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Davide Marenduzzo1 ,Somendra M. Bhattacharjee2,3, Amos Maritan1,4 , Enzo Orlandini3 and Flavio Seno3
We report studies of the equilibrium and the dynamics of a general set of lattice models which
capture the essence of the force-induced or mechanical DNA unzipping transition. Besides yielding
the whole equilibrium phase diagram in the force vs temperature plane, which reveals the presence
of an interesting re-entrant unzipping transition for low T , these models enable us to characterize
the dynamics of the process starting from a non-equilibrium initial condition. The thermal melting
of the DNA strands displays a model dependent time evolution. On the contrary, our results suggest
that the dynamical mechanism for the unzipping by force is very robust and the scaling behaviour
does not depend on the details of the description we adopt.
The replication of DNA is a correlated process involving many proteins and other molecules [1] working at different points in space and time. An understanding of the
nature and origin of this correlation is expected to shed
light on this complex mechanism. It has recently been
shown [26] that the force induced unzipping of DNA is a
genuine phase transition different from the thermal melting transition of DNA. It was then hypothesized [2] that
the initiation of replication at the origins along the DNA,
e.g, by dnaA for E.Coli [1,7] or by the origin recognition
complex (ORC) in eukaryotes [8] is like this unzipping
near the critical threshold (with dnaA or ORC acting
as the force-inducing agent) and the resulting correlation during unzipping leads the co-operativity required
for replication.
In contrast to real biological situations, techniques
like laser tweezers [9], atomic force microscopes (AFM)
[1012] etc have been used to study DNA by pulling at
one end. This has led to strand separation by force. In
particular, AFM experiments reported hysteresis in the
unzipping process, indicating the presence of a first order transition. These mechanical unzipping experiments
have opened up new ways of thinking about DNA, just as
similar stretching experiments of DNA showed the possibility of several structures other than the most prevalent B-DNA [13]. The activities of polymerases, topoisomerase etc on single stranded DNA have now been analyzed in terms of the force they exert or the force applied
against them [1416]. What needs to be investigated, to
mimic the biological situation, is the coupling between
the opening of the strands and the subsequent events
during replication. Such a study involves the dynamics
of the unzipping process [3].
The purpose of this paper is to define a set of simpler models, in the spirit of Poland and Sheraga [17], for
which the unzipping transition can be studied exactly.
On the basis of this, the dynamics can be understood.
The proposed lattice models (bubble models: b-models)
1
Bubbles
m
f
FIG. 1. A typical configuration of the two DNA-strands as
modelled on a square lattice. Dashed lines indicate monomers
which are in contact. The quantities m and x are graphically
represented.
FIG. 2. The plot of the force vs. temperature phase diagram for the model on the directed lattice.
x1
where dn (x) represents the fixed distance partition function, i.e., the sum over all interacting pairs of directed
chains whose last monomers are at distance x [18] and
F is the free energy density. The quantity dn (x) whose
dependence has been omitted, obeys simple recursion
relations. In d = 2, on the square lattice, the recursion
relation is
dn+1 (x) = [2dn (x) + dn (x + 1) + dn (x 1)]
1 + e 1 x,1 ,
(2)
n=0
z n Zn (, f ).
(3)
This Y-model will be extremely useful to study the unzipping dynamics and it presents a phase diagram similar to the one previously obtained but, for example, with
Tm = log1 2 , f0 = 1 and fmax = 1.282143... [24] in d=2.
fc (T ) = T cosh
1 , (4)
2 1 e 1 + e
Dynamics. We now consider the dynamics of the models previously introduced, the b-model of directed walks
and the simplified Y-model. In both cases, we start from
a non-equilibrium zero-temperature initial condition
2
FIG. 3. Plot of
(5)
0.1
m(t)/N
0.01
0.001
0.0001
N=100
N=1000
N=4000
N=8000
N=12000
0.0001
0.001
0.01
0.1
10
t
4
N3
4
3
and 1 = 43 .
where N is the length of the chains and Gm,x are two scaling functions. Eq. 6 also defines the exponents d1,2 and
z1,2 for the two variables. Note that 1 = dz11 , 2 = dz22 and
that d1,2 can be obtained through equilibrium considert
t
ations as one requires m(t) N d1 and x(t) N d2 .
The crossover to the equilibrium behavior is described
by the dynamic exponents z1,2 . The possibility of the
two quantities having different relaxations is kept open
by two different exponents.
The values of the exponents in Eqs. (5) and (6) obtained from simulations, for both the Y-model and the
b-model, are shown in Table I. They were obtained by
collapsing Monte-Carlo data according to eq. (6) and by
using a recently proposed search algorithm [26] (see Fig.
3)
1e-05
vs
1e-05
1e-06
m(t)
N
100
t/N4/3
Regime
A:Y
A:b
B:Y
B:b
C:Y
seb C:b
D:Y
D:b
E:Y
E:b
annealed
<1/2
pure 2
?
<1
quenched
1
0.5
Tm
0
0.5
?
<1
1.5
Ta
2
1
1
3/4
1/2
1/2
1
3/4
1/2
1/2
1/3
1/3
d2
1/2
1/2
1/2
1/2
1
1
1
1
1
1
z2
3/2
3/2
2
2
2
2
2
2
3
3
2
1/3
1/3
1/4
1/4
1/2
1/2
1/2
1/2
1/3
1/3
1/2
1.5
z1
1
4/3
2
2
1
4/3
2
2
3
3
d1
1
1
1
1
1
1
1
1
1
1
2.5
[19]
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[18] Notice that along the x-direction the configurations are
those of two interacting random walks which never intersect each other. This differs from the model considered
by Poland and Scheraga [17] with f = 0, where the two
[20]
[21]
[22]
[23]
[24]
[25]
[26]
[27]
t
l(t)2
12
= t2 .
(m)
[28] At f = 0, N dFdm
displays also a subleading (for large
1
. This
m) entropic contribution which in d = 2 is 2m
should not affect the mapping proposed in the text except perhaps just at the critical temperature Tm .
[29] M. Doi, S. F. Edwards, The Theory of Polymer Dynamics
(Clarendon Press, Oxford) (1986).
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Solomon Annals of Probability 3, 1 (1975).