Stereodynamics of ribodinucleoside monophosphates in aqueous solution

Abstract

Arguments are presented which show that conformations II and III proposed by Lee and Tinoco [Lee, C.H., and Tinoco, I., Jr. (1977), Biochemistry 16, 5403] for ribodinucleoside monophosphates in aqueous solution are untenable. It has been shown that ribodinucleoside monophosphates exist in aqueous solution as an equilibrium blend of the classically recognized right-handed stack (g-g-), loop stack (g+g+), skewed (g+t), and extended arrays. In order to determine the effect of epsilonA base on the conformer distribution in the equilibrium blend, detailed ring-current calculations were performed and the isoshielding curves for epsilonA were derived. Use of these curves vis-a-vis dimerization shift data indicates that introduction of epsilonA perturbs the equilibrium blend which causes an increase in the population of skewed (g+t) arrays.

Conformational flexibility of the 3' acceptor end of transfer ribonucleic acid

“…The difficulty in arriving at quantitative information about the sugar-base torsion angle (x) by NMR measurements has been discussed in extenso elsewhere (Lee et al, 1976;Ezra et al, 1977;Dhingra et al, 1978). As in the earlier work, the preponderance of shift evidence favors a sugar-base torsion in the anti domain.…”

“…A normally preferred stacked arrangement for nucleic acids is the one in which the phosphodiester bonds exist in g-,g- (w N 290' and w' = 290') domains. We have discussed elsewhere (Lee et al, 1976;Ezra et al, 1977;Dhingra et al, 1978) that a g-,garrangement will result in the deshielding of the interior H5' by the 2'-OH of the nucleotide unit at the 5' end. The data show that in the ApCp-segment of ApCpC, the interior H5' is deshielded by 0.296 ppm, clearly suggesting the dominant stacked array for the ApCp-segment to be g-,g-.…”

“…As in the earlier work, the preponderance of shift evidence favors a sugar-base torsion in the anti domain. It has been shown (Lee et al, 1976;Ezra et al, 1977;Dhingra et al, 1978;Evans & Sarma, 1976; that the 2E -3E shift is associated with a reduction in the magnitude of x in the anit domain.…”

“…These studies revealed the presence of a coupled set of base sequence dependent conformational parameters and interdependent structural changes linked to base stacking interactions (Lee et al, 1976;Ezra et al, 1977;Dhingra et al, 1978;Evans & Sarma, 1976;Cheng & Sarma, 1977). A natural extension is the investigation of the spatial configuration and conformational properties of higher oligomers.…”

Ab-initio Quantum Mechanical Calculations of NMR Chemical Shifts in Nucleic Acids Constituents III Chemical Shift Variations due to Base Stacking

“…The chemical shifts measured for the base protons in dinucleoside or trinucleoside phosphates (1-3), short duplexes (5)(6)(7)(8) or nucleic acids (9)(10)(11) can be accounted for, quite satisfactorily in many cases, by adding to the value of their chemical shift in the mononucleotide (or in a base pair for the imino protons) the ring current effect and the local magnetic anisotropy contribution of the other residues of the polymer (5,10,(12)(13)(14)(15)(16)(17) while the carbon 13 spectra which have been reported for some of these molecules (18)(19)(20)(21)(22) show that the chemical shifts of the carbon nuclei of a given base undergo with polymerization or duplex formation, variations which are very different from those observed for the protons of the same molecule, they can even be in opposite directions.…”