Excitation Energies of Stacked DNA Base Pair
نویسندگان
چکیده
منابع مشابه
Single-molecule derivation of salt dependent base-pair free energies in DNA.
Accurate knowledge of the thermodynamic properties of nucleic acids is crucial to predicting their structure and stability. To date most measurements of base-pair free energies in DNA are obtained in thermal denaturation experiments, which depend on several assumptions. Here we report measurements of the DNA base-pair free energies based on a simplified system, the mechanical unzipping of singl...
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Strand separation is a fundamental molecular process essential for the reading of the genetic information during DNA replication, transcription and recombination. However, DNA melting in physiological conditions in which the double helix is expected to be stable represents a challenging problem. Current models propose that negative supercoiling destabilizes the double helix and promotes the spo...
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DNA size markers are widely used to estimate the size of DNA samples on agarose or polyacrylamide gelelectrophoresis (PAGE). DNA markers can be prepared by mixing PCR products with definite sizes.Alternatively, they are prepared by restriction enzyme digestion of the genomic DNA of bacteriophages ornatural and synthetic DNA plasmids. The present study describes engineering of ...
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A complete set of harmonic force constants describing the DNA deformation energetics at the base pair level was obtained using unrestrained atomic-resolution molecular dynamics simulations of selected duplex oligonucleotides and subsequent analysis of structural fluctuations from the simulated trajectories. The deformation was described by the six base pair conformational parameters (buckle, pr...
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Brutlag, D., Atkinson, M. R., Setlow, P. & Kornberg, A. (1969) Biochem. Biophys. Res. Commun. 37, 982-989 Joyce, C. M. & Grindley, N. D. F. (1983) Proc. Natl. Acad. Sci. U .S .A . 80, 183G1834 Joyce, C. M., Ollis, D. L., Ruch, J., Steitz, T. A,, Knigsber, W. H. & Grindley, N. D. F. (19850) in Protein Structure. Function and Design (Oxender, D. ed.), UCLA Symposia in Molecular and Cellular Biolo...
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ژورنال
عنوان ژورنال: Journal of Computer Aided Chemistry
سال: 2010
ISSN: 1345-8647
DOI: 10.2751/jcac.11.25