DNA: An Extensible Molecule Author(s): Philippe Cluzel, Anne Lebrun, Christoph Heller, Richard Lavery, Jean-Louis Viovy, Didier Chatenay, François 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 Your use of the JSTOR archive indicates your acceptance of JSTOR's Terms and Conditions of Use, available at http://www.jstor.org/page/info/about/policies/terms.jsp. JSTOR's Terms and Conditions of Use provides, in part, that unless you have obtained prior permission, you may not download an entire issue of a journal or multiple copies of articles, and you may use content in the JSTOR archive only for your personal, non-commercial use. Please contact the publisher regarding any further use of this work. Publisher contact information may be obtained at http://www.jstor.org/action/showPublisher?publisherCode=aaas. Each copy of any part of a JSTOR transmission must contain the same copyright notice that appears on the screen or printed page of such transmission. JSTOR is a not-for-profit service that helps scholars, researchers, and students discover, use, and build upon a wide range of content in a trusted digital archive. We use information technology and tools to increase productivity and facilitate new forms of scholarship. For more information about JSTOR, please contact
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wherek is the Boltzmannconstant,T is the temperaturein 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 cooperativetransition, leadsto an excellentfit (10) (see full line in Fig. 2A). If, as suggestedabove, the plateauis the resultof a DNA conformationaltransition, a drasticchange could be expected in the presenceof intercalatingagents.The transition indeeddisappearsin the presenceof 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
160 120 -
e
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Relative length
Fig. 3. Force versus extension curve in the presence of 10 pLg/mlof ethidium bromide at a pulling 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 forcerisesat a largervalueof the extension and the extendedform. than withoutan intercalator,in 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. Vostretchingprocess,performedwith the prologodskii, Macromolecules 27, 5623 (1994); J. gramJUMNA (Fig. 4), also leadsto a plaMarkoand E. D. Siggia, ibid., 28, 8759 (1995). teau in the force-displacementcurve (Fig. 6. D. Bensimon et al., Phys. Rev. Lett. 74, 4754 (1995); A. Bensimon et al., Science 265, 2096 (1994). 2C). The structureof 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 not take into account reductionin helical diameterand a strong 10. the entropicelasticity,it becomes rapidlyinaccuratefor 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 required.Additionalelasticitymay also arisefromdistortions of bond angles (15) or from a dependence of Fraseron stretchedDNA fibers (11). The energies on base paircontent and sequence. strongbase inclinationinducedby stretch- 11. transition M. J. Fraser and R. D. B. Fraser, Nature 167, 760 ing suggestsan 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). loss of basestackingor wouldrequireDNA 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 R. G. Cox, J. FluidMech. 44, 791 (1970). (12, 13) to speculateon the biologicalim- 17. 18. EMBL3 X DNA (16) was labeled at the right end for 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 which is a putativeintermediateduringrelabeling 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 maybe an intermediatestep in such triplex was multilabeled (about 150 ligands) on both formation.The role of RecA might thus be strands with biotin by the ligation, by means of an
Fig. 4. DNAstretchingwas modeledwith use of the JUMNAmolecularmechanics programdeveloped for studyingnucleic acid conformations(21-23). An all-atom force fieldis used, and efficientminimization is allowedby a reducedvariablerepresentationinvolvinghelicoidaland internal variables(bondrotationsand valenceangles). Solvent and counterioneffects are representedby a distance-dependentdielectricfunctionand reduced phosphate charges. An infiniteDNA polymer was studied with the use of helicalsymmetry constraintsand a repeatof 10 nucleotide pairs. Stretchinginvolvedminimizingthe energyper turnof the polymeras a functionof the lengthof one of its strands(imposed witha quadraticdistanceconstraint betweenC5' and C3' atoms separatedby 10 nucleotides).Resultsare presentedfor an alternatingATsequence. The figureshows space-filling TheelongatedDNA graphicsof the relaxedlinearDNA(left)and DNAstretchedby a factorof 1.7 (right). is characterized bya strongbase pairinclination, a narrowminorgroove,anda diameterroughly30%less thanthatof B-DNA.Thebase pairs,whichareexposed on the majorgrooveside of the doublehelix,are stillboundby a singlehydrogenbond, and stronginterstrand stackingbetweenadeninescan be seen. Thisconformational change occurs progressivelyand cooperativelyduringstretching.Modeling,however, indicatesthat the finalconformationand the energetics of stretchingdepend both on base sequence and on whichstrandterminiare tetheredduringstretching.
19.
20. 21.
22. 23. 24.
adapter, of a 700-base pair fragment labeled with biotin by the polymerase chain reaction. The exact value of the initialextension, which is related 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 obtained by fittingthe steep rise of the entropicforce at the vicinityof the fullcontourlengthextension (4, 5). This 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 centration,but a quantitativestudy of salt effects would requirea 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 Armees, the European Ecothe DRET/Ministbre nomic CommunityBiomed Program, and the French Supercomputing Centre IDRIS.We 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
