Opposite effect of counterions on the persistence length of nicked and non-nicked DNA

Journal of Molecular Biology

Volumn 266, Issue 4, 1997, Pages 711-721

  Furrer, Patrick ^a,b   Bednar, Jan ^a,c   Stasiak, Alicja Z ^a   Katritch, Vsevolod ^a,d   Michoud, Didier ^a,e   Stasiak, Andrzej ^a   Dubochet, Jacques ^a  

^a UNIVERSITY OF LAUSANNE   (Switzerland)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF MASSACHUSETTS   (United States)

^d RUTGERS UNIVERSITY   (United States)

^e Ecl Polytech Fe'derale L   (Switzerland)

Author keywords

Cryo electron microscopy; DNA flexibility; DNA nicking; DNA persistence length; DNA structure

Indexed keywords

DOUBLE STRANDED DNA; SODIUM CHLORIDE;

ARTICLE; DNA CONFORMATION; DNA NICK TRANSLATION; DNA SEQUENCE; DNA STRUCTURE; ELECTRON MICROSCOPY; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL;

EID: 0031557391     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0825     Document Type: Article

References (26)

1. Bednar J., Furrer P., Katritch V., Stasiak A. Z., Dubochet J., Stasiak A. Determination of DNA persistence length by cryo-electron microscopy. Separation of the static and dynamic contributions to the apparent persistence length of DNA. J. Mol. Biol. 254:1995;579-591.
2. Bolshoy A., McNamara P., Harrington R. E., Trifonov E. N. Curved DNA without A-A: experimental estimations of all 16 DNA wedge angles. Proc. Natl Acad. Sci. USA. 88:1991;2312-2316.
3. Dubochet J, Adrian M., Chang J., Homo J., Lepault J., McDowall W., Schultz P. Cryo-electron microscopy of vitrified specimens. Quart. Rev. Biophys. 21:1988;129-228.
4. Dubochet J., Adrian M., Dustin I., Furrer P., Stasiak A. Cryo-electron microscopy of DNA molecules in solution. Methods in Enzymolgy. 1992;Academic Press, Inc. New York.
5. Dubochet J., Bednar J., Furrer P., Stasiak A. Z., Stasiak A., Bolshoy A. A. Determination of the DNA helical repeat by cryo-electron microscopy. Nature Struct. Biol. 1:1994;361-363.
6. Dustin I., Furrer P., Stasiak A., Dubochet J., Langowski J., Egelman E. Spatial visualisation of DNA in solution. J. Struct. Biol. 107:1991;15-21.
7. Erie D. A., Jones R. A., Olson W. K., Sinha N. K., Breslauer K. J. Melting behavior of a covalently closed, single-stranded, circular DNA. Biochemistry. 28:1989;268-273.
8. Frontali C., Dore E., Ferrauto A., Gratton E., Bettini A., Pozzan M. R., Valdevit E. An absolute method for the determination of the persistence length of native DNA from electron micrographs. Biopolymers. 18:1979;1353-1373.
9. Hagerman K. R., Hagerman P. J. Helix rigidity of DNA: the meroduplex as an experimental paradigm. J. Mol. Biol. 260:1996;207-223.
10. Haran T. I., Kahn J. D., Crothers D. M. Sequence elements responsible for DNA curvature. J. Mol. Biol. 244:1994;135-143.
11. Kahn J. D., Yun E., Crothers D. M. Detection of localized DNA flexibility. Nature. 368:1994;163-166.
12. Katritch V., Bednar J., Furrer P., Pinol-i-Margalef F., Kunt M., Vologodskii A., Stasiak A., Dubochet J. Persistence length of DNA molecules confined to a thin liquid layer. II. From stereo-micrographs of DNA molecules to their reconstructed 3-D trajectories. An automatic procedure for filament recognition and its application to the measurements of DNA persistence length. J. Mol. Biol. 254:1995;591-594.
13. Kroeker W. D., Kowalski D. Gene-sized pieces produced by digestion of linear duplex DNA with mung bean nuclease. Biochemistry. 17:1978;3236-3243.
14. Landau L. D., Lifshitz E. M. Statistical Physics, Course of Theoretical Physics. 1958;Pergamon, London.
15. Le Cam E., Fack F., Ménissier-de Murcia J., Cognet J. A. H., Barbin A., Sarantoglou V., Révet B., Delain E., de Murcia G. Conformational analysis of a 139 base-pair DNA fragment containing a single-stranded break and its interaction with human poly(AD-ribose) polymerase. J. Mol. Biol. 235:1994;1062-1071.
16. Lerman L. S., Silverstein K. Computational simulation of DNA melting and its application to denaturing gradient gel electrophoresis. Methods Enzymol. 155:1987;482-501.
17. Mills J. B., Cooper J. P., Hagerman P. J. Electrophoretic evidence that single-stranded regions of one or more nucleotides dramatically increase the flexibility of DNA. Biochemistry. 33:1994;1797-1803.
18. Pieters J. M. L., Mans R. M. W., van den Elst H., van der Marel G. A., van Boom J. H., Altona C. Conformational and thermodynamic consequences of the introduction of a nick in duplex DNA fragments: an NMR study augmented by biochemical experiments. Nucl. Acids Res. 17:1989;4551-4564.
19. Porschke D. Persistence length and bending dynamics of DNA from electro-optical measurements at high salt concentrations. Biophys. Chem. 40:1991;169-179.
20. Shaw S. Y., Wang J. C. Knotted DNA rings: probability of formation and resolution of the two chiral trefoils. Science. 260:1993;533-536.
21. Snowden-Ifft E. A., Wemmer D. E. Characterization of the structure and melting of DNAs containing backbone nicks and gaps. Biochemistry. 29:1990;6017-6025.
22. Studer D., Michel M., Wohlwend M., Hunziker E. B., Buschmann M. Vitrification of articular cartilage by high pressure freezing. J. Microsc. 179:1995;321-332.
23. Taylor W. H., Hagerman P. J. Application of the method of phage T4 DNA ligase-catalysed ring-closure to the study of DNA structure. II. NaCl-dependence of DNA flexibility and helical repeat. J. Mol. Biol. 212:1990;363-376.
24. Trifonov E. N., Tan R. K. Z., Harvey S. C. Static persistence length of DNA. Olson W. K., Sarma M. H., Sarma R. H., Sundaralinjam M. S.,. Structure and Expression. 1988;Adenine Press, Albany.
25. Vologodskii A. V. Topology and Physics of Circular DNA. 1992;CRC Press, Boca Raton.
26. Wilson R. W., Bloomfield V. A. Counterion-induced condensation of deoxyribonucleic acid. A light scattering study. Biochemisry. 18:1979;2192-2196.