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

Abstract

The intimate details of the conformational features and dynamics of the trinucleoside diphosphates CpCpA and ApCpC in aqueous solution have been arrived at by the complete analysis of their proton magnetic resonance spectra. In addition to the right-handed stacked species in which the phosphodiester torsions conform to the gauche-gauche domains, sugar puckers 3E, C4'-C5 approximately equal to 60 degrees, C5'-O5' approximately 180 degrees, C3'-O3' approximately equal to 205 degrees, and chi CN approximately equal to 40 degrees, the trimers display a variety of spatial configurations, an important one being a bulged configuration in which the central nucleotide unit is bulged out, enabling stacking interactions between the end units. It is further shown that the 3' acceptor end of tRNA, CpCpA, displays considerable flexibility for the terminal adenine nucleotide unit. Theoretical NMR calculations demonstrate that the predominant solution conformation does not conform to the CCA terminus of tRNA as reported by four independent crystallographic studies of tRNAPhe. It is shown that the preferred intramolecular order of CCA in solution is such that chi 1 = chi 2 = chi 3 = 40 degrees, all the three sugars are in 3E, psi 1 = psi 2 = psi 3 = 60 degrees, phi 2 and phi 3 = 170 and 180 degrees, respectively, phi 1 = phi 2' = 205 degrees, and omega 1/omega 1 and omega 2/omega 2' = 240/205 degrees and 295/265 degrees, respectively.

Conformational analysis of a modified ribotetranucleoside triphosphate: m62A-U-m62A-U studied in aqueous solution by nuclear magnetic resonance at 500 MHz1

“…We conclude that the existence of special conformers in the A(M)U(2)A(3) fragment is not reflected in higher conformational purityaround any C4' -C5' bond. Conformation around C5' -05' (8) .~~~~~~~~~~~~~~~T he fractional population Pt of the preferred trans rotamer St around the C5' -05' bond is calculated23 from the formula Pt = (25-E')/20.8, where E= JS'P + J5"P. The highest conformational purity is found between A (3) and U(4) due to the good stacking properties of fragment A(3)U(4). In contrast, the conformational freedom of B(2) and B(3) is similar to that in the monomers mA and iprU (75S5% 8t).…”

Thermodynamic and Structural Properties of r(ACC) as Revealed by Ultraviolet Electronic Absorption, Circular Dichroism,1H-NMR Spectroscopy and Monte Carlo Simulations

“…::\~, . ::\Hx and T m( equations [1] and [2] ), were obtained from the plot of the UV absorbance as a function of the temperature. Four states in equilibrium were considered: the free unstacked state (FU) with chemical shift &FU, the free stacked state (X) with population P x(T) and chemical shift variation 1\x, the associated unstacked state (AU) with population P A(l-Px) and chemical shift variation .…”

“…In the case of the vicinal coupling constant data, the experimental values reported by Cheng eta/. (2) at 353K for a 10 mM sample were used as theoretical values for the unstacked population. The Oro values were used to represent the unstacked population for the chemical shift data.…”

“…Cheng et al (2) proposed a variety of spatial configurations based on NMR data including the aforementioned one in which the central nucleotide unit is bulged out enabling stacking between the end units. This contention was supported by Lee and Tinoco (3) who studied thirteen trinucleotide diphosphates by NMR spectroscopy and found evidence from next nearest-neighbour effects for bulged structures.…”

“…As regards experimental chemical shift data, it has been shown (16) that the effect of self-association is not negligeable even in the case of dilute ( < 5mM) samples. Such effects were not considered in much of the earlier work (2)(3)(4)(5)(6). Ring-current induced chemical shift variations can be established for theoretical structures using the results of pioneering studies based on ab initio calculations (17).…”