Abstract A-form DNA is one of the biologically active double helical structure. The study of A-DNA structure has an extensive application for developing the field of DNA packaging in biotechnology. In aqueous solution, the A-DNA structure will have a free transformation, the A-DNA structure will be translated into B-form structure with the evolution of time, and eventually stabilized in the B-DNA structure. To explore the stability function of the bivalent metal ions on the A-DNA structure, a series of molecular dynamics simulations have been performed on the A-DNA of sequence (CCCGGCCGGG). The results show that bivalent metal ions (Mg2+, Zn2+, Ca2+) generate a great effect on the structural stability of A-DNA in the environment of high concentration. As the interaction between metal ions and electronegative DNA chains, the stability of A-DNA in solution is gradually improved with the increasing solution concentration of ions. In metal salt solution with high concentration, metal ions can be easily distributed in the solvation shells around the phosphate groups and further lead to the formation of shorter and more compact DNA structure. Also, under the condition of the same concentration and valency of the metal ions, the stability of A-DNA structure is different. The calculations indicate that the structure of A-DNA in CaCl2 solution is less stable than in MgCl2 and ZnCl2 solution.
Fund: This work was supported by the National Natural Science Foundation of China (Grant No. 11564015), the Foundation of Educational Committee of Jiangxi Province, China (Grant No. GJJ211112), and the Fund for Distinguished Young Scholars of Jiangxi Science & Technology Normal University (Grant No. 2015QN-BJRC002).
Jingjing Xue(薛晶晶), Xinpeng Li(李新朋), Rongri Tan(谈荣日), and Wenjun Zong(宗文军) Molecular dynamics simulations of A-DNA in bivalent metal ions salt solution 2022 Chin. Phys. B 31 048702
[1] Thanbichler M, Wang S C and Shapiro L 2005 J. Cell. Biochem. 96 506 [2] Patel D J, Pardi A and Itakura K 1982 Science216 581 [3] Nugent C I and Lundblad V 1998 Genes Dev. 12 1073 [4] Watson J D and Crick F H 1953 Nature171 737 [5] Wilkins M H, Stokes A R and Wilson H R 1953 Nature171 738 [6] Lavery R, Moakher M, Maddocks J H, Petkeviciute D and Zakrzewska K 2009 Nucl. Acids. Res. 37 5917 [7] Kilpatrick J E, Pitzer K S and Spitzer R 1947 J. Am. Chem. Soc. 69 2483 [8] Altona C and Sundaralingam M 1972 J. Am. Chem. Soc. 94 8205 [9] Dickerson R E, Drew H R, Conner B N, Wing R M, Fratini A V and Kopka M L 1982 Science216 475 [10] Ghosh A and Bansal M 2003 Acta Crystall. D:Biol. Crystallogr. 59 620 [11] Wu H M, Dattagupta N and Crothers D M 1981 Proc. Natl. Acad Sci. USA78 6808 [12] Daley J 2019 Nature576 S12 [13] Gibson D 2002 Pharmacogen. J. 2 275 [14] Oram M, Sabanayagam C and Black L W 2008 J. Mol. Biol. 381 61 [15] Seeman N C and Sleiman H F 2017 Nat. Rev. Mater. 3 1 [16] Wolk S, Thurmes W N, Ross W S, Hardin C C and Tinoco I Jr 1989 Biochemistry28 2452 [17] Omichinski J G, Clore G, Schaad O, Felsenfeld G, Trainor C, Appella E, Stahl S and Gronenborn A 1993 Science261 438 [18] Zimmerman S B and Pheiffer B H 1979 J. Mol. Biol. 135 1023 [19] Cheatham III T and Kollma P 1996 J. Mol. Biol. 259 434 [20] Waters J T, Lu X J, Galindo-Murillo R, Gumbart J C, Kim H D, Cheatham T E and Harvey S C 2016 J. Phys. Chem. B120 8449 [21] Lai C T and Schatz G C 2018 J. Phys. Chem. B122 7990 [22] Pasi M, Maddocks J H and Lavery R 2015 Nucl. Acids Res. 43 2412 [23] Yoo J and Aksimentiev A 2012 J. Phys. Chem. B116 12946 [24] Alder B J and Wainwright T E 1959 J. Chem. Phys. 31 459 [25] Hays F A, Teegarden A, Jones Z J, Harms M, Raup D, Watson J, Cavaliere E and Ho P S 2005 Proc. Natl. Acad. Sci. USA102 7157 [26] Li W, Nordenskiöld L and Mu Y 2011 J. Phys. Chem. B115 14713 [27] Mukherjee S and Bhattacharyya D 2013 J. Biomol. Struct. Dyn. 31 896 [28] Abraham M J, Murtola T, Schulz R, Páll S, Smith J C, Hess B and Lindahl E 2015 Softwarex1 19 [29] Cornell W D, Cieplak P, Bayly C I, Gould I R, Merz K M, Ferguson D M, Spellmeyer D C, Fox T, Caldwell J W and Kollman P A 1995 J. Am. Chem. Soc. 117 5179 [30] Darden T, York D and Pedersen L 1993 J. Chem. Phys. 98 10089 [31] Berendsen H, Grigera J and Straatsma T 1987 J. Phys. Chem. 91 6269 [32] Liu J H, Zhang X, Bao L, Zhang X H and Tan Z J 2019 Biophys. J. 117 74 [33] Hyndman R J and Koehler A B 2006 Int. J. Forecast. 22 679 [34] Barciszewski J, Jurczak J, Porowski S, Specht T and Erdmann V A 1999 Eur. J. Biochem. 260 293 [35] Bao L, Zhang X, Shi Y Z, Wu Y Y and Tan Z J 2017 Biophys. J. 112 1094 [36] Zgarbova M, Jurecka P, Sponer J and Michal O 2018 J. Chem. Theor. Comput. 14 1319 [37] Drew H R, Wing R M, Takano T, Broka C, Tanaka S, Itakura K and Dickerson R E 1981 Proc. Natl. Acad. Sci. USA78 2179 [38] Heinemann U, Alings C and Bansal M 1992 EMBO J. 11 1931 [39] Richmond T J and Davey C A 2003 Nature423 145 [40] Fu H, Zhang C, Qiang X W, Yang Y J, Dai L, Tan Z J and Zhang X H 2020 Phys. Rev. Lett. 124 058101 [41] Pan F, Roland C and Sagui C 2020 Nucl. Acids Res. 42 13981 [42] Drozdetski A V, Tolokh I S, Pollack Lois, Baker N and Onufriev V 1986 Phys. Rev. Lett. 117 028101 [43] Tolokh I S, Pabit S A, Katz A M, Chen Y, Drozdetski A, Baker N, Pollack L and Onufriev A V 2014 Nucl. Acids Res. 14 2737 [44] Wu Y Y, Zhang Z L, Zhang J S, Zhu X L and Tan Z J 2015 Nucl. Acids Res. 43 6156 [45] Long M P, Alland S, Martin M E and Isborn C M 2011 J. Phys. Chem. B115 14713 [46] Nishimura Y, Torigoe C and Tsuboi M 2020 Phys. Chem. Chem. Phys. 22 5584 [47] Eichhorn G L and Clark P 1965 Proc. Natl. Acad. Sci. USA23 050502 [48] Pasi M, Maddocks J H and Lavery R 2015 Nucl. Acids Res. 43 2421 [49] Feig M and Pettitt B M 1999 Biophys. J. 77 1769 [50] Tan Z J and Chen S J 2006 Biophys. J. 90 1175 [51] Madhumalar A and Bansal M 2003 Biophys. J. 85 1805 [52] Soliva R, Luque F J, Alhambra C and Orozco M 1999 J. Biomol. Struct. Dyn. 17 89 [53] Bujold K E, Lacroix A and Sleiman H F 2018 Chem4 495
Altmetric calculates a score based on the online attention an article receives. Each coloured thread in the circle represents a different type of online attention. The number in the centre is the Altmetric score. Social media and mainstream news media are the main sources that calculate the score. Reference managers such as Mendeley are also tracked but do not contribute to the score. Older articles often score higher because they have had more time to get noticed. To account for this, Altmetric has included the context data for other articles of a similar age.
