Conformational Analysis of the Single-Stranded Ribonucleic Acid A-A-C-C. A One-Dimensional and Two-Dimensional Proton NMR Study at 500 MHz

Abstract

Proton NMR studies at 300 MHz and 500 MHz are reported on the ribotetranucleotide A‐A‐C‐C. The complete 1H‐NMR spectral assignment at 20°C is given. Two‐dimensional NMR was used to elucidate spin multiplets in ‘crowded’ regions. Nuclear Overhauser enhancement (NOE) experiments made an unambiguous spectral assignment possible and yielded information on interproton distances. The N/S equilibrium of the riboses and the rotamer populations around some backbone torsion angles are presented. A large preference for N‐type ribose and γ+ and βt backbone torsions is observed, in particular in the central A – C unit of A‐A‐C‐C. Information on distances between protons of different nucleotide units, obtained from NOE experiments, constitutes a probe of base‐base stacking. It is concluded that A‐A‐C‐C offers a good model for RNA single‐strand conformation.

Synthesis complete1H assignments and conformations of the self-complementary hexadeoxyribonucleotide [d(CpGpApTpCpG)]2and its fragments by high field NMR

“…In addition, NOE difference measurements have provided information on the orientation of bases with respect to the suqar residues in both single and duplex strands (31)(32)(33)(34)(35)(36)(37)(38). The non-exchangeable 1H resonances of the hexamer (shown in Fig.…”

Benchmarking AMBER Force Fields for RNA: Comparisons to NMR Spectra for Single-Stranded r(GACC) Are Improved by Revised χ Torsions

“…In particular, the nuclear Overhauser effect (NOE) differs by roughly 20-fold between syn and anti conformations of a base relative to its ribose, the ribose pucker can be determined from 3 J 1′2′ coupling constants, and various NOEs report on base–base stacking. 47−49 For example, single-stranded AACC RNA exhibits base–base stacking, especially for the middle nearest neighbor of A-C.(50) Similarly, single-stranded GAAAC has adenine–adenine stacking both as DNA and RNA. (51) NMR spectra of CAAU, C M A M A M U M , and C L A M A L U M , where M and L stand for 2′O-methyl and locked nucleic acid (LNA) sugars (i.e., ribose with a methylene bridge between the 2′ oxygen and 4′ carbon), respectively, revealed helical preorganization, especially for oligonucleotides with LNA residues.…”

A nuclear magnetic resonance study of the ribotrinucleoside dlphophate UpUpC

“…13C-NMR spectroscopy is particularly useful for the determination of the sugar phosphate backbone conformation via carbon-phosphorus coupling constants (6,7), which can easily be determined from proton decoupled 13C-NMR spectra. To date most 1H-NMR studies on oligoribonucleotides containing complete assignments of base and sugar protons have dealt with dimers (8,10), and only a few trimers (10,12) and two tetramers (13,14) have been investigated. (For a recent review on 1H-NMR studies see ref.…”