"http://pubs.acs.org/toc/jctcce/9/1" . . "The Dickerson-Drew dodecamer (DD) d[CGCGAATTCGCG](2) is a prototypic B-DNA molecule whose sequence-specific structure and dynamics have been investigated by many experimental and computational studies. Here, we present an analysis of DD properties based on extensive atomistic molecular dynamics (MD) simulations using different ionic conditions and water models. The 0.6-2.4-mu s-long MD trajectories are compared to modern crystallographic and NMR data. In the simulations, the duplex ends can adopt an alternative base-pairing, which influences the oligomer structure. A clear relationship between the BI/BII backbone substates and the basepair step conformation has been identified, extending previous findings and exposing an interesting structural polymorphism in the helix. For a given end pairing, distributions of the basepair step coordinates can be decomposed into Gaussian-like components associated with the BI/BII backbone states." . . . . "1"^^ . . . "10.1021/ct300671y" . "000313378700071" . . . . "Lanka\u0161, Filip" . . . . . "Dr\u0161ata, Tom\u00E1\u0161" . "I, P(ED1.1.00/02.0068), P(GAP208/11/1822)" . "1" . "RIV/00216224:14740/13:00067939" . . . . "Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer"@en . "\u0160poner, Ji\u0159\u00ED" . . "Orozco, Modesto" . "RIV/00216224:14740/13:00067939!RIV14-MSM-14740___" . "15"^^ . "108423" . . "Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer" . "MOLECULAR-DYNAMICS SIMULATIONS; UNIQUE TETRANUCLEOTIDE SEQUENCES; NUCLEIC-ACID STRUCTURES; B-DNA DODECAMER; BASE-PAIR LEVEL; X-RAY; COUPLING-CONSTANTS; MONOVALENT CATIONS; CRYSTAL-STRUCTURES; ATOMIC-RESOLUTION"@en . "Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer"@en . . . . "[42FC9C8D3299]" . . "Perez, Alberto" . "Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer" . . "1549-9618" . "Journal of Chemical Theory and Computation" . "6"^^ . . "Morozov, Alexandre V" . "14740" . "US - Spojen\u00E9 st\u00E1ty americk\u00E9" . "The Dickerson-Drew dodecamer (DD) d[CGCGAATTCGCG](2) is a prototypic B-DNA molecule whose sequence-specific structure and dynamics have been investigated by many experimental and computational studies. Here, we present an analysis of DD properties based on extensive atomistic molecular dynamics (MD) simulations using different ionic conditions and water models. The 0.6-2.4-mu s-long MD trajectories are compared to modern crystallographic and NMR data. In the simulations, the duplex ends can adopt an alternative base-pairing, which influences the oligomer structure. A clear relationship between the BI/BII backbone substates and the basepair step conformation has been identified, extending previous findings and exposing an interesting structural polymorphism in the helix. For a given end pairing, distributions of the basepair step coordinates can be decomposed into Gaussian-like components associated with the BI/BII backbone states."@en . . "9" .