types in Uniformly13C-Labeled RNAs

Ramachandran, Ramadurai; Sich, Christian; Ohlenschläger, Oliver; Brown, L. R.

doi:10.1006/jmre.1996.7490

Cited by 2 publications

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References 6 publications

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“…For a detailed description of this approach as applied to the 19mer studied here, see Ramachandran et al (1996). For the through-space approach via NOESY spectroscopy Moore, 1995), a 400 ms 2D ( 1 H, 1 H) NOESY experiment (Kumar et al, 1980) as well as a 400 ms 2D ( 1 H, 1 H) purine/pyrimidine-selective NOESY experiment (Ramachandran et al, 1997) was recorded. The latter experiment provides NOE subspectra for NOEs arising from purine H8 and pyrimidine H6 hydrogens, respectively, thereby simplifying the sequential assignment procedure.…”

Section: Preparation Of Monomeric Stem-loop Structuresmentioning

confidence: 99%

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Structure of an RNA Hairpin Loop with a 5‘-CGUUUCG-3‘ Loop Motif by Heteronuclear NMR Spectroscopy and Distance Geometry

et al. 1997

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Structural features of a 19-nucleotide RNA hairpin loop (5'-GGCGUACGUUUCGUACGCC-3'), a loop motif which occurs in eukaryotic 18S rRNA, have been derived using multidimensional heteronuclear NMR spectroscopy in combination with local conformational analysis and torsion angle distance geometry followed by restrained energy minimization. A method to obtain both the 3JC4'P3' and 3JC4'P5' coupling constants from a set of spin-echo difference constant time HSQC spectra is introduced, and it is shown how these couplings can be assigned to the backbone angles beta and epsilon. A total of 280 distance constraints as well as 132 homo- and heteronuclear three-bond scalar coupling constants were derived from the NMR data. The structure which has been determined is a pentaloop rather than a triloop with no base pairing between G8 and C12. G8 is pointed to the minor groove where it forms a base triplet with C7-G13 that is further stabilized by hydrogen bonding to the 2'-hydroxyl group of C7. C12 is directed to the major groove where its conformation is stabilized by hydrogen bonding between O2 and HO2'. The NMR data suggest two possible, interconverting conformations with stacking of bases U10-G8 or U11-C7. Overall, the loop provides a variety of interaction sites for RNA or protein interactions.

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Section: Preparation Of Monomeric Stem-loop Structuresmentioning

confidence: 99%

“…The latter experiment provides NOE subspectra for NOEs arising from purine H8 and pyrimidine H6 hydrogens, respectively, thereby simplifying the sequential assignment procedure. For a detailed description of this approach applied to the present 19-mer, see Ramachandran et al (1997).…”

Section: Preparation Of Monomeric Stem-loop Structuresmentioning

confidence: 99%

Structure of an RNA Hairpin Loop with a 5‘-CGUUUCG-3‘ Loop Motif by Heteronuclear NMR Spectroscopy and Distance Geometry

et al. 1997

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Leppert

Heise

Ramachandran

2000

Journal of Biomolecular NMR

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An approach to the determination of the 2-(13)C' chemical shift (CS) tensor orientation in pyrimidine bases via heteronuclear MAS NMR spectroscopy is presented. Considering a dipolar coupled spin 1/2 network of the type S1-I-S2 consisting of directly bonded heteronuclear spins, we have carried out numerical simulations to assess the sensitivity of I-S REDOR spinning sidebands to the Euler angles defining the orientation of the I-S1 and I-S2 dipolar vectors in the I spin CS tensor principal axes system. Our investigations clearly demonstrate the potential of I-S REDOR studies in IS1S2 systems for obtaining with high reliability and accuracy the I spin chemical shift tensor orientation in the molecular frame spanned by the two internuclear vectors I-S1 and I-S2. The significant contribution to the observed REDOR sideband intensities from anti-phase operator terms which are present at the start of the data acquisition is illustrated. The procedure for the recording and analysis of the I-S REDOR spectra in IS1S2 systems is presented and the measurement of the 2-(13)C' CS tensor orientation in a polycrystalline sample of [1,3-(15)N2, 2-(13)C] uracil, which is one of the four bases in RNA, is experimentally demonstrated.

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Identification of Ribose-Base Sequential NOEs According to Base Types in Uniformly13C-Labeled RNAs

Cited by 2 publications

References 6 publications

Structure of an RNA Hairpin Loop with a 5‘-CGUUUCG-3‘ Loop Motif by Heteronuclear NMR Spectroscopy and Distance Geometry

Structure of an RNA Hairpin Loop with a 5‘-CGUUUCG-3‘ Loop Motif by Heteronuclear NMR Spectroscopy and Distance Geometry

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