Characterization of the dynamic behavior of r(ACC) and r(AAC) with NMR relaxation data and both metropolis monte carlo and molecular dynamics simulations

• Published in: Biopolymers Vol. 39; no. 4; pp. 549 - 571
• Main Authors: Bouchemal-Chibani, N., du Penhoat, C. Hervé, Abdelkafi, M., Ghomi, M., Turpin, P. Y.
• Format: Journal Article
• Language: English
• Published: Hoboken Wiley Subscription Services, Inc., A Wiley Company 01-10-1996
• ISSN: 0006-3525; 1097-0282
• DOI: 10.1002/(SICI)1097-0282(199610)39:4<549::AID-BIP7>3.0.CO;2-X

The solution‐state behavior of two triribonucleotides, adenylyl(3′‐5′) adenylyl (3′‐5′) cytidine [r(AAC)] and adenylyl (3′‐5′) cytidylyl (3′‐5′) cytidine [r(ACC)], was studied with spectroscopic and molecular modeling methods. Melting temperatures of 299 and 294 K for r(AAC) and r(ACC), respectively, were obtained from ultraviolet absorption (UV) and circular dichroism (CD) temperature profiles of the order‐disorder transition. The behavior of the Raman marker modes is consistent with greater stability of r(AAC) compared to that of r(ACC). Nuclear magnetic resonance (nmr) relaxation data (homonuclear cross‐relaxation rates, proton selective and nonselective longitudinal relaxation times, and carbon longitudinal relaxation times) were measured at 283, 296, and 318 K for both trimers. In parallel, the major types of conformations were explored with Metropolis Monte Carlo (MMC) and molecular dynamics (MD) simulations to obtain representations of both slow and fast events. Fitting of experimental data showed that although the MMC conformations do not represent an exhaustive list of conformers in solution, the canonical helical form (A‐RNA type) should coexist at low temperature with significant populations of other less classical conformers such as half‐stacked (HS), bulged (BU), and reverse‐stacked (RS). Fitting of the experimental relaxation data ensemble at 283 K led to very different representations for the two trimers. r(AAC) was shown to have a fairly compact, rigid structure (angular order parameter, S2ang ∼ 0.9, correlation time for internal motion, τe ∼ 0.1 ns), which undergoes fairly rapid overall tumbling characterized by the correlation time τc ∼ 0.6 ns, whereas r(ACC) exhibits much more flexibility (S2ang ∼ 0.7, τe ∼ 0.1 ns) and slower molecular reorientation (τc ∼ 1.0 ns). The values of S2ang tended to confirm that large amplitude fluctuations did not occur on the relaxation timescale (ns). In the course of this paper, a widely accepted concept was shown to be questionable. As regards the nmr relaxation data, simulations show that for fairly small nucleic acids (τc < 2.0 ns) the second term of the model‐free spectral densities is not negligible for representative motional models (S2ang values < 0.9 and τe values in the 0.05–0.2 ns range). The difference in the dynamic behavior of r(AAC) and r(ACC) can be explained by the greater propensity of the A‐A sequence to stack as compared to that of A‐C. © 1996 John Wiley & Sons, Inc.