8/3/2019 Philippe Cluzel, Anne Lebrun, Christoph Heller, Richard
Lavery, Jean-Louis Viovy, Didier Chatenay and Franois Caro
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DNA: An Extensible MoleculeAuthor(s): Philippe Cluzel, Anne
Lebrun, Christoph Heller, Richard Lavery, Jean-Louis ViovyDidier
Chatenay, Franois CaronSource: Science, New Series, Vol. 271, No.
5250 (Feb. 9, 1996), pp. 792-794Published by: American Association
for the Advancement of ScienceStable URL:
http://www.jstor.org/stable/2889888
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8/3/2019 Philippe Cluzel, Anne Lebrun, Christoph Heller, Richard
Lavery, Jean-Louis Viovy, Didier Chatenay and Franois Caro
4/4
wherek is the Boltzmann onstant,T is thetemperaturen kelvin, y =
x/N - (1 +12)/2,N is the numberof elements (nucle-otide pairs), Al
= (12 - 1), and x is theextension of the chain (in
micrometers).Poor fits are obtained orw -> 0. Takingwequalto -
16.6kj/molperbasepair,whichdisfavors isolated S-form or B-form
ele-ments and impliesa cooperative ransition,leads o an
excellentfit (10) (seefull line inFig. 2A).If, as suggested bove,
the plateau s theresultof a DNA conformationalransition,a
drasticchange could be expectedin thepresenceof intercalating
gents.The tran-sition indeed disappearsn the presenceof10 ,ug/mlof
ethidiumbromide Fig. 3). Atthe present tage, one can note the
follow-ing: First, he rise of the force with exten-sion is smoother
than shown in Fig. 2A,both beforeor after the plateau.This may
160 -
120 -
e 80 -
40 -
0.6 0.8 1 1.2 1.4 1.6 1.8Relative lengthFig. 3. Force versus
extension curve in the pres-ence of 10 pLg/mlf ethidium bromide at
a pullingrate of 10 ,um/s, other conditions being identicalto those
of Fig. 2A. The relative length is againdefined with respect to the
B-form contour length(15.1 ,um).
be a resultof exchangeof the intercalatorduring he
stretchingprocess.Second,theforcerisesat a larger alueof the
extensionthanwithout an intercalator,n agreementwith the well-known
engtheningand un-windingof DNA inducedby intercalatingagents and
with earlier observationsbySmith et al. (4).Molecular modeling of
the DNAstretchingprocess,performedwith the pro-gramJUMNA(Fig. 4),
also leads to a pla-teau in the force-displacementurve (Fig.2C).
The structure f the S form,modeledby stretching he ends of one
strandof theduplex (compatiblewith our experimenthere),
suggeststhat extension involves areduction n helicaldiameteranda
strongbase pair inclinationthat maintainsbothbase stackingand
pairinguntil a relativelength of 2.0. This finding
correlateswithearly spectroscopic tudies by FraserandFraser n
stretchedDNA fibers(11). Thestrongbaseinclination nducedby
stretch-ing suggests n explanation or the cooper-ative natureof the
transition,becausedis-continuities in inclination would implyaloss
of basestackingor wouldrequireDNAkinking.The 1.6 times extensionof
DNA at theend of the force plateau s close enoughtothe extension
inducedby RecA fixation(12, 13) to speculateon the biological
m-portanceof an extendedform of isolatedDNA. The purposeof
extendingand un-windingDNA, in the case of RecA, is tofacilitate
the formationof a triplex (14),which is a putative ntermediate
uringre-combination.A pre-extendedDNA formmaybe an intermediate
tepin suchtriplexformation.The role of RecA mightthus be
Fig. 4. DNA tretchingwas modeledwithuse of the
JUMNAmolecularmechanicsprogramdeveloped for studying nucleicacid
conformations21-23). An all-atomforce field s used, and
efficientminimiza-tion s allowedby a reducedvariable
ep-resentationnvolving elicoidal nd internalvariables bond
rotations nd valence an-gles). Solvent and counterion ffects
arerepresentedby a distance-dependent i-electric unctionand reduced
phosphatecharges. An infiniteDNA polymer wasstudied with the use of
helical ymmetryconstraints nda repeatof 10 nucleotidepairs.
Stretching nvolvedminimizingheenergyperturnof the polymer s a
func-tionof the lengthof one of its strands im-posedwitha quadratic
istanceconstraintbetweenC5'andC3'atomsseparatedby10
nucleotides).Resultsare presented or an alternating Tsequence. The
figure hows space-fillinggraphics f the relaxed inearDNA left) nd
DNA tretchedby a factorof 1.7 (right). heelongatedDNAis
characterizedya strongbase pair nclination,narrowminor roove,anda
diameter oughly 0% essthan hatof B-DNA.The base pairs,whichare
exposed on the major rooveside of the doublehelix, restillboundbya
singlehydrogenbond, and strong nterstrandtackingbetweenadeninescan
be seen.Thisconformationalhange occurs progressively nd
cooperatively uring tretching.Modeling, ow-ever, indicates hat the
finalconformation nd the energeticsof stretchingdepend both on
basesequenceand on which trand ermini re tetheredduring
tretching.
to induce such a transitionby means ofspecific
interactionsbetween the proteinandthe extended orm.REFERENCESAND
NOTES
1. M. H. F. Wilkins t al., Nature 171, 738 (1953).2. M. H. F.
Wilkins t al., ibid. 167, 759 (1951).3. F. H. C. Crick and J. D.
Watson, Proc. R. Soc. Lon-don Ser. A 223, 80 (1954).4. S. B. Smith
et al., Science 258, 1122 (1992).5. C. Bustamante et al., ibid.
265, 1599 (1994); A. Vo-logodskii, Macromolecules 27, 5623 (1994);
J.Marko and E. D. Siggia, ibid., 28, 8759 (1995).6. D. Bensimon et
al., Phys. Rev. Lett.74, 4754 (1995);A. Bensimon et al., Science
265, 2096 (1994).7. A. Kishino and T. Yanagida, Nature334, 74
(1988).8. S. B. Smith et al., Biophys. J. 68, A250 (1995).9. T. L.
Hill,J. Chem. Phys. 30, 383 (1959); B. Zimmand J. Bragg, ibid. 31,
526 (1959).10. Because this simple model does not take into
accountthe entropicelasticity, t becomes rapidly
naccurateorextensionsoutside the plateauregion.For a
completedescription,a theory aking ntoaccount the degrees offreedom
relatedto the exchange between states, aswell as those related to
entropic elasticity(5), will berequired.Additionallasticitymay also
arise romdistor-tions of bond angles (15) or from a dependence
oftransitionnergieson base paircontent and sequence.11. M. J.
Fraser and R. D. B. Fraser, Nature 167, 760(1951).12. A. Stasiak
and E. diCapua, ibid. 299,185 (1982).13. M. M. Cox and 1. R.
Lehman, Annu. Rev. Biochem.56, 229 (1987).14. B. J. Rao, M.
Dutreix,C. M. Radding, Proc. Natl.Acad. Sci. U.S.A. 88, 2984
(1991).15. J. L.Viovy,C. Heller,F. Caron, Ph. Cluzel, D. Chat-enay,
C. R. Acad. Sci. Paris 317, 795 (1994).16. A.-M. Frischauf,H.
Lehrach, A. Poustka, N. Murray,J. Mol. Biol. 170, 827 (1983).17. R.
G. Cox, J. FluidMech. 44, 791 (1970).18. EMBL3XDNA(16) was labeled
at the rightend forattachment to a polystyrene microbead
(Poly-science; 2.8 ,um)covered with antibody to digoxi-genin
(anti-DIG) by ligation of a modified 12-meroligonucleotide,
complementary to the 5' protrud-ing right end of XDNA. The
modification consists oflabeling the oligonucleotide with terminal
trans-ferase in the presence of
DIG2'3'-dideoxyuridine-5'-triphosphate (Boehringer). At the left
end, DNAwas multilabeled (about 150 ligands) on bothstrands with
biotin by the ligation, by means of anadapter, of a 700-base pair
fragment labeled withbiotin by the polymerase chain reaction.19.
The exact valueof the initial xtension,whichis relatedto the
positionof the beadwithrespectto the anchoringof DNAon the fiber,
is known only to within 3 j,m;therefore, ntemalreferencewith a 1
jim accuracywasobtainedbyfittinghe steep riseof the entropic orce
atthevicinity f the full ontour engthextension (4, 5).
Thisfityieldsa persistencelengthsmaller hanthat obtainedby others
(5) by a factor of 3 to 4. This decrease
isqualitativelyonsistentwithour use of a higher
altcon-centration,but a quantitativetudyof salt effects
wouldrequire higheraccuracy n he low-forcedomainand isbeyond the
scope of ourwork here.20. E.-L. Florin,V. T. Moy, E. Gaub, Science
264, 415(1994).21. R. Lavery, nStructureand Expression,vol.3 of
DNABending and Curvature,W. K. Olson, R. H. Sarma,M. H. Sarma, M.
Sundaralingam, Eds. (AdeninePress, New York, 1988), pp. 191-211.22.
R. Lavery, K. Zakrzewska, H. Sklenar, Comput.Phys. Commun. 91,135
(1995).23. R. Lavery,Adv. Comput. Biol. 1, 69 (1994).24. The
authorsacknowledge support from the Chemis-try Departmentof the
CNRS,the Ultimatechprogram,the DRET/Ministbrees Armees, the
EuropeanEco-nomic CommunityBiomed Program,and the
FrenchSupercomputing CentreIDRIS.We thank J. Malth6teand J.
Davidovits or helpfuldiscussions concemingthe chemistryof these
experiments,A. Laigle orhelp-fulpreparatory xperiments,and F.
Breton for techni-cal assistance.15 September 1995; accepted 15
November 1995
