title: Sequence and temperature dependence of the end-to-end collision dynamics of single-stranded DNA.
abstract: Intramolecular collision dynamics play an essential role in biomolecular folding and function and, increasingly, in the performance of biomimetic technologies. To date, however, the quantitative studies of dynamics of single-stranded nucleic acids have been limited. Thus motivated, here we investigate the sequence composition, chain-length, viscosity, and temperature dependencies of the end-to-end collision dynamics of single-stranded DNAs. We find that both the absolute collision rate and the temperature dependencies of these dynamics are base-composition dependent, suggesting that base stacking interactions are a significant contributor. For example, whereas the end-to-end collision dynamics of poly-thymine exhibit simple, linear Arrhenius behavior, the behavior of longer poly-adenine constructs is more complicated. Specifically, 20- and 25-adenine constructs exhibit biphasic temperature dependencies, with their temperature dependences becoming effectively indistinguishable from that of poly-thymine above 335 K for 20-adenines and 328 K for 25-adenines. The differing Arrhenius behaviors of poly-thymine and poly-adenine and the chain-length dependence of the temperature at which poly-adenine crosses over to behave like poly-thymine can be explained by a barrier friction mechanism in which, at low temperatures, the energy barrier for the local rearrangement of poly-adenine becomes the dominant contributor to its end-to-end collision dynamics.
authors.affiliation: Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan.
authors.forename: Takanori
authors.initials: T
authors.lastname: Uzawa
authors.forename: Takashi
authors.initials: T
authors.lastname: Isoshima
authors.forename: Yoshihiro
authors.initials: Y
authors.lastname: Ito
authors.forename: Koichiro
authors.initials: K
authors.lastname: Ishimori
authors.forename: Dmitrii E
authors.initials: DE
authors.lastname: Makarov
authors.forename: Kevin W
authors.initials: KW
authors.lastname: Plaxco
mesh_terms: D001483:Base Sequence; D004277:DNA, Single-Stranded / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D017276:Friction; D017711:Nonlinear Dynamics; D015203:Reproducibility of Results; D013696:Temperature; D013816:Thermodynamics
chemical_list: D004277:DNA, Single-Stranded