Конформационная динамика нуклеиновых кислот при взаимодействии с лигандами (1098269), страница 46
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—Vol. 40, no. 16. — Pp. 8119–8128.324. Hud N. V. [et al.] Binding sites and dynamics of ammonium ions in a telomererepeat DNA quadruplex // Journal of molecular biology. — 1999. — Jan. —Vol. 285, no. 1. — Pp. 233–243.325. Vairamani M., Gross M. L. G-quadruplex formation of thrombin-binding aptamer detected by electrospray ionization mass spectrometry // Journal of theAmerican Chemical Society. — 2003.
— Jan. — Vol. 125, no. 1. — Pp. 42–43.326. Majhi P. R. [et al.] Heat capacity changes associated with guanine quadruplex formation: an isothermal titration calorimetry study // Biopolymers. —2008. — Apr. — Vol. 89, no. 4. — Pp. 302–309.327. Car, Parrinello Unified approach for molecular dynamics and densityfunctional theory // Physical review letters. — 1985. — Nov. — Vol. 55, no.22. — Pp. 2471–2474.328. Eichinger M. [et al.] A hybrid method for solutes in complex solvents: Density functional theory combined with empirical force fields // The Journal ofChemical Physics. — 1999. — Vol.
110, no. 21. — P. 10452.329. Smirnov I., Shafer R. H. Effect of loop sequence and size on DNA aptamerstability // Biochemistry. — 2000. — Feb. — Vol. 39, no. 6. — Pp. 1462–1468.330. Aptamers specific for biomolecules and methods of making.331. Baldrich E., O'Sullivan C. K. Ability of thrombin to act as molecular chaperone, inducing formation of quadruplex structure of thrombin-binding ap-305tamer // Analytical biochemistry. — 2005. — June. — Vol. 341, no.
1. —Pp. 194–197.332. Tsiang M. [et al.] Functional mapping of the surface residues of human thrombin // The Journal of biological chemistry. — 1995. — July. — Vol. 270, no.28. — Pp. 16854–16863.333. Hazel P. [et al.] Loop-length-dependent folding of G-quadruplexes. // J AmChem Soc. — 2004. — Dec. — Vol. 126, no. 50. — Pp.
16405–15.334. Smargiasso N. [et al.] G-quadruplex DNA assemblies: loop length, cationidentity, and multimer formation. // J Am Chem Soc. — 2008. — Aug. —Vol. 130, no. 31. — Pp. 10208–16.335. Gaudin A. [et al.] How long is too long? Effects of loop size on G-quadruplexstability.
// Nucleic Acids Res. — 2010. — Nov. — Vol. 38, no. 21. —Pp. 7858–68.336. Risitano A., Fox K. Influence of loop size on the stability of intramolecularDNA quadruplexes. // Nucleic Acids Res. — 2004None. — Vol. 32, no. 8. —Pp. 2598–606.337. Phillips K. [et al.] The crystal structure of a parallel-stranded guanine tetraplexat 0.95 A resolution. // J Mol Biol.
— 1997. — Oct. — Vol. 273, no. 1. —Pp. 171–82.338. Ida R., Wu G. Direct NMR detection of alkali metal ions bound to Gquadruplex DNA. // J Am Chem Soc. — 2008. — Mar. — Vol. 130, no. 11. —Pp. 3590–602.306339. Hazel P., Parkinson G., Neidle S. Predictive modelling of topology and loopvariations in dimeric DNA quadruplex structures. // Nucleic Acids Res. —2006None. — Vol. 34, no.
7. — Pp. 2117–27.340. Rueda M., Luque F., Orozco M. G-quadruplexes can maintain their structurein the gas phase. // J Am Chem Soc. — 2006. — Mar. — Vol. 128, no. 11. —Pp. 3608–19.341. Li H., Cao E., Gisler T. Force-induced unfolding of human telomeric Gquadruplex: a steered molecular dynamics simulation study.
// Biochem Biophys Res Commun. — 2009. — Jan. — Vol. 379, no. 1. — Pp. 70–5.342. Pagano B. [et al.] Stability and cations coordination of DNA and RNA 14-merG-quadruplexes: a multiscale computational approach. // J Phys Chem B. —2008. — Sept. — Vol. 112, no. 38. — Pp. 12115–23.343. Petraccone L. [et al.] An integrated molecular dynamics (MD) and experimental study of higher order human telomeric quadruplexes. // Biopolymers. —2010.
— June. — Vol. 93, no. 6. — Pp. 533–48.344. Spacková N., Berger I., Sponer J. Structural dynamics and cation interactionsof DNA quadruplex molecules containing mixed guanine/cytosine quartets revealed by large-scale MD simulations. // J Am Chem Soc. — 2001. — Apr. —Vol. 123, no. 14. — Pp. 3295–307.345. Cavallari M. [et al.] Stability and migration of metal ions in G4-wires bymolecular dynamics simulations.
// J Phys Chem B. — 2006. — Dec. — Vol.110, no. 51. — Pp. 26337–48.346. Cavallari M., Garbesi A., Di Felice R. Porphyrin intercalation in G4-DNAquadruplexes by molecular dynamics simulations. // J Phys Chem B. —2009. — Oct. — Vol. 113, no. 40. — Pp. 13152–60.307347. Fadrní E. [et al.] Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields // Journal of Chemical Theoryand Computation. — 2009.
— Vol. 5, no. 9. — Pp. 2514–2530. — eprint:http://pubs.acs.org/doi/pdf/10.1021/ct900200k.348. Mao X., Marky L., Gmeiner W. NMR structure of the thrombin-binding DNAaptamer stabilized by Sr2+. // J Biomol Struct Dyn. — 2004. — Aug. — Vol.22, no. 1. — Pp. 25–33.349. Marathias V., Bolton P.
Determinants of DNA quadruplex structural type: sequence and potassium binding. // Biochemistry. — 1999. — Apr. — Vol. 38,no. 14. — Pp. 4355–64.350. Marathias V., Bolton P. Structures of the potassium-saturated, 2:1, and intermediate, 1:1, forms of a quadruplex DNA. // Nucleic Acids Res. — 2000. —May. — Vol. 28, no. 9. — Pp. 1969–77.351. Trajkovski M., Sket P., Plavec J. Cation localization and movement withinDNA thrombin binding aptamer in solution. // Org Biomol Chem.
— 2009. —Nov. — Vol. 7, no. 22. — Pp. 4677–84.352. Jing N. [et al.] Mechanism of inhibition of HIV-1 integrase by G-tetradforming oligonucleotides in Vitro. // J Biol Chem. — 2000. — July. — Vol.275, no. 28. — Pp. 21460–7.353. Schultze P., Macaya R., Feigon J. Three-dimensional solution structure ofthe thrombin-binding DNA aptamer d(GGTTGGTGTGGTTGG). // J MolBiol.
— 1994. — Feb. — Vol. 235, no. 5. — Pp. 1532–47.354. Cordomí A., Edholm O., Perez J. J. Effect of Force Field Parameters onSodium and Potassium Ion Binding to Dipalmitoyl Phosphatidylcholine Bilayers // Journal of Chemical Theory and Computation. — 2009. — Vol. 5,308no. 8. — Pp. 2125–2134. — eprint: http://pubs.acs.org/doi/pdf/10.1021/ct9000763.355.
Van Der Spoel D. [et al.] GROMACS: fast, flexible, and free. // J ComputChem. — 2005. — Dec. — Vol. 26, no. 16. — Pp. 1701–18.356. Payne M. C. [et al.] Iterative minimization techniques for <i>ab initio</i>total-energy calculations: molecular dynamics and conjugate gradients // Rev.Mod. Phys. — 1992. — Oct. — Vol. 64, issue 4. — Pp. 1045–1097.357. Pant M., Rajagopal A. Theory of inhomogeneous magnetic electron gas //Solid State Communications. — 1972. — Vol. 10, no. 12. — Pp. 1157–1160.358. Perdew J. [et al.] Atoms, molecules, solids, and surfaces: Applications of thegeneralized gradient approximation for exchange and correlation.
// Phys RevB Condens Matter. — 1992. — Sept. — Vol. 46, no. 11. — Pp. 6671–6687.359. Vanderbilt D. Soft self-consistent pseudopotentials in a generalized eigenvalueformalism. // Phys Rev B Condens Matter. — 1990. — Apr. — Vol. 41, no.11. — Pp. 7892–7895.360. Grimme S. Accurate description of van der Waals complexes by density functional theory including empirical corrections.
// J Comput Chem. — 2004. —Sept. — Vol. 25, no. 12. — Pp. 1463–73.361. Biswas P., Gogonea V. A regularized and renormalized electrostatic couplingHamiltonian for hybrid quantum-mechanical-molecular-mechanical calculations. // J Chem Phys. — 2005. — Oct. — Vol. 123, no. 16. — P.
164114.362. Hoover W. Canonical dynamics: Equilibrium phase-space distributions. //Phys Rev A. — 1985. — Mar. — Vol. 31, no. 3. — Pp. 1695–1697.309363. Špačkoví N., Berger I., Šponer J. Nanosecond Molecular Dynamics Simulations of Parallel and Antiparallel Guanine Quadruplex DNA Molecules //Journal of the American Chemical Society. — 1999. — Vol. 121, no. 23. —Pp. 5519–5534. — eprint: http://pubs.acs.org/doi/pdf/10.1021/ja984449s.364. Fadrná E. [et al.] Molecular dynamics simulations of Guanine quadruplexloops: advances and force field limitations. // Biophys J.
— 2004. — July. —Vol. 87, no. 1. — Pp. 227–42.365. Zacharias M. Simulation of the structure and dynamics of nonhelical RNAmotifs. // Curr Opin Struct Biol. — 2000. — June. — Vol. 10, no. 3. —Pp. 311–7.366. Faralli C. [et al.] The solvation dynamics of Na+ and K+ ions in liquidmethanol // Theoretical Chemistry Accounts. — 2007. — Vol. 118, no.
2. —Pp. 417–423.367. Hancock R. D. [et al.] The structure of the 11-coordinate bariumcomplex of the pendant-donor macrocycle 1,4,7,10-tetrakis(carbamoylmethyl)-1,4,7,10-tetraazacyclododecane: an analysis of the coordination numbers of barium(II) in its complexes // Inorganica Chimica Acta. — 2004. —Vol. 357, no. 3. — Pp. 723–727.368. Reshetnikov R. [et al.] Structural Dynamics of Thrombin-Binding DNA Aptamer d(GGTTGGTGTGGTTGG) Quadruplex DNA Studied by Large-ScaleExplicit Solvent Simulations // Journal of Chemical Theory and Computation.
— 2010. — Vol. 6, no. 10. — Pp. 3003–3014. — eprint: http://pubs.acs.org/doi/pdf/10.1021/ct100253m.310369. Hong E. [et al.] Mass spectrometric studies of alkali metal ion binding onthrombin-binding aptamer DNA. // J Am Soc Mass Spectrom. — 2010. —July. — Vol. 21, no. 7. — Pp. 1245–55.370. Shim J., Tan Q., Gu L. Single-molecule detection of folding and unfolding ofthe G-quadruplex aptamer in a nanopore nanocavity. // Nucleic Acids Res.
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