DNA: An Extensible Molecule Author(s): Philippe Cluzel, Anne Lebrun, Christoph Heller, Richard Lavery, Jean-Louis Viovy, Didier

Chatenay, Franois Caron Source: Science, New Series, Vol. 271, No. 5250 (Feb. 9, 1996), pp. 792-794 Published by: American Association for the Advancement of Science Stable URL: http://www.jstor.org/stable/2889888 Accessed: 22/02/2010 12:51
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wherek is the Boltzmann constant,T is the in temperature kelvin, y = x/N - (1 + 12)/2,N is the numberof elements (nucleotide pairs), Al = (12 - 1), and x is the extension of the chain (in micrometers). Poorfits are obtainedfor w -> 0. Takingw equal to - 16.6 kj/mol per basepair,which disfavors isolated S-form or B-form elements and impliesa cooperative transition, leadsto an excellentfit (10) (see full line in Fig. 2A). If, as suggested above, the plateauis the resultof a DNA conformational transition, a drasticchange could be expected in the presenceof intercalating agents.The transition indeeddisappears the presenceof in 10 ,ug/mlof ethidiumbromide(Fig. 3). At the presentstage,one can note the following: First,the rise of the force with extension is smoother than shown in Fig. 2A, both beforeor after the plateau.This may

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Fig. 3. Force versus extension curve in the presence of 10 pLg/ml ethidium bromide at a pulling of rate of 10 ,um/s, other conditions being identical to those of Fig. 2A. The relative length is again defined with respect to the B-form contour length (15.1 ,um).

be a resultof exchangeof the intercalator to induce such a transition by means of duringthe stretchingprocess.Second, the specific interactionsbetween the protein valueof the extension and the extendedform. forcerisesat a larger in than withoutan intercalator, agreement REFERENCESAND NOTES with the well-knownlengtheningand unwinding of DNA inducedby intercalating 1. M. H. F. Wilkinset al., Nature 171, 738 (1953). 2. M. H. F. Wilkinset al., ibid. 167, 759 (1951). agents and with earlier observationsby 3. F. H. C. Crickand J. D. Watson, Proc. R. Soc. LonSmith et al. (4). don Ser. A 223, 80 (1954). Molecular modeling of the DNA 4. S. B. Smith et al., Science 258, 1122 (1992). 5. C. Bustamante et al., ibid. 265, 1599 (1994); A. Vowith the prostretchingprocess,performed logodskii, Macromolecules 27, 5623 (1994); J. gramJUMNA (Fig. 4), also leadsto a plaMarkoand E. D. Siggia, ibid., 28, 8759 (1995). curve (Fig. teau in the force-displacement 6. D. Bensimon et al., Phys. Rev. Lett. 74, 4754 (1995); A. Bensimon et al., Science 265, 2096 (1994). of 2C). The structure the S form,modeled 7. A. Kishinoand T. Yanagida, Nature 334, 74 (1988). by stretchingthe ends of one strandof the 8. S. B. Smith et al., Biophys. J. 68, A250 (1995). duplex (compatible with our experiment 9. T. L. Hill,J. Chem. Phys. 30, 383 (1959); B. Zimm and J. Bragg, ibid. 31, 526 (1959). here), suggeststhat extension involves a Because this simple model does reductionin helical diameterand a strong 10. the entropicelasticity,it becomes not take into account rapidly inaccuratefor base pair inclination that maintainsboth extensions outside the plateau region. For a complete description,a theorytakingintoaccount the degrees of base stacking and pairinguntil a relative freedom related to the exchange between states, as length of 2.0. This finding correlateswith well as those related to entropic elasticity (5), will be early spectroscopicstudies by Fraserand elasticitymay also arisefromdistorAdditional required. tions of bond angles (15) or from a dependence of on Fraser stretchedDNA fibers (11). The strongbase inclinationinducedby stretch- 11. transitionenergies on base paircontent and sequence. M. J. Fraser and R. D. B. Fraser, Nature 167, 760 an ing suggests explanationfor the cooper(1951). ative natureof the transition,becausedis- 12. A. Stasiak and E. diCapua, ibid. 299,185 (1982). 13. M. M. Cox and 1. R. Lehman, Annu. Rev. Biochem. continuities in inclination would imply a 56, 229 (1987). DNA loss of basestackingor wouldrequire 14. B. J. Rao, M. Dutreix, C. M. Radding, Proc. Natl. Acad. Sci. U.S.A. 88, 2984 (1991). kinking. 15. J. L. Viovy, C. Heller, F. Caron, Ph. Cluzel, D. ChatThe 1.6 times extensionof DNA at the enay, C. R. Acad. Sci. Paris 317, 795 (1994). end of the force plateauis close enough to 16. A.-M. Frischauf, H. Lehrach, A. Poustka, N. Murray, J. Mol. Biol. 170, 827 (1983). the extension induced by RecA fixation 44, 791 J. Fluid (12, 13) to speculateon the biologicalim- 17. R. G. Cox,DNA (16)Mech.labeled at(1970). end for the right was 18. EMBL3 X portanceof an extended form of isolated attachment to a polystyrene microbead (Polyscience; 2.8 ,um) covered with antibody to digoxiDNA. The purposeof extending and ungenin (anti-DIG)by ligation of a modified 12-mer winding DNA, in the case of RecA, is to oligonucleotide, complementary to the 5' protrudfacilitate the formationof a triplex (14), ing right end of XDNA. The modification consists of duringrewhich is a putativeintermediate labeling the oligonucleotide with terminal transferase in the presence of DIG 2'3'-dideoxyuridinecombination.A pre-extendedDNA form 5'-triphosphate (Boehringer). At the left end, DNA step maybe an intermediate in such triplex was multilabeled (about 150 ligands) on both The role of RecA might thus be formation. strands with biotin by the ligation, by means of an
19. adapter, of a 700-base pair fragment labeled with biotin by the polymerase chain reaction. extension, which is related The exact value of the initial to the positionof the bead withrespect to the anchoring of DNA on the fiber, is known only to within 3 j,m; therefore,intemalreferencewitha 1-jim accuracy was the obtained by fitting steep rise of the entropicforce at the vicinity the fullcontourlengthextension (4, 5). This of fityieldsa persistence lengthsmallerthan that obtained by others (5) by a factor of 3 to 4. This decrease is consistent withour use of a highersalt conqualitatively study of salt effects would centration,but a quantitative a require higheraccuracyinthe low-forcedomainand is beyond the scope of our work here. E.-L. Florin,V. T. Moy, E. Gaub, Science 264, 415 (1994). R. Lavery,in Structureand Expression, vol.3 of DNA Bending and Curvature,W. K. Olson, R. H. Sarma, M. H. Sarma, M. Sundaralingam, Eds. (Adenine Press, New York, 1988), pp. 191-211. R. Lavery, K. Zakrzewska, H. Sklenar, Comput. Phys. Commun. 91,135 (1995). R. Lavery,Adv. Comput. Biol. 1, 69 (1994). The authors acknowledge support from the ChemistryDepartmentof the CNRS, the Ultimatechprogram, des the DRET/Ministbre Armees, the European Economic CommunityBiomed Program, and the French We Supercomputing Centre IDRIS. thank J. Malth6te and J. Davidovitsfor helpfuldiscussions conceming the chemistryof these experiments, A. Laiglefor helpful preparatoryexperiments, and F. Breton for technical assistance. 15 September 1995; accepted 15 November 1995

Fig. 4. DNAstretching was modeledwith use of the JUMNA molecularmechanics programdeveloped for studyingnucleic acid conformations (21-23). An all-atom force fieldis used, and efficient minimization is allowedby a reducedvariable representation involving helicoidal internal and variables (bondrotations and valenceangles). Solvent and counterioneffects are representedby a distance-dependent dielectricfunctionand reduced phosphate charges. An infiniteDNA polymer was studied with the use of helicalsymmetry constraints a repeatof 10 nucleotide and the pairs. Stretchinginvolvedminimizing energyper turnof the polymer a funcas tionof the lengthof one of its strands(imposed witha quadratic distanceconstraint betweenC5' and C3' atoms separatedby AT 10 nucleotides). Resultsare presentedfor an alternating sequence. The figureshows space-filling The graphics the relaxedlinear of DNA(left) DNAstretchedby a factorof 1.7 (right). elongatedDNA and is characterized a strongbase pair 30%less by inclination,narrow a minor groove,anda diameter roughly thanthatof B-DNA. base pairs,whichareexposed on the major The grooveside of the doublehelix,are stillboundby a singlehydrogen bond, and stronginterstrand stackingbetweenadeninescan be seen. howThisconformational change occurs progressively cooperatively and during stretching. Modeling, and the energetics of stretchingdepend both on base ever, indicatesthat the finalconformation are sequence and on whichstrandtermini tetheredduring stretching.

20. 21.

22. 23. 24.