Stretched and overwound DNA forms a Pauling-like structure with exposed bases.

We investigate structural transitions within a single stretched and supercoiled DNA molecule. With negative supercoiling, for a stretching force >0.3 pN, we observe the coexistence of B-DNA and denatured DNA from sigma approximately -0.015 down to sigma = -1. Surprisingly, for positively supercoiled DNA (sigma > +0.037) stretched by 3 pN, we observe a similar coexistence of B-DNA and a new, highly twisted structure. Experimental data and molecular modeling suggest that this structure has approximately 2.62 bases per turn and an extension 75% larger than B-DNA. This structure has tightly interwound phosphate backbones and exposed bases in common with Pauling's early DNA structure [Pauling, L. & Corey, R. B. (1953), Proc. Natl. Acad. Sci. USA 39, 84-97] and an unusual structure proposed for the Pf1 bacteriophage [Liu, D. J. & Day, L. A. (1994) Science 265, 671-674].

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

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

[3]  T. Strick,et al.  Behavior of supercoiled DNA. , 1998, Biophysical journal.

[4]  Steven M. Block,et al.  Transcription Against an Applied Force , 1995, Science.

[5]  O. Mandelboim,et al.  Protection from Natural Killer Cell-Mediated Lysis by HLA-G Expression on Target Cells , 1996, Science.

[6]  Eric J. Brown,et al.  Decreased Resistance to Bacterial Infection and Granulocyte Defects in IAP-Deficient Mice , 1996, Science.

[7]  D. Liu,et al.  Pf1 virus structure: helical coat protein and DNA with paraxial phosphates. , 1994, Science.

[8]  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.

[9]  D. Lilley,et al.  Structural alteration in alternating adenine-thymine sequences in positively supercoiled DNA. , 1991, Journal of molecular biology.

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

[11]  Heinz Sklenar,et al.  JUMNA (junction minimisation of nucleic acids) , 1995 .

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

[13]  R. Lavery,et al.  Defining the structure of irregular nucleic acids: conventions and principles. , 1989, Journal of biomolecular structure & dynamics.

[14]  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.

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

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

[17]  Nidhi Arora,et al.  Strength of hydrogen bonds in α helices , 1997 .

[18]  Structure models for DNA in filamentous viruses with phosphates near the center. , 1979, Nucleic acids research.

[19]  Z. Wang,et al.  Differential control of transcription‐induced and overall DNA supercoiling by eukaryotic topoisomerases in vitro. , 1996, The EMBO journal.

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

[21]  R Lavery,et al.  Modelling extreme stretching of DNA. , 1996, Nucleic acids research.