TY - JOUR
T1 - The influence of salt on the structure and energetics of supercoiled DNA
AU - Schlick, T.
AU - Li, B.
AU - Olson, W. K.
N1 - Funding Information:
We thank Nathan Hunt, John Hearst, Gerald Manning, Irwin Tobias, Alex Vologodskii, and James Wang for valuable discussions and for sharing the results of recent work, Attilio De Falco and Andrew Olson for assistance with computer graphics, and one reviewer for pointing us to important experiments. Our research was generously supported by the National Science Foundation (CHE-9002146, PYI Award ASC-9157582, and Grand Challenge Award ASC-9318159, the latter co-funded by ARPA), the U.S. Public Health Ser- vice (GM-34809), National Institutes of Health (CI-0474), the Searle Schol- ars Program/The Chicago Community Trust, the Whitaker and Sloan Foun- dations, and the Howard Hughes Medical Institute.
PY - 1994
Y1 - 1994
N2 - We present a detailed computational study of the influence of salt on the configurations, energies, and dynamics of supercoiled DNA. A potential function that includes both elastic and electrostatic energy components is employed. Specifically, the electrostatic term, with salt-dependent coefficients, is modeled after Stigter's pioneering work on the effective diameter of DNA as a function of salt concentration. Because an effective charge per unit length is used, the electrostatic formulation does not require explicit modeling of phosphates and can be used to study long DNAs at any desired resolution of charge. With explicit consideration of the electrostatic energy, an elastic bending constant corresponding to the nonelectrostatic part of the bending contribution to the persistence length is used. We show, for a series of salt concentrations ranging from 0.005 to 1.0 M sodium, how configurations and energies of supercoiled DNA (1000 and 3000 base pairs) change dramatically with the simulated salt environment. At high salt, the DNA adopts highly compact and bent interwound states, with the bending energy dominating over the other components, and the electrostatic energy playing a minor role in comparison to the bending and twisting terms. At low salt, the DNA supercoils are much more open and loosely interwound, and the electrostatic components are dominant. Over the range of three decades of salt examined, the electrostatic energy changes by a factor of 10. The buckling transition between the circle and figure-8 is highly sensitive to salt concentration: this transition is delayed as salt concentration decreases, with a particularly sharp increase below 0.1 M. For example, for a bending-to-twisting force constant ratio of A/C = 1.5, the linking number difference (delta LK) corresponding to equal energies for the circle and figure-8 increases from 2.1 to 3.25 as salt decreases from 1.0 to 0.005 M. We also present in detail a family of three-lobed supercoiled DNA configurations that are predicted by elasticity theory to be stable at low delta Lk. To our knowledge, such three-dimensional structures have not been previously presented in connection with DNA supercoiling. These branched forms have a higher bending energy than the corresponding interwound configurations at the same delta Lk but, especially at low salt, this bending energy difference is relatively small in comparison with the total energy, which is dominated by the electrostatic contributions. Significantly, the electrostatic energies of the three-lobed and (straight) interwound forms are comparable at each salt environment.(ABSTRACT TRUNCATED AT 400 WORDS)
AB - We present a detailed computational study of the influence of salt on the configurations, energies, and dynamics of supercoiled DNA. A potential function that includes both elastic and electrostatic energy components is employed. Specifically, the electrostatic term, with salt-dependent coefficients, is modeled after Stigter's pioneering work on the effective diameter of DNA as a function of salt concentration. Because an effective charge per unit length is used, the electrostatic formulation does not require explicit modeling of phosphates and can be used to study long DNAs at any desired resolution of charge. With explicit consideration of the electrostatic energy, an elastic bending constant corresponding to the nonelectrostatic part of the bending contribution to the persistence length is used. We show, for a series of salt concentrations ranging from 0.005 to 1.0 M sodium, how configurations and energies of supercoiled DNA (1000 and 3000 base pairs) change dramatically with the simulated salt environment. At high salt, the DNA adopts highly compact and bent interwound states, with the bending energy dominating over the other components, and the electrostatic energy playing a minor role in comparison to the bending and twisting terms. At low salt, the DNA supercoils are much more open and loosely interwound, and the electrostatic components are dominant. Over the range of three decades of salt examined, the electrostatic energy changes by a factor of 10. The buckling transition between the circle and figure-8 is highly sensitive to salt concentration: this transition is delayed as salt concentration decreases, with a particularly sharp increase below 0.1 M. For example, for a bending-to-twisting force constant ratio of A/C = 1.5, the linking number difference (delta LK) corresponding to equal energies for the circle and figure-8 increases from 2.1 to 3.25 as salt decreases from 1.0 to 0.005 M. We also present in detail a family of three-lobed supercoiled DNA configurations that are predicted by elasticity theory to be stable at low delta Lk. To our knowledge, such three-dimensional structures have not been previously presented in connection with DNA supercoiling. These branched forms have a higher bending energy than the corresponding interwound configurations at the same delta Lk but, especially at low salt, this bending energy difference is relatively small in comparison with the total energy, which is dominated by the electrostatic contributions. Significantly, the electrostatic energies of the three-lobed and (straight) interwound forms are comparable at each salt environment.(ABSTRACT TRUNCATED AT 400 WORDS)
UR - http://www.scopus.com/inward/record.url?scp=0027961109&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=0027961109&partnerID=8YFLogxK
U2 - 10.1016/S0006-3495(94)80732-5
DO - 10.1016/S0006-3495(94)80732-5
M3 - Article
C2 - 7696459
AN - SCOPUS:0027961109
SN - 0006-3495
VL - 67
SP - 2146
EP - 2166
JO - Biophysical journal
JF - Biophysical journal
IS - 6
ER -