Overstretching B-DNA: The Elastic Response of Individual Double-Stranded and Single-Stranded DNA Molecules

Abstract

Single molecules of double-stranded DNA (dsDNA) were stretched with force-measuring laser tweezers. Under a longitudinal stress of approximately 65 piconewtons (pN), dsDNA molecules in aqueous buffer undergo a highly cooperative transition into a stable form with 5.8 angstroms rise per base pair, that is, 70% longer than B form dsDNA. When the stress was relaxed below 65 pN, the molecules rapidly and reversibly contracted to their normal contour lengths. This transition was affected by changes in the ionic strength of the medium and the water activity or by cross-linking of the two strands of dsDNA. Individual molecules of single-stranded DNA were also stretched giving a persistence length of 7.5 angstroms and a stretch modulus of 800 pN. The overstretched form may play a significant role in the energetics of DNA recombination.

Single DNA molecule stretching measures the activity of chemicals that target the HIV-1 nucleocapsid protein

“…The stretching curve for ssDNA in the presence of 10 nM HIV-1 NCp7 (open circles) measured previously in 25 mM Na + (31), indicates major changes in the elasticity of ssDNA upon protein binding. The theoretical force-extension curves given by the worm-like chain (WLC) model for dsDNA (left solid line) and freely jointed chain (FJC) model for ssDNA (right solid line) in the absence of protein (40) are also shown, for comparison.…”

“…ΔF is the difference in the forces at which the tangent to the experimental stretching curve of λ-DNA with NC intersects the tangents to the experimental stretching curves for dsDNA and ssDNA with NC bound on it. The left and right solid lines are the theoretical stretching curves for naked dsDNA and naked ssDNA given by the WLC and FJC models, respectively (40). Data are taken in 50 mM Na + (45 mM NaCl and 5 mM NaOH), 10 mM HEPES, pH 7.5, and room temperature.…”

Stretching single DNA molecules to demonstrate high‐force capabilities of holographic optical tweezers

“…Before every experiment, both the chamber and the beads were washed with 10 mg/ml bovine serum albumin (BSA) to prevent non-specific interactions between the beads and glass surfaces. Experiments were conducted in a buffer solution (150 mM NaCl, 10 mM Tris and 1 mM EDTA, pH 8.0) in which the overstretch transition of dsDNA is expected to occur at 65 pN [25].…”

Honey, I shrunk the DNA: DNA length as a probe for nucleic‐acid enzyme activity

“…Single-stranded DNA, on the other hand, is not constrained by a helical geometry and can be stretched to lengths $70% larger than the doublestranded form. 53 A crossover point at 6 pN defines the forces below which single-stranded DNA is shorter than the duplex form and above which it can be considerably longer. As will be discussed in greater detail in this review, these welldefined differences in length can be utilized to characterize the activity of enzymes that convert one form of DNA into the other.…”

“…53,54 The exact nature of this transition is not well understood. Measurements of the transition free energy associated with overstretching under a variety of biochemical conditions are consistent with DNA denaturation and unwinding, possibly indicating a melting transition of double-stranded to singlestranded DNA.…”