Remington, Jacob M.; McCullagh, Martin; Kohler, Bern published the artcile< Molecular Dynamics Simulations of 2-Aminopurine-Labeled Dinucleoside Monophosphates Reveal Multiscale Stacking Kinetics>, Quality Control of 452-06-2, the main research area is mol dynamics simulation aminopurine dinucleoside monophosphate stacking kinetics.
Mol. dynamics (MD) simulations of 2-aminopurine (2Ap)-labeled DNA dinucleoside monophosphates (DNMPs) were performed to investigate the hypothesis that base stacking dynamics occur on timescales sufficiently rapid to influence the emission signals measured in time-resolved fluorescence experiments Anal. of multiple microsecond-length trajectories shows that the DNMPs sample all four coplanar stacking motifs. In addition, three metastable unstacked conformations are detected. A hidden Markov-state model (HMSM) was applied to the simulations to estimate transition rates between the stacked and unstacked states. Transitions between different stacked states generally occur at higher rates when the number of nucleobase faces requiring desolvation is minimized. Time constants for structural relaxation range between 1.6 and 25 ns, suggesting that emission from photoexcited 2Ap, which has an excited-state lifetime of 10 ns, is sensitive to base stacking kinetics. A master equation model for the excited-state population of 2Ap predicts multiexponential emission decays that reproduce the sub-10 ns emission decay lifetimes and amplitudes seen in experiments Combining MD simulations with HMSM anal. is a powerful way to understand the dynamics that influence 2Ap excited-state relaxation and represents an important step toward using observed emission signals to validate MD simulations.
Journal of Physical Chemistry B published new progress about Conformation. 452-06-2 belongs to class imidazoles-derivatives, and the molecular formula is C5H5N5, Quality Control of 452-06-2.
Referemce:
Imidazole – Wikipedia,
Imidazole | C3H4N2 – PubChem