Distinguishing Inter- and Intrastrand NOEs Involving Exchangeable Protons in RNA Duplexes

Sich, Christian; Flemming, J.; Ramachandran, Ramadurai; Brown, L. R.

doi:10.1006/jmrb.1996.0142

Cited by 4 publications

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“…As has been observed by NMR for several hairpin loop motifs, e.g., the 5′-CUUG-3′ tetraloop (Aboul-ela et al, 1994), the 5′-CGGUUCG-3′ motif (Sich et al, 1996), and the 5′-CGUUUCG-3′ motif studied here, there is a propensity in solution to form duplexes containing bulges with unusual base pairs. Furthermore, in X-ray crystallography it is often observed that hairpin loop motifs crystallize as duplex structures (Holbrook et al, 1991;Lietzke et al, 1996;Gru ¨ne et al, 1996a).…”

Section: Discussionsupporting

confidence: 80%

“…This tetraloop sequence is a good example in which either hairpin loop or duplex conformations exist in solution depending on the solution conditions. We have also shown that the 5′-GUU-3′ triloop motif with a stem length of four nucleotides forms a duplex with three unusual base pairs at concentrations used for NMR spectroscopy, and alternative NMR methods to verify monomer or duplex formation by 15 N-labeled RNA molecules have been proposed (Sich et al, 1996). For the 5′-CGUUUCG-3′ loop motif, the rapid interconversion of monomeric and dimeric forms of the 11mer might be related to loop-loop interactions such as those observed in "kissing complexes" (Marino et al, 1995a) since three consecutive UU base pairs are present in the duplex form (unpublished results).…”

Section: Discussionmentioning

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: Discussionsupporting

confidence: 80%

Section: Discussionmentioning

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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Lapham

Rife

Moore

et al. 1997

Journal of Biomolecular NMR

117

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Pulsed field-gradient NMR experiments can be used to measure the diffusion constants of nucleic acids. The diffusion constants measured in this way for double-helical DNAs of defined length agree well both with theory and with measurements done using other techniques. When applied to RNAs, this experiment easily distinguishes duplex RNAs from RNA hairpins and thus it can solve one of the perennial problems faced by RNA spectroscopists, i.e. assessing whether their samples are monomeric or not.

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Distinguishing Inter- and Intrastrand NOEs Involving Exchangeable Protons in RNA Duplexes

Cited by 4 publications

References 4 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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