Albany 2013: Book of Abstracts

category image Albany 2013
Conversation 18
June 11-15 2013
©Adenine Press (2012)

Kinetics of DNA overstretching: Melting vs B-to-S transition

Single B-form DNA molecules undergo an overstretching transition at force Fov to a ~1.7-fold longer form when stretched. The nature of overstretched DNA has been debated for over 10 years. Either peeled (PL DNA), internally melted (M DNA), or unwound double-helical (S DNA) forms of overstretched DNA have been suggested. Here we characterize the kinetics of the overstretching transition in polymeric torsionally unconstrained double stranded (ds) DNA molecules. We pull ~50 Kbp λ−DNA molecules using optical tweezers with rates ν ~10 nm/s to 5.104 nm/s, (over-stretching time between 0.2 and 103 s). The Fov (ν, [Na+]) dependence measured over a broad range of rates and solution ionic strength suggests the existence of all three forms of the overstretched DNA. Thus, at [Na+]>50mM and the stretching time >>1s, internal melting dominates overstretching. This B-to-M transition is highly cooperative (involves ~100 bp), and slow (on/off time ~1000s). Faster overstretching during ≤1 s leads to B-to-S DNA transition, which is less cooperative (involves ~10 bp) and faster (on/off time ~1s). In contrast, in lower salt ([Na+]<50mM) the overstretching during >1s leads to DNA peeling. However, on the faster time scale of 0.2-1 s, even in low salt, the DNA overstretches into S DNA, as peeling becomes kinetically prohibited. Our conclusions are supported by several independent lines of evidence, including the salt and rate dependence of both the slope of the overstretched DNA force-extension curve and the value of the second transition force (from M or PL DNA into S DNA).

Micah J. McCauley 1
Ioulia Rouzina2
Mark C.Williams1

1Northeastern University
Dept. of Physics
110 Forsyth St
Boston, MA, 02115
2University of Minnesota
Dept. of Biochemistry
Molecular Biology
and Biophysics
321 Church Str.
Minneapolis, MN, 55455

Ph: 651-354-6006 (IR)