An AT-barrier mechanically controls DNA reannealing under tension

• Published in: Nucleic acids research 2016-09, Vol.44 (16), p.7954-7962
• Main Authors: Bongini, L, Pongor, C, Falorsi, G, Pertici, I, Kellermayer, M, Lombardi, V, Bianco, P
• Format: Article
• Language: English
• Subjects: AT Rich Sequence - genetics; Bacteriophage lambda; Base Sequence; Biomechanical Phenomena; DNA, Viral - metabolism; Kinetics; Nucleic Acid Denaturation; Osmolar Concentration; Structural Biology
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkw604

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.