Gapped DNA and Cyclization of Short DNA Fragments

Overview

Journal Biophys J

Publisher Cell Press

Specialty Biophysics

Date 2005 Mar 22

PMID 15778443

Citations 18

Authors

Quan Du

Maria Vologodskaia

Heiko Kuhn

Maxim Frank-Kamenetskii

Alexander Vologodskii

Affiliations

Soon will be listed here.

Abstract

We use the cyclization of small DNA molecules, approximately 200 bp in length, to study conformational properties of DNA fragments with single-stranded gaps. The approach is extremely sensitive to DNA conformational properties and, being complemented by computations, allows a very accurate determination of the fragment's conformational parameters. Sequence-specific nicking endonucleases are used to create the 4-nt-long gap. We determined the bending rigidity of the single-stranded region in the gapped DNA. We found that the gap of 4 nt in length makes all torsional orientations of DNA ends equally probable. Our results also show that the gap has isotropic bending rigidity. This makes it very attractive to use gapped DNA in the cyclization experiments to determine DNA conformational properties, since the gap eliminates oscillations of the cyclization efficiency with the DNA length. As a result, the number of measurements is greatly reduced in the approach, and the analysis of the data is greatly simplified. We have verified our approach on DNA fragments containing well-characterized intrinsic bends caused by A-tracts. The obtained experimental results and theoretical analysis demonstrate that gapped-DNA cyclization is an exceedingly sensitive and accurate approach for the determination of DNA bending.

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References

Frank-Kamenetskii M, Lukashin A, Anshelevich V, Vologodskii A . Torsional and bending rigidity of the double helix from data on small DNA rings. J Biomol Struct Dyn. 1985; 2(5):1005-12. DOI: 10.1080/07391102.1985.10507616. View

Hillisch A, Lorenz M, Diekmann S . Recent advances in FRET: distance determination in protein-DNA complexes. Curr Opin Struct Biol. 2001; 11(2):201-7. DOI: 10.1016/s0959-440x(00)00190-1. View

Kahn J, Crothers D . Measurement of the DNA bend angle induced by the catabolite activator protein using Monte Carlo simulation of cyclization kinetics. J Mol Biol. 1998; 276(1):287-309. DOI: 10.1006/jmbi.1997.1515. View

Wang J, Davidson N . Cyclization of phage DNAs. Cold Spring Harb Symp Quant Biol. 1968; 33:409-15. DOI: 10.1101/sqb.1968.033.01.047. View

MILLS J, Vacano E, Hagerman P . Flexibility of single-stranded DNA: use of gapped duplex helices to determine the persistence lengths of poly(dT) and poly(dA). J Mol Biol. 1999; 285(1):245-57. DOI: 10.1006/jmbi.1998.2287. View

Shore D, Langowski J, Baldwin R . DNA flexibility studied by covalent closure of short fragments into circles. Proc Natl Acad Sci U S A. 1981; 78(8):4833-7. PMC: 320266. DOI: 10.1073/pnas.78.8.4833. View

Hagerman P . Flexibility of DNA. Annu Rev Biophys Biophys Chem. 1988; 17:265-86. DOI: 10.1146/annurev.bb.17.060188.001405. View

Protozanova E, Yakovchuk P, Frank-Kamenetskii M . Stacked-unstacked equilibrium at the nick site of DNA. J Mol Biol. 2004; 342(3):775-85. DOI: 10.1016/j.jmb.2004.07.075. View

Barbic A, Zimmer D, Crothers D . Structural origins of adenine-tract bending. Proc Natl Acad Sci U S A. 2003; 100(5):2369-73. PMC: 151347. DOI: 10.1073/pnas.0437877100. View

10.

MILLS J, Cooper J, Hagerman P . Electrophoretic evidence that single-stranded regions of one or more nucleotides dramatically increase the flexibility of DNA. Biochemistry. 1994; 33(7):1797-803. DOI: 10.1021/bi00173a024. View

11.

Vologodskaia M, Vologodskii A . Contribution of the intrinsic curvature to measured DNA persistence length. J Mol Biol. 2002; 317(2):205-13. DOI: 10.1006/jmbi.2001.5366. View

12.

Tchernaenko V, Radlinska M, Drabik C, Bujnicki J, Halvorson H, Lutter L . Topological measurement of an A-tract bend angle: comparison of the bent and straightened states. J Mol Biol. 2003; 326(3):737-49. DOI: 10.1016/s0022-2836(02)01468-7. View

13.

Smith C, Jordan J, Vinograd J . In vivo effects of intercalating drugs on the superhelix density of mitochondrial DNA isolated from human and mouse cells in culture. J Mol Biol. 1971; 59(2):255-72. DOI: 10.1016/0022-2836(71)90050-7. View

14.

Tchernaenko V, Halvorson H, Lutter L . Topological measurement of an A-tract bend angle: variation of duplex winding. J Mol Biol. 2003; 326(3):751-60. DOI: 10.1016/s0022-2836(02)01360-8. View

15.

Inners L, Felsenfeld G . Conformation of polyribouridylic acid in solution. J Mol Biol. 1970; 50(2):373-89. DOI: 10.1016/0022-2836(70)90199-3. View

16.

Ulanovsky L, Bodner M, Trifonov E, Choder M . Curved DNA: design, synthesis, and circularization. Proc Natl Acad Sci U S A. 1986; 83(4):862-6. PMC: 322970. DOI: 10.1073/pnas.83.4.862. View

17.

Cherny D, Fourcade A, Svinarchuk F, Nielsen P, Malvy C, Delain E . Analysis of various sequence-specific triplexes by electron and atomic force microscopies. Biophys J. 1998; 74(2 Pt 1):1015-23. PMC: 1302582. DOI: 10.1016/S0006-3495(98)74026-3. View

18.

Hardwidge P, Wu J, Williams S, Parkhurst K, Parkhurst L, Maher 3rd L . DNA bending by bZIP charge variants: a unified study using electrophoretic phasing and fluorescence resonance energy transfer. Biochemistry. 2002; 41(24):7732-42. DOI: 10.1021/bi020213w. View

19.

Xu Y, Lunnen K, Kong H . Engineering a nicking endonuclease N.AlwI by domain swapping. Proc Natl Acad Sci U S A. 2001; 98(23):12990-5. PMC: 60812. DOI: 10.1073/pnas.241215698. View

20.

Shore D, Baldwin R . Energetics of DNA twisting. I. Relation between twist and cyclization probability. J Mol Biol. 1983; 170(4):957-81. DOI: 10.1016/s0022-2836(83)80198-3. View