Conformational features of benzo-homologated yDNA duplexes by molecular dynamics simulation

摘要: yDNA is a base-modified nucleic acid duplex containing size-expanded nucleobases. Base-modified acids could expand the genetic alphabet and thereby enhance functional potential of DNA. Unrestrained 100 ns MD simulations were performed in explicit solvent on NMR sequence [5'(yA T yA T)2 ] two modeled duplexes, [5'(yC yC G G)2 [(yT5' yT A yG C T3')•(yA5' A3')]. The force field parameters for bases derived consistent with well-established AMBER field. Our results show that DNA backbone can withstand stretched size retaining Watson-Crick base pairing duplexes. duplexes retained their double helical structure throughout accommodating strain due to expanded torsion angles, sugar pucker parameters. effect benzo-expansion clearly reflected extended C1'-C1' distances enlarged groove widths. modification leads reduction pair twist resulting larger overlapping area between stacked bases, enhancing inter intra strand stacking interactions comparison BDNA. This geometry favour enhanced binders binding proteins., 2016. © 2015 Wiley Periodicals, Inc. Biopolymers 105: 55-64,