title: An AT-barrier mechanically controls DNA reannealing under tension.
abstract: Regulation of genomic activity occurs through the manipulation of DNA by competent mechanoenzymes. Force-clamp optical tweezers that allow the structural dynamics of the DNA molecule to be measured were used here to investigate the kinetics of mechanically-driven strand reannealing. When the force on the torsionally unconstrained λ-phage DNA is decreased stepwise from above to below the overstretching transition, reannealing occurs via discrete shortening steps separated by exponentially distributed time intervals. Kinetic analysis reveals a transition barrier 0.58 nm along the reaction coordinate and an average reannealing-step size of ∼750 bp, consistent with the average bp interval separating segments of more than 10 consecutive AT bases. In an AT-rich DNA construct, in which the distance between segments of more than 10 consecutive AT is reduced to ∼210 bps, the reannealing step reduces accordingly without changes in the position of the transition barrier. Thus, the transition barrier for reannealing is determined by the presence of segments of more than 10 consecutive AT bps independent of changes in sequence composition, while the length of the reannealing strand changes according to the distance between poly-AT segments at least 10 bps long.
authors.affiliation: PhysioLab, Department of Biology, University of Florence, Via G. Sansone 1, I-50019 Sesto Fiorentino, Italy.
authors.forename: L
authors.initials: L
authors.lastname: Bongini
authors.affiliation: Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó u. 37-47 Budapest IX, H-1094 Hungary.
authors.forename: C
authors.initials: C
authors.lastname: Pongor
authors.affiliation: PhysioLab, Department of Biology, University of Florence, Via G. Sansone 1, I-50019 Sesto Fiorentino, Italy.
authors.forename: G
authors.initials: G
authors.lastname: Falorsi
authors.affiliation: PhysioLab, Department of Biology, University of Florence, Via G. Sansone 1, I-50019 Sesto Fiorentino, Italy.
authors.forename: I
authors.initials: I
authors.lastname: Pertici
authors.affiliation: Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó u. 37-47 Budapest IX, H-1094 Hungary.
authors.forename: M
authors.identifier: 0000-0002-5553-6553
authors.initials: M
authors.lastname: Kellermayer
authors.affiliation: PhysioLab, Department of Biology, University of Florence, Via G. Sansone 1, I-50019 Sesto Fiorentino, Italy vincenzo.lombardi@unifi.it.
authors.forename: V
authors.initials: V
authors.lastname: Lombardi
authors.affiliation: PhysioLab, Department of Biology, University of Florence, Via G. Sansone 1, I-50019 Sesto Fiorentino, Italy.
authors.forename: P
authors.initials: P
authors.lastname: Bianco
mesh_terms: D020856:AT Rich Sequence / Q000235:genetics*; D010582:Bacteriophage lambda; D001483:Base Sequence; D001696:Biomechanical Phenomena; D004279:DNA, Viral / Q000378:metabolism*; D007700:Kinetics; D009691:Nucleic Acid Denaturation; D009994:Osmolar Concentration
chemical_list: D004279:DNA, Viral