biostudies-literatureDrsata TNHGRI NIH HHS707-721https://www.ebi.ac.uk/biostudies/studies/S-EPMC3748671biostudies-literatureUnknown9(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-µs-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 givenJournal of chemical theory and computationStructure, Stiffness and Substates of the Dickerson-Drew Dodecamer.PMC3748671R01 HG004708Sponer JPerez AOrozco MLankas FDrsata TMorozov AVfalseStructure, Stiffness and Substates of the Dickerson-Drew Dodecamer.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-µs-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 given2013-01-01T00:00:00Z20132026-05-30T01:41:54.263Z2026-04-08T06:29:44.927ZS-EPMC37486712397688610.1021/ct300671y