The solution structure of the circular trinucleotide cr(GpGpGp) determined by NMR and molecular mechanics calculation

Abstract

The 3'-5' circular trinucleotide cr(GpGpGp) was studied by means of 1D and 2D high resolution NMR techniques and molecular mechanics calculations. Analysis of the J-couplings, obtained from the 1H and 13C-NMR spectra, allowed the determination of the conformation of the sugar rings and of the 'circular' phosphate backbone. In the course of the investigations it was found that the Karplus-equation most recently parametrized for the CCOP J-coupling constants could not account for the measured J(C4'P) of 11.1 Hz and a new parametrization for both HCOP and CCOP coupling constants is therefore presented. Subsequent analysis of the coupling constants yielded 'fixed' values for the torsion angles beta and delta (with beta = 178 degrees and delta = 139 degrees). The value of the latter angle corresponds to an S-type sugar conformation. The torsion angles gamma and epsilon are involved in a rapid equilibrium in which they are converted between the gauche(+) and trans and between the trans and gauche(-) domain respectively. We show that the occurrence of epsilon in the gauche(-) domain necessitates S-type sugar conformations. Given the aforementioned values for beta, gamma, delta and epsilon the ring closure constraints for the ring, formed by the phosphate backbone can only be fulfilled if alpha and zeta adopt some special values. After energy minimization with the CHARMm force field only two combinations of alpha and zeta result in energetically favourable structures, i.e. the combination alpha (t)/zeta(g-) in case gamma is in a gauche(+) and epsilon is in a trans conformation, and the combination alpha (t)/zeta (g+) for the combination gamma (t)/epsilon (g-). The results are discussed in relation to earlier findings obtained for cd(ApAp) and cr(GpGp), the latter molecule being a regulator of the synthesis of cellulose in Acetobacter xylinum.

Exploratory Studies to Investigate a Linked Prebiotic Origin of RNA and Coded Peptides

“…Ignoring, for the moment, their provenance, we considered the possibility of the (coded) conversion of the cyclic trinucleotides 32 into 25 and 26 (Scheme 8). The preferred conformational isomers of the cyclic trinucleotide 32 (B 1 B 2 B 3 G, sodium salt) in aqueous solution have been determined by 1 H-NMR analysis and molecular mechanics calculation [47]. In the lowest energy conformer, the nucleobases are in an axial position with respect to the 18-membered ring, and we reasoned that similar conformers of 32 (in general) or the activated derivative 33 might bind a-amino acids (in the presence of Mg 2 ).…”

“…We have recently shown that a cytidine ribonucleotide can be produced by sequential assembly of the base on a sugar phosphate template (Scheme 10) [56]. Specifically, arabinose-3-phosphate (46) was converted under potentially prebiotic conditions to cytidine-2',3'-cyclic phosphate (47). The sequence involved reaction of 46 with cyanamide giving the amino-oxazoline 48, [9].…”

The detailed structure of tandem G·A mismatched base-pair motifs in RNA duplexes is context dependent

“…Estimates of 3 J HP coupling constants derived from the 1 H-31 P HETCOR experiment were converted to torsion angle constraints using a recently reparametrized Karplus equation (Mooren et al, 1994) to constrain the b and e torsion angles.…”

Conformational evaluation of labeled C3′‐O‐P‐13CH2‐O‐C4″ phosphonate internucleotide linkage, a phosphodiester isostere

“…Vicinal couplings (given with 32,33 gives the best agreement between these three observed and calculated J-values for angle e about 21258 in both 6a and 6b. This value falls into the range between 2608 and 21808 allowed for angle e for steric reasons.…”