Behavior of supercoiled DNA.

We study DNA supercoiling in a quantitative fashion by micromanipulating single linear DNA molecules with a magnetic field gradient. By anchoring one end of the DNA to multiple sites on a magnetic bead and the other end to multiple sites on a glass surface, we were able to exert torsional control on the DNA. A rotating magnetic field was used to induce rotation of the magnetic bead, and reversibly over- and underwind the molecule. The magnetic field was also used to increase or decrease the stretching force exerted by the magnetic bead on the DNA. The molecule's degree of supercoiling could therefore be quantitatively controlled and monitored, and tethered-particle motion analysis allowed us to measure the stretching force acting on the DNA. Experimental results indicate that this is a very powerful technique for measuring forces at the picoscale. We studied the effect of stretching forces ranging from 0.01 pN to 100 pN on supercoiled DNA (-0.1 < sigma < 0.2) in a variety of ionic conditions. Other effects, such as stretching-relaxing hysteresis and the braiding of two DNA molecules, are discussed.

[1]  D. Natale,et al.  Stable DNA unwinding, not "breathing," accounts for single-strand-specific nuclease hypersensitivity of specific A+T-rich sequences. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[2]  P. Gennes.  Scaling Concepts in Polymer Physics , 1979 .

[3]  S. Smith,et al.  Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads. , 1992, Science.

[4]  Leroy F. Liu,et al.  Transcription generates positively and negatively supercoiled domains in the template , 1988, Cell.

[5]  A. Bensimon,et al.  The Elasticity of a Single Supercoiled DNA Molecule , 1996, Science.

[6]  F. Reif,et al.  Fundamentals of Statistical and Thermal Physics , 1965 .

[7]  H. Patterton,et al.  Negative supercoiling and nucleosome cores. I. The effect of negative supercoiling on the efficiency of nucleosome core formation in vitro. , 1993, Journal of molecular biology.

[8]  C. Benham,et al.  Energetics of the strand separation transition in superhelical DNA. , 1992, Journal of molecular biology.

[9]  E. Siggia,et al.  Fluctuations and supercoiling of DNA. , 1994, Science.

[10]  J Langowski,et al.  Modulation of intramolecular interactions in superhelical DNA by curved sequences: a Monte Carlo simulation study. , 1995, Biophysical journal.

[11]  A Bensimon,et al.  Alignment and sensitive detection of DNA by a moving interface. , 1994, Science.

[12]  M Frank-Kamenetskii,et al.  Conformational and thermodynamic properties of supercoiled DNA. , 1992, Journal of molecular biology.

[13]  R. Wiegand,et al.  Uptake of homologous single-stranded fragments by superhelical DNA. II. Characterization of the reaction. , 1977, Journal of molecular biology.

[14]  N R Cozzarelli,et al.  Structure of plectonemically supercoiled DNA. , 1990, Journal of molecular biology.

[15]  M. Sheetz,et al.  Tracking kinesin-driven movements with nanometre-scale precision , 1988, Nature.

[16]  J. Sikorav,et al.  Forces on chromosomal DNA during anaphase. , 1996, Biophysical journal.

[17]  R. Wiegand,et al.  Uptake of homologous single-stranded fragments by superhelical DNA. IV. Branch migration. , 1977, Journal of molecular biology.

[18]  Marko,et al.  Statistical mechanics of supercoiled DNA. , 1995, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[19]  Elaine A. Ostrander,et al.  Local domains of supercoiling activate a eukaryotic promoter in vivo , 1993, Nature.

[20]  A Bensimon,et al.  pH-dependent specific binding and combing of DNA. , 1997, Biophysical journal.

[21]  L Pauling,et al.  A Proposed Structure For The Nucleic Acids. , 1953, Proceedings of the National Academy of Sciences of the United States of America.

[22]  E. Paleček,et al.  Local supercoil-stabilized DNA structures. , 1991, Critical reviews in biochemistry and molecular biology.

[23]  E. Siggia,et al.  Entropic elasticity of lambda-phage DNA. , 1994, Science.

[24]  R. Lavery,et al.  DNA: An Extensible Molecule , 1996, Science.

[25]  Z. Wang,et al.  Long-range effects in a supercoiled DNA domain generated by transcription in vitro. , 1997, Journal of molecular biology.

[26]  J. Dubochet,et al.  The twist, writhe and overall shape of supercoiled DNA change during counterion-induced transition from a loosely to a tightly interwound superhelix. Possible implications for DNA structure in vivo. , 1994, Journal of molecular biology.

[27]  R. Watson,et al.  The twisted circular form of polyoma viral DNA. , 1965, Proceedings of the National Academy of Sciences of the United States of America.

[28]  D. Moras,et al.  Self-fitting and self-modifying properties of the B-DNA molecule. , 1995, Journal of molecular biology.

[29]  T Schlick,et al.  Supercoiled DNA energetics and dynamics by computer simulation. , 1992, Journal of molecular biology.

[30]  M. Mézard,et al.  Elastic rod model of a supercoiled DNA molecule , 1998, cond-mat/9904018.

[31]  J. Marko.  Supercoiled and braided DNA under tension , 1997 .

[32]  R. Wiegand,et al.  Uptake of homologous single-stranded fragments by superhelical DNA: a possible mechanism for initiation of genetic recombination. , 1975, Proceedings of the National Academy of Sciences of the United States of America.

[33]  James H. White.  Self-Linking and the Gauss Integral in Higher Dimensions , 1969 .

[34]  M. Mézard,et al.  Elasticity model of a supercoiled DNA molecule , 1997, cond-mat/9706050.

[35]  C. Bustamante,et al.  Overstretching B-DNA: The Elastic Response of Individual Double-Stranded and Single-Stranded DNA Molecules , 1996, Science.