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CurrOpinDNA2000.pdf
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Single-molecule studies of DNA mechanics
Carlos Bustamante*†§, Steven B Smith*, Jan Liphardt‡ and Doug Smith†
During the past decade, physical techniques such as optical
tweezers and atomic force microscopy were used to study the
mechanical properties of DNA at the single-molecule level.
Knowledge of DNA’s stretching and twisting properties now
permits these single-molecule techniques to be used in the
study of biological processes such as DNA replication and
transcription.
Addresses
*Department of Molecular and Cell Biology, † Department of Physics
and ‡ Department of Chemistry, University of California, Berkeley,
CA 94720, USA
§ e-mail: [email protected]
Current Opinion in Structural Biology 2000, 10:279–285
0959-440X/00/$ — see front matter
© 2000 Elsevier Science Ltd. All rights reserved.
Abbreviations
AFM
atomic force microscopy
bp
base pair
ds
double-stranded
FJC
freely jointed chain
ss
single-stranded
WLC
worm-like chain
Introduction
Until recently, physical and chemical studies of DNA were
performed in bulk, whereby large numbers of molecules
were sampled simultaneously. Inherent averaging in such
measurements makes it difficult to resolve the timedependent stresses and strains that develop in DNA
during the course of its biological reactions. Processes like
protein-induced DNA bending, induced-fit molecular
recognition between proteins and DNA, and the
mechanochemical energy transduction of DNA-binding
molecular motors were not directly accessible to study.
In the past decade, this situation has changed dramatically.
New methods to manipulate single molecules now offer
researchers the opportunity to directly measure the forces
generated in biochemical reactions and, even, to exert
external forces to alter the fate of these reactions.
Stretching DNA
The elastic behavior of dsDNA has been investigated in
various laboratories using a variety of forces, for example,
hydrodynamic drag [1–3], magnetic beads [4], glass needles [5] and optical traps [6,7]. Magnetic beads attached to
the ends of DNA by biotin–avidin can be pulled by external magnets. These magnetic tweezers are a useful tool,
particularly in the range between 0.01 and 10 pN. Slightly
higher force regimes can be probed with optical tweezers,
which allow one to apply and sense forces on micron-sized
dielectric particles, such as plastic microspheres, in an
aqueous environment [8,9]. A trap is formed by focusing a
laser beam onto a micron-sized spot through a microscope
objective. A particle with an index of refraction higher than
that of the surrounding medium experiences a force equal
to the rate of change of momentum of the refracted trapping beam. For a laser beam with a Gaussian profile, this
force attracts the bead and traps it at the center of the beam
near the focus. External forces acting on the bead can be
measured by observing either the particle position in the
trap or the corresponding deflection of the trapping beam.
Trapping forces typically range between 0.1 and 100 pN.
In atomic force microscopy (AFM), a tip at the end of a
flexible cantilever of known force constant is scanned over
the sample. Bending of the cantilever can be monitored by
the deflection of a laser beam reflected off its back [10,11].
If a molecule is attached between the tip and a surface, and
the tip is lifted upward, a force/extension curve can be
obtained. Typical forces range from 10 to 10,000 pN.
Complex behavior has been revealed by elasticity studies of
individual dsDNA molecules. In this case, the range of forces
applied to the molecule determines the nature and length
scale involved in the elastic response, with higher forces
probing shorter length units. So far, at least four different
force/extension regimes have been characterized for dsDNA.
The force/extension regimes of DNA
Entropic elasticity regime
A dsDNA molecule in solution bends and curves locally as
a result of thermal fluctuations. Such fluctuations shorten
the end-to-end distance of the molecule, even against an
applied force. This elastic behavior is thus purely entropic
in origin. Two models are often used to describe the
entropic elasticity of DNA. In the freely jointed chain
(FJC) model, the molecule is made up of rigid, orientationally independent Kuhn segments whose length, b, is a
measure of chain stiffness. The alignment of segments by
tension is described by the Boltzmann distribution. In the
inextensible worm-like chain (WLC) model, the molecule
is treated as a flexible rod of length L that curves smoothly as a result of thermal fluctuations. The rod’s local
direction decorrelates at distance s along the curve according to e–s/P, where the decay length, P, is the persistence
length of the chain. The stiffer the chain, the longer the
persistence length. For dsDNA in physiological salt, the
persistence length is approximately 50 nm. Forces of the
order kBT/P = 0.1 pN, where kB is the Boltzmann constant
and T is temperature, are required to align polymer segments with these dimensions.
Extension experiments have provided the strictest test to
date of these two models [4,6,7,12,13•]. Results, shown in
Figure 1, indicate that, even though the FJC model can
describe the behavior of dsDNA in the limit of low forces, it
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Nucleic acids
Thus, dsDNA behaves as a linear spring with a Hooke’s
constant kDNA = 3kBT/2PL, that is, inversely proportional
to the length of the molecule and its persistence length. A
10 µm dsDNA molecule, for example, has a spring constant of approximately 10–5 pN-nm–1. An identical
expression is predicted by the FJC model, within this force
limit, if the size of a Kuhn segment is taken to be twice the
persistence length of the chain [17].
Figure 1
100
dsDNA
FJC
WLC interpolated
WLC exact
Hooke's law
-11
10
Intrinsic elasticity regime
Figure 1 shows deviation from the model above 10 pN.
Indeed, the end-to-end distance becomes longer than its
theoretical B-form contour length L, indicating the existence of a finite stretch modulus. Thus, at these high
forces, the chemical structure of DNA is being altered and
the elastic response is not merely entropic. Experiments
performed with laser tweezers [6,7] give a clearer view of
the linear elasticity regime, as shown in Figure 2, in which
the molecule behaves as a stretchable solid. Assuming that
the contour length of the molecule increases linearly with
the applied force [6,18], the following formula can be used
between 5 and 50 pN:
Force (pN)
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0.1
0.01
0
0.2
0.4
0.6
0.8
1
1.2
Extension (x/L)
1/2
Current Opinion in Structural Biology
Force versus extension data (red crosses) for λ phage dsDNA
(48,502 bp) pulled by magnetic beads in 10 mM Na+ buffer [4]. The data
are fit to a WLC model solved numerically (WLC exact) or using Equation
3 (WLC interpolated), both assuming P = 53 nm. The FJC curve assumes
b = 2P = 106 nm. The Hooke’s law force curve is from Equation 2.
fails at intermediate and high forces. The WLC model, on
the other hand, provides an excellent description of molecular elasticity at low and intermediate forces. The exact force
(F) required to induce an end-to-end distance extension of x
in a chain of contour length L must be obtained numerically [14–16], but a useful approximation is given by [14]:
FP
1
x 1
=
+ − .
2
k BT
L
4
 x
4 1− √
L↵
x = L 1−
1 k BT
F
√ +
2 FP ↵
S
(3)
where S is the stretch modulus of the molecule. S equals
approximately 1000 pN in 150 mM Na+. The stretch modulus of a simple elastic rod is related to its intrinsic
persistence length, Pi, as:
Pi = Sr2/4kBT
(4)
where r is the rod’s radius. An intrinsic persistence length
of 60 nm is thus obtained for dsDNA, assuming its radius
is 1 nm, in fair agreement with the value obtained from the
entropic elasticity measurements.
The overstretching transition
(1)
The inextensible WLC model fits dsDNA data at forces
up to 10 pN, as shown in Figure 1. Setting P = 53 nm gave
the best fit to the force/extension data of Smith et al. [4],
which were taken in 10 mM Na+ buffer.
The Hookian spring: ‘Ut tensio, sic vis’
At the lowest forces accessible in these studies, the molecule behaves as a Hookian spring and its extension is
proportional to the force applied at its end. The expansion
of Equation 1 for small values of x/L gives:
When the molecule is subjected to forces of 65 pN or
more, it suddenly changes form, stretching up to 70%
beyond its canonical B-form contour length [5,6]. Various
models for the structure of this so-called S-form DNA
have been proposed [19–21] and await experimental verification. The B-to-S overstretching transition occurs
within a narrow range of forces (see the flat plateau in
Figure 2), suggesting a cooperative process [22,23]. Sform DNA is stable in high salt up to forces of between
approximately 150 pN (for random sequence) and
300 pN [for poly(dG–dC)] [24••,25•]. Above these forces,
S-DNA melts into single strands that exhibit the characteristic force/extension behavior of ssDNA (Figure 2).
Breaking covalent bonds in DNA
F=
3k BT x
√.
2P L ↵
(2)
What force is needed to cause bond scission in DNA?
Bond potential theory predicts an excess of 5000 pN is
needed, but experiments in which bulk DNA was
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Single-molecule studies of DNA mechanics Bustamante et al.
sheared in flowing buffer have yielded values of only
100–300 pN. Single molecules of dsDNA were broken
with a receding water meniscus [26] at forces estimated
to be 960 pN (correcting Young’s modulus doubles the
published scission force of 480 pN). Short dsDNA molecules pulled with an AFM tip [27] sustained forces
over 1700 pN. The ‘correct’ tensile strength is difficult
to define because it depends on the rate of stretching,
the length of the molecule (number of bonds) and solvent factors, such as bond hydrolysis at sites of DNA
depurination. Similarly, covalent bond strength of
approximately 1000 pN was determined by AFM experiments on polysaccharide molecules in water [28•].
Stretching single-stranded DNA
By attaching dsDNA between beads and melting off the
unlabeled strand with distilled water or formaldehyde, a
single strand connecting two beads is obtained [6]. As
shown in Figure 2, ssDNA is more contractile than
dsDNA because of its high flexibility, but it can be
stretched to a greater length because it no longer forms a
helix. Although the force/extension curve can be fit with
an FJC model modified by including a stretch modulus
(ad hoc) [6], almost as good a fit can be obtained with a
simple WLC model using the correct sugar–phosphate
distance without need for a stretch modulus. However,
both models fail in high salt (perhaps due to hairpin formation) and in low salt (probably due to excluded volume
effects) [6]. Further theoretical and experimental work is
clearly needed here.
281
Figure 2
S-DNA melts
100
100
Inextensible WLC
dsDNA solid stretch
10
10
Force (pN)
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1
dsDNA
WLC-53
ssDNA 5 Mg++
ssDNA 2 Na+
ssDNA 150 Na+
0
0.5
1
Extension/B-form
1.5
2
Current Opinion in Structural Biology
Force/extension behavior of dsDNA and ssDNA. Different DNA
molecules were pulled with force-measuring laser tweezers [6]. Both
pulling and relaxing curves are shown, so all force curves were
reversible. Dashed line data (WLC-53) are from Equation 1, assuming
P = 53 nm. The dsDNA curve was taken using a 10.4 kbp restriction
fragment in 50 mM Na+ and 5 mM Mg++ buffer [25•]. The same
fragment and buffer were used to make ssDNA (labeled ssDNA
5 Mg++) [40••]. The ssDNA curves in 150 mM Na+ and 2 mM Na+
were taken using 48 kbp λ phage DNA [6]. See text for further details.
Unzipping the double helix
Essevaz-Roulet et al. [29] performed the mechanical separation of the complementary strands of an individual λ
phage dsDNA molecule. They used the bending of a glass
microneedle to determine the forces required to pull apart
the 3′ and 5′ extremities of the molecule. Strand unzipping
occurred abruptly at 12–13 pN and displayed a reproducible ‘saw-tooth’ force variation pattern with an
amplitude of +/– 0.5 pN along the DNA. As shown in
Figure 3, this force variation pattern was found to match
the corresponding variation in the GC content of DNA
averaged over 100 bp. An upper bound for the maximum
spatial resolution of such an experiment is set by thermal
fluctuations and by the entropic elasticity of the ssDNA
portions of the molecule.
Higher resolution can be obtained using shorter, stiffer linker
molecules. In our laboratory, we have recently used laser
tweezers to monitor the unwinding of a 12 bp poly(GC) DNA
hairpin flanked by 600 bp dsDNA handles. At about 16 pN,
the rapid increase of force that defines the stretchable solid
regime of the handles is interrupted by a short region in which
the force remains constant over the approximately 10 nm distance required to unwind the hairpin (Figure 3). Once the
hairpin has been fully opened, the behavior of the handles
reduces to the conventional double-stranded case. Similar
forces were also obtained by Rief et al. [24••] using short AFM
cantilevers. They unzipped poly(dG–dC) at approximately
20 pN and poly(dA–dT) at approximately 10 pN.
Bockelmann et al. [30] used equilibrium statistical
mechanics to model the force/extension obtained experimentally. Agreement between simulation and experiment
was remarkable, indicating that the force variations reflect
DNA sequence composition, specifically the GC content.
More importantly, it shows that, unlike macroscopic slipstick processes, the ‘molecular stick-slip’ motion observed
in this case does not involve instabilities. Instead, each
point on the force/extension curves corresponds to an
equilibrium position.
These forces may be interpreted, therefore, as being equilibrium forces and thermodynamic state quantities, such as
free energy (∆G), can be obtained by the integration of the
force along the distance of the unwinding plateau. For our
12 bp hairpin, integration yields a ∆G per GC base pair of
about 9 kJ/mol, which is equal to the value obtained in
conventional bulk experiments.
Mechanical supercoiling of DNA
Strick et al. [12,13•] devised an elegant experiment in
which they attached both strands of a dsDNA molecule
to a flat surface at one end and to a magnetic bead at the
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Figure 3
(a)
% GC (100 bp avg)
14
13.5
60%
13
50%
Force (pN)
70%
12.5
40%
5000
7000
9000
11000
13000
15000
λ DNA base
WLCpair index
(b)
20
Force (pN)
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10
A T
T
A
CG
GC
CG
GC
CG
CG
CG
CG
GC
GC
GC
GC
5'
Mechanical unzipping of DNA. (a) A
comparison between the force signal and
average GC content along a segment from
5000 to 15,000 bp of the sequence of λ DNA
from [29]. The smooth curve is %GC
averaged over 100 bases and the jagged
curve is the force signal (versus sequencenormalized distance) obtained by mechanical
opening. (b) Unzipping of a 12 bp poly(GC)
hairpin. A single-stranded region able to form
a short hairpin (see small panel) was flanked
by two dsDNA handles. The handles were
end-labeled with biotin (5′ handle, 531 bp) or
digoxigenin (3′ handle, 613 bp) and thus
attached to appropriately labeled polystyrene
beads. Unzipping was fully reversible and was
performed in standard force-measuring laser
tweezers as described in [6] in a 150 mM Na+
buffer (pH 7.0).
dsDNA
10nm
DNA
hairpin
5
300
350
Extension (nm)
400
Current Opinion in Structural Biology
other. By external rotation of a magnetic field, the DNA
molecules became supercoiled. The authors then determined how the elasticity depended on the twist. Small
twists (< 1% change in linking number) in either direction cause molecules to increase in contractility relative
to relaxed DNA. Such an effect is predicted for a rod that
alleviates excess torsional energy by forming plectonemes (i.e. twisted loops that branch laterally from the
direct end-to-end path in the rod) [31]. Extending the
rod converts writhe into twist, at the expense of extra
tension. Unlike the simple rod, the tension in underwound dsDNA reaches a critical value (F c–) of
approximately 0.5 pN and then plateaus as the molecule
is stretched. Apparently, the DNA strands separate
(melt) to absorb the molecule’s linking number deficit
and remove plectonemes, consistent with reports [32,33]
that negatively supercoiled DNA cannot change its twist
by more than approximately 1%. Molecules with large
positive linking numbers display a different force
plateau at a higher critical force, Fc+, of approximately
3 pN. Apparently, local regions of the DNA adopt a new
form, named ‘P-DNA’, with very short helical pitch
(hypercoiled DNA).
Ionic effects
Ions strongly affect the bending behavior of DNA in
processes like chromosome formation, viral packaging,
replication and transcription. DNA’s bending rigidity is
described by the worm-like model of a polyelectrolyte as
being composed of two parts: the electrostatic persistence
length (Pe) due to intrachain repulsion and the intrinsic
persistence length (Pi) due to base stacking. Typical estimates of Pi are around 45 nm. The overall persistence
length is then P = Pi + Pe.
Single-molecule experiments in various buffer conditions
are now revealing how ions modify the rigidity of
DNA [7,34]. In monovalent salt (e.g. Na+), the measured
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Single-molecule studies of DNA mechanics Bustamante et al.
persistence length is consistent with an electrostatic contribution that varies inversely with the ionic strength, as
predicted by theory [35,36]. In this case, Pe is related to the
Debye–Hückel screening length κ–1 and the Bjerrum
length lb (0.7 nm in water/monovalent ions) by
Pe = κ–2/4lb. The model fails, however, with multivalent
ions like Co(NH3)63+ and spermidine3+. Measurements
with these ions gave P values of 25–30 nm, lower than the
‘intrinsic’ persistence length Pi. Perhaps DNA locally
bends towards the transiently bound multivalent ions,
shortening the intrinsic persistence length [34].
The eventual limitations of the ‘mechanical’ description of
dsDNA as a rod are revealed by changes in ionic strength.
Lowering the ionic strength increases the measured persistence length, but seems to reduce DNA’s elastic stretch
modulus, contradicting the elastic rod model (Equation 4).
Reversibility versus hysteresis
The free energy change in a single molecule can be
obtained by integration of a reversible force/extension
curve. In this case, the molecule passes only through a
succession of time-independent equilibrium states [37].
Thus, measurements must be made slower than the
slowest relaxation process in the molecule/bead system.
Slow processes may include transport of stretch
(Rouse–Zimm modes), transport of twist [38•], formation
of plectonemes [13•], DNA zipping and rezipping, and
protein binding. The hallmark of thermodynamic
reversibility is the retracing of the force/extension curve
upon contraction, that is, the relaxation curve coincides
with the stretching curve. Force curve hysteresis is a sensitive indicator of the kinetics of protein–DNA binding
and refolding (see chromatin below).
283
of RecA–DNA filaments in the presence of various
cofactors. The stretch modulus for a dsDNA–RecA fiber
was a stiff 5 nN fiber in [γ-thio]-ATP, but decreased to a
softer 2 nN in ATP. In this case, variation of stretch modulus with cofactor coincides with RecA’s function, as
ATP hydrolysis reduces the protein’s affinity for DNA
and, hence, the structural integrity of the filament.
Replication and transcription studies
Single-molecule measurements have been used to investigate mechanochemical properties of polymerases, such as
their stall forces [40••,41–46]. Yin et al. [41,42] immobilized
Escherichia coli RNA polymerase on a surface and provided
a DNA template attached to a bead. An optical trap was
used to pull on the DNA and oppose translocation.
Polymerization velocity was fairly insensitive to force until
it stalled reversibly at 25 pN [41,42].
A different method was used in the recent study of T7
DNA polymerase by Wuite et al. [40••], who pulled on
both ends of the template and observed changes in its
elastic properties as ssDNA was converted to dsDNA by
the enzyme. As ssDNA and dsDNA have different
force/extension properties (Figure 2), the progress of
polymerases along their ssDNA templates could be monitored in real time by fitting the force/extension data to a
combination of ssDNA and dsDNA stretching curves. T7
DNA polymerase velocity was sensitive to template tension: rates increased to a maximum at 6 pN, but then fell
linearly with tension until the enzyme reversibly stalled
at 34 pN. In contrast to RNA polymerase, the rate-limiting step for the polymerization reaction in DNA
polymerase is apparently force-sensitive. Higher template tensions (approximately 40 pN) triggered a fast
3′→5′ exonucleolysis.
Protein–DNA interactions
Special mechanical properties of DNA are frequently
invoked to explain protein binding and it is now possible
to directly test some of those models with single-molecule
experiments. Furthermore, forces can be applied to the
composite DNA–protein structure that probe its biologically active conformation. Studies of RecA–DNA filaments
have helped to quantify the role of DNA’s bending rigidity in its biological function.
The mechanics of RecA–DNA filaments
RecA is a small bacterial protein that catalyzes homologous recombination and repair of DNA. When coated
with RecA, DNA is 1.5 times longer and less twisted
than B-form DNA (20° per base pair versus 35° per base
pair). Shivashankar et al. [39] anchored λ phage DNA at
one end to a glass coverslip and at the other end to an
optically trapped polystyrene bead. From force/extension measurements in the presence of RecA and ATP,
they obtained the persistence length of the RecA–DNA
complex and the detailed kinetics of the polymerization
reaction. Using similar techniques, Hegner et al. [25•]
characterized the stretch modulus and bending rigidity
Chromatin studies
Little is known about the forces that stabilize the variously
compacted forms of chromatin and how these factors control the accessibility of chromosomes to transcription and
replication. To explore these issues, Cui and Bustamante
[47•] stretched and relaxed chicken erythrocyte chromatin
fibers with laser tweezers. In the low force regime (< 8 pN),
force/extension curves were reversible and individual fibers
could be cycled many times with identical results. From
these force/extension measurements, the internucleosomal
attractive energy is approximately 3.4 kBT at physiological
ionic strength. This value for the interaction energy suggests a mechanism for the local access of trans-acting factors
to chromatin: on average, two adjacent nucleosomes should
be found in an open (accessible) state about 4% of the time.
In the intermediate force range, the curves are hysteretic,
but repeatable, indicating reversible rearrangement of the
nucleosomes on a slower timescale than the relaxation of
the molecule. At higher forces (> 2 pN), the nucleosomal
core particles begin to disassociate from the DNA and the
force/extension curve never retraces its path.
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Outlook
Started less than a decade ago, single-molecule experiments with DNA and proteins are helping us answer questions about biological function that would be difficult or
impossible to address in bulk experiments. Further refinement of the current manipulation methods, including the
incorporation of single-chromophore fluorescence detection, is likely to occur in the immediate future. Scientists
may soon learn how to use mechanical force to control the
dynamics, time evolution and fate of chemical and biochemical reactions. Conversely, it may be possible to
understand how chemical reactions lead to the generation
of force and movement in molecular machines.
Update
In a very recent study, single-molecule twisting techniques (described above) have been used to study the
relaxation of DNA supercoils by individual topoisomerase
molecules [48]. Here, DNA plectonemes were observed
to relax, two turns at a time, by individual ATP-dependent catalytic turnovers. These relaxation events were
recorded as discrete jumps (~90 nm) in the extension of a
DNA molecule held under constant force (0.7 pN). These
experiments directly measured enzyme turnover as a
function of applied force. Unexpectedly, too much torque
decreased the turnover rate, an effect never observed with
bulk experiments.
References and recommended reading
Papers of particular interest, published within the annual period of review,
have been highlighted as:
• of special interest
•• of outstanding interest
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•
supercoiled DNA. Biophys J 1998, 74:2016-2028.
This paper, together with [12], introduces methods for studying the elastic
behavior of mechanically supercoiled DNA molecules.
14. Bustamante C, Marko JF, Siggia ED, Smith S: Entropic elasticity of
lambda-phage DNA. Science 1994, 265:1599-1601.
15. Marko J, Siggia E: Stretching DNA. Macromolecules 1995,
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16. Vologodskii AV: DNA extension under the action of an external
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17.
Grosberg AY, Khokhlov AR: Statistical Physics of Macromolecules.
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24. Rief M, Clausen-Schaumann H, Gaub HE: Sequence-dependent
•• mechanics of single DNA molecules. Nat Struct Biol 1999,
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The identification of a tension-induced melting transition at high force and its
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25. Hegner M, Smith SB, Bustamante C: Polymerization and
•
mechanical properties of single RecA-DNA filaments. Proc Natl
Acad Sci USA 1999, 96:10109-10114.
The application of mechanical manipulation techniques to the study of RecA
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