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Are isolated nucleic acid bases really planar? A Car-Parrinello molecular dynamics study


, : Are isolated nucleic acid bases really planar? A Car-Parrinello molecular dynamics study. Journal of Physical Chemistry. B 111(13): 3476-3480

Car-Parrinello molecular dynamics simulations of the flexibility of isolated DNA bases have been carried out. The comparison of lowest ring out-of-plane vibrations calculated by using MP2/cc-pvdz and BLYP/PW methods reveals that the DFT method with the plane wave basis set reasonably reproduces out-of-plane deformability of the pyrimidine ring in nucleic acid bases and could be used for reliable modeling of conformational flexibility of nucleobases. The conformational phase space of pyrimidine rings in thymine, cytosine, guanine, and adenine has been investigated by using the ab initio Car-Parrinello molecular dynamics method. It is demonstrated that all nucleic acid bases are highly flexible molecules and possess a nonplanar effective conformation of the pyrimidine ring despite the fact that the planar geometry corresponds to a minimum on the potential energy surface. The population of the planar geometry of the pyrimidine ring does not exceed 30%. Among the nonplanar conformations of the pyrimidine rings, the boat-like and half-chair conformations are the most populated.

US$19.90

PMID: 17388492

DOI: 10.1021/jp070857j


Other references

Davila, M.; Kaeppler, S., 2000: Molecular analysis of mutations induced by tissue culture in maize. The objective of this work was to uncover the molecular basis for the differential expression of cob colour in culture-derived lines in maize. Plants previously identified as P-locus mutants were selfed in the field and the seeds obtained from the...

Damager, I.; Buchini, S.; Amaya, M.F.; Buschiazzo, A.; Alzari, P.; Frasch, A.C.; Watts, A.; Withers, S.G., 2008: Kinetic and mechanistic analysis of Trypanosoma cruzi trans-sialidase reveals a classical ping-pong mechanism with acid/base catalysis. The trans-sialidase from Trypanosoma cruzi catalyzes the transfer of a sialic acid moiety from sialylated donor substrates to the terminal galactose moiety of lactose and lactoside acceptors to yield alpha-(2,3)-sialyllactose or its derivatives w...

Moore, M.D., 2016: Harnessing the Power of Difference: Colonialism and British Chronic Disease Research, 1940-1975. Recent studies of post-war chronic disease epidemiology have generally focused on the histories of research in the USA and UK. Using the archival records of a major British funding body, the Colonial Medical Research Committee and its successor th...

Kopple, J.D., 2007: Phenylalanine and tyrosine metabolism in chronic kidney failure. In chronic kidney failure, there is impairment in the conversion of phenylalanine to tyrosine. As a result, tyrosine and the tyrosine/phenylalanine ratio are reduced in plasma and many tissues, and phenylalanine concentrations tend to be normal or...

Rothschild, G.H.L.; Vickers, R.A.; Jones, E.L., 1982: Control of oriental fruit moth (Cydia molesta (Busck)) by mating disruption in S.E. Australia. Studies in south-eastern Australia in 1971-75 showed that mating disruption of the fruit pest Cydia molesta (Busck) with synthetic female sex pheromone could reduce fruit and shoot infestation to levels similar to those achieved with a standard pe...

Gregorio, A.; Castellano, F., 1989: Aspecific rhinoreactivity in the diagnosis of vasomotor rhinopathy: rhinomanometric study. The authors examined 70 patients divided into three groups: 15 normal, 20 affected by allergic rhinitis in a non critical period, 35 with vasomotor rhinitis. The aim was to evaluate the reactions induced through cold water stimulation (5 degrees C...

Quick James E.; Sinigoi Silvano; Mayer Adriano; Zari Sylvia, 1994: Is a continental crust-mantle transition exposed in the Ivrea-Verbano Zone?. Eos, Transactions, American Geophysical Union 75(44, Suppl

Ullberg, T.; Glader, E-Lotta.; Zia, E.; Petersson, J.; Eriksson, M.; Norrving, B., 2017: Associations between Ischemic Stroke Follow-Up, Socioeconomic Status, and Adherence to Secondary Preventive Drugs in Southern Sweden: Observations from the Swedish Stroke Register (Riksstroke). Currently, the knowledge that one has on adequate stroke follow-up practices is limited. We report associations between 90-day stroke follow-up, socio-economy and adherence to secondary prevention in southern Sweden. Data on 5,602 patients with is...

Thiel, RP., 1980: Unusual vehicle caused mortality in red crossbills. Passenger Pigeon, 421: 23-24

Chen, F.; Demers, L.M.; Vallyathan, V.; Lu, Y.; Castranova, V.; Shi, X., 1999: Involvement of 5'-flanking kappaB-like sites within bcl-x gene in silica-induced Bcl-x expression. The present study investigated the involvement of the transcription factor NF-kappaB in the expression of an anti-apoptotic gene, bcl-x, using a murine macrophage cell line and peritoneal macrophages from both wild type (p50(+/+)) and NF-kappaB p5...