In this paper we report direct measurement of large low frequency temperature
fluctuations in double stranded (ds) DNA when it undergoes thermal denaturation
transition. The fluctuation, which occurs only in the temperature range where
the denaturation occurs, is several orders more than the expected equilibrium
fluctuation. It is absent in single stranded (ss) DNA of the same sequence. The
fluctuation at a given temperature also depends on the wait time and vanishes
in a scale of few hours. It is suggested that the large fluctuation occurs due
to coexisting denaturated and closed base pairs that are in dynamic equilibrium
due to transition through a potential barrier in the scale of
25-30k_{B}T_{0}(T_{0}=300K).Comment: 4 pages, 5 figures, Replaced with revised versio

Chatterji, Dipankar

Nagapriya, K. S.

Raychaudhuri, A. K.

English

arXiv

In this letter, we report direct measurement of large low frequency temperature fluctuations in double stranded DNA when it undergoes a denaturation transition. The fluctuation, which occurs only in the temperature range where the denaturation occurs, is several orders more than the expected equilibrium fluctuation. It is absent in single stranded DNA of the same sequence. The fluctuation at a given temperature also depends on the wait time and vanishes in a scale of a few hours. It is suggested that the large fluctuation occurs due to coexisting denaturated and closed base pairs that are in dynamic equilibrium due to the transition through a potential barrier in the scale of 25-30kBT0 (T0=300 K)

Publications of the IAS Fellows

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06
Direct observation of large temperature fluctuations during DNA thermal
denaturation
K. S. Nagapriya∗, A. K. Raychaudhuri†
Department of Physics, Indian Institute of Science, Bangalore 560 012, India.
Dipankar Chatterji
Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
(Dated: February 13, 2006)
In this paper we report direct measurement of large low frequency temperature fluctuations in
double stranded (ds) DNA when it undergoes thermal denaturation transition. The fluctuation,
which occurs only in the temperature range where the denaturation occurs, is several orders more
than the expected equilibrium fluctuation. It is absent in single stranded (ss) DNA of the same
sequence. The fluctuation at a given temperature also depends on the wait time and vanishes in a
scale of few hours. It is suggested that the large fluctuation occurs due to coexisting denaturated
and closed base pairs that are in dynamic equilibrium due to transition through a potential barrier
in the scale of 25− 30kBT0(T0 = 300K).
PACS numbers:
I. INTRODUCTION
The physics of thermal denaturation has been a topic
of investigation for the past four decades [1, 2, 3, 4, 5].
In thermal denaturation, which we call melting transition
(also known as helix-coils transition) the hydrogen bonds
between the base pairs of the double stranded DNA (ds-
DNA) break and the dsDNA separates into two single
stranded DNA (ssDNA). It occurs over a range of tem-
perature and there are distinct steps which depend on
the sequence as well as the length of the DNA (number
of base pairs) [6]. The AT segments with lower binding
energy melt at lower temperatures compared to the GC
segments. The melting of DNA starts with creation of
denaturation bubbles. As the denaturation process pro-
ceeds the number of bound pairs decrease.
In this paper we address the issue of temperature
fluctuations during the process of thermal denaturation
which we believe has not been addressed before. We
present the first direct measurement of the temperature
fluctuations in a number of double stranded DNA under-
going denaturation. These include heterogeneous poly-
mers like a 40 kbps T7 bacteriophage, 7250 bps plasmid
(both ssDNA and dsDNA), 100bp heteropolymeric ds-
DNA fragment and a 100bps homopolymer (...ATAT...).
Our experimental results show that the process of ther-
mal denaturation is associated with large low frequency
fluctuations. These grow as the temperature enters the
melting regime and die down once the melting process is
complete. At a given temperature in the melting regime,
the increased fluctuation shows a time dependence. It
first grows and then decays. The basic process of ther-
∗Electronic mail: ksnaga@physics.iisc.ernet.in
†Electronic mail: arup@physics.iisc.ernet.in, currently at S.N.Bose
National Centre for Basic Sciences, Salt Lake, Kolkata 700098
DNA
Rth
Thermal
bath
Lock-in-
Amplifier
16 Bit
ADC Card
Computer
(a)
(b)
R1 R2
Pt film
Substrate
Pt film
FIG. 1: (a) Schematic of the calorimeter, (b) schematic of
the noise measurement setup.
mal detection is explained in the schematic of figure 1.
The calorimeter consists of a substrate (heat capacity
Csub ≈ 30mJ/K) and a thin film of Pt as a thermometer.
The calorimeter is connected to a temperature controlled
copper thermal bath (heat capacity Cbath ≈ 60J/K)
through a link of thermal resistance Rth ≈ 800K/W .The
total heat capacity of the system is the heat capacity
of the sample Cs plus that of the substrate Csub. But
Cs being much less (∼ 10
−6J/K), the total heat capac-
ity is ≈ Csub. The calorimeter has a relaxation time
τ = RthCsub. We use two calorimeters connected in
a bridge arrangement which enhances the sensitivity of
the experiment and also reduces the effect of small ther-
210-19
10-17
10-15
10-13
10-11
0.01 0.1 1 10
10-19
10-17
10-15
10-13
10-11
S(
f) 
(b)
T=307K
 Sth With DNA
 Sth Empty calorimeter
 
 
S(
f) 
(V
2 /H
z)
Measured SV(f)
 With DNA
 Empty calorimeter
Increase in S(f) due to DNA melting
(c)
 
 
T = 326K
S(
f) 
(V
2 /H
z)
f (Hz)
(a)
S
th
S
Pt
+S
th
S(f)
measured
 = S
Sample
+S
Pt
+S
th
 
 
 
 
FIG. 2: (a) Cartoon of the three contributions to the
observed SV (f). (b) The observed SV (f) and Sth at
T = 307K(<< temperature where the denaturation sets in)
for empty calorimeter (open symbols) and calorimeter with
7250bp dsDNA (closed symbols) (c) the observed SV (f) and
Sth at T = 326K for empty calorimeter (open symbols) and
calorimeter with 7250bp dsDNA (closed symbols).
mal drifts. The sample (DNA) is mounted on the sub-
strate. When the strands separate out the DNA absorbs
energy from the calorimeter leading to lowering of the
calorimeter temperature in a time scale that is faster
than the thermal relaxation time (τ) of the calorime-
ter. At a longer timescale the calorimeter equilibrates
with the heat bath. In the timescale < τ , if the energy
exchanged by the DNA with the calorimeter/substrate
is ∆U , the temperature change ∆T of the calorimeter
is ∆T ≈ ∆U/Csub. As the denaturation transition pro-
ceeds, the process of energy exchange thus leads to a
fluctuation in the temperature of the calorimeter (about
its average temperature). The temperature change ∆T
of the calorimeter arising from the energy exchange leads
to a resistance change ∆R of the thermometer. The ther-
mometer being current biased, this is detected as a volt-
age change (∆V ). The voltage fluctuation thus arising
from the temperature fluctuation is given by:
〈(∆V )2〉
V 2
= (βT )2
〈(∆T )2〉
T 2
(1)
where V is the voltage across the Pt thermometer. β(=
1
R
dR
dT
) of the platinum thermometer was determined from
the calibration of the thermometers and ≈ 3.8× 10−3/K
around 300K. The thermal link of the calorimeter deter-
mines the bandwidth of the detection system which is
10-2 10-1 100
10-12
10-10
10-8
10-6
 
 
S T
(S
am
pl
e)
 (K
2 /H
z)
f (Hz)
FIG. 3: An example of the PSD of the temperature fluctua-
tion ST (Sample) for 7250 bps dsDNA at T=326K (shown by
cirles). The PSD of temperature fluctuation due to the tem-
perature fluctuation of the bath is shown by a dotted line.
like a low pass filter with a roll off at fc =
1
2piτ .
The temperature fluctuations of the calorimeter can
be characterized by the power spectral density (PSD)
and the mean square temperature fluctuation 〈(∆T )2〉.
The observed temperature fluctuation though finite is
small and a digital signal processing technique [7] was
used to eliminate the different background contributions
(described later on). Briefly, the voltage fluctuation
(and from it the temperature fluctuation) was deter-
mined by digitizing the ∆V of the thermometer as a
function of time at a digitization rate of 1024 /sec. To
reduce the contribution of the noise of the detector elec-
tronics, the voltage fluctuation was measured using a
frequency modulation technique where the fluctuation
appears as a side band around a carrier frequency(∼
230Hz) [7]. The data is digitally filtered and deci-
mated and the PSD of voltage fluctuation SV (f) was
obtained by a fast fourier transform (FFT). As described
later, from the observed SV (f), the Nyquist noise and
the 1/f noise of the thermometer (predetermined exper-
imentally using the empty calorimeter) were subtracted
out to obtain the PSD of fluctuation from the sample
SSample(f). The mean square fluctuation 〈(∆V )
2〉/V 2
=
∫ f2
f1
SSample(f)df where f1 and f2 are the lower (≈
10−3Hz) and upper (≈ 10Hz) frequency limits. The
temperature fluctuation 〈(∆T )2〉/T 2 was then obtained
from 〈(∆V )2〉/V 2 by equation 1. The determination
of 〈(∆T )2〉/T 2 through PSD was necessary for proper
subtraction of the contribution of Nyquist noise and the
thermometer 1/f noise.
A few µg to a few tens of µg of a solution of the DNA in
water are put on the substrate using a micropipette and
the solution is allowed to evaporate off. DNA with sol-
vent evaporated off harbours about 66% bound water [8]
and the conformation of the DNA does not undergo any
change. We have observed similar fluctuations near the
denaturation temperature when the experiment is carried
with DNA in a buffer. We have used DNA with solvent
3evaporated off because DNA in solution reduces the sen-
sitivity of the experiment due to the thermal mass of the
solvent.
Figure 2 shows the observed SV (f) across the Pt film
taken with an empty calorimeter as well as that taken
with a sample of 7250bp dsDNA. It can be seen from
figure 2(b) that at T = 307K both the data are nearly the
same. However at T = 326K (figure 2(c)) the observed
fluctuation with DNA is much larger. This is an example
of a typical data. The observed SV (f) can be written
(shown in figure 2(a)) as:
SV (f) = Sth + Spt + Ssample (2)
Here Sth is the white Nyquist noise given by 4kBTR
(≈ 10−18V 2/Hz) and Spt is predominantly the 1/f noise
of the Pt film resistor. The sum Sth + Spt (that con-
stitutes the background) is measured by doing the runs
on an empty calorimeter and is subtrated out from the
measured SV (f) to obtain Ssample. (Note: Sth can be
independently obtained by digitizing the out-of- phase
signal from the lock-in amplifier [7].)
In figure 3 we show an example of the PSD of the tem-
perature fluctuation ST (Sample) (obtained from Ssample
using the relation ST (sample)(f) = (βV )
−2Ssample(f)) for
the 7250 bp dsDNA at T=326K. This figure shows that
there is a large temperature fluctuation that has a pre-
dominant low frequency component. In the same figure
we also show the expected contribution from the bath
fluctuation by a dotted line [9]. It can be seen that this
is several orders smaller than the fluctuations due to the
sample.
The data were taken using two different procedures.
In the first procedure, the temperature was stabilized at
a particular value and two data sets were taken. Imme-
diately the temperature was raised to the next desired
value. At temperatures below that of the onset of melt-
ing, the observed voltage fluctuation is mostly the 1/f
noise of the thermometer. By slowly increasing the tem-
perature we find the onset temperature where there are
additional contributions to the fluctuations. Using this
procedure we obtained data as a function of temperature
for fixed wait time tw at every temperature. In the sec-
ond method, the thermal bath was stabilized at a tem-
perature where one sees significant fluctuations (which
is known from data got using the first procedure). Data
were taken at that temperature at different time intervals
until the additional fluctuations fell below the detection
limit. This way, using different wait time tw we can follow
the approach to equilibrium.
In figure 4 we show the 〈(∆T )2〉/T 2 as a function of
temperature for the different DNA samples. The figure
shows that in a certain region in temperature the ds-
DNA shows a large fluctuation which is absent in the ss-
DNA with the same sequence. We find that 〈(∆T )2〉/T 2
can be rather large, reaching close to 1ppm in the tem-
perature range of interest . In the inset of figure 4 we
show the UV absorption data for the T7 DNA. We can
see that the melting temperature matches very well with
290 300 310 320 330 340 350 360 370 380
10-16
10-15
10-14
10-13
10-12
300 315 330 345
0
20
40
60
80
100
 
 
<D
T2
/T
2 >
T (K)
 100bp heterogeneous DNA
 100bp ..ATAT..
 7250bp dsDNA
 7250bp ssDNA
 40kbps T7
Da
 (%
)
 
 
 T (K)
FIG. 4: The relative mean temperature fluctuation 〈(∆T )
2〉
T2
as a function of temperature in the different DNA samples.
0 50 100 150 200 250
0
2x10-13
4x10-13
6x10-13
 
 
<D
T2
/T
2 >
t (min)
0.0 2.0x10-10 4.0x10-10 6.0x10-10
10-3
10-2
10-1
100    Wait Time
 0 min
 40 min
 72 min
 110 min
 145 min
 183 min
 221 min
 
 
P 
(D
T)
DT2 (K2)
FIG. 5: (a) 〈(∆T )
2〉
T2
as a function of the wait time tw at 329K
for the T7 DNA. (b) the PDF of temperature fluctuation as
a function of the wait time tw at 329K for the T7 DNA. The
data are offset for clarity. The deviation from the Gaussian
behavior is seen as deviation from the straight lines.
that of increased fluctuation. Thus we can relate the
observed temperature fluctuation in the dsDNA to the
process of thermal denaturation. The fluctuation is ab-
sent both in the fully zipped and fully unzipped state.
The range in temperature where the excess noise persists
depends on the length and heterogeneity, being maxi-
mum for the T7 DNA (δT ≈ 15K ) and smallest for the
100bps homopolymer (δT ≈ 5K). It can also be seen that
while in the 100bp heteropolymer the fluctuation jumps
by more than an order of magnitude during melting, in
the 100bp homopolymer the change is much lesser. In
the case of the T7 DNA, the fluctuation during melting
is about three orders higher than that of the background
fluctuation. It is clear from these observations that both
length and heterogeniety play important roles in deter-
mining the magnitude of fluctuation. To summarize, the
4fluctuation is larger in longer DNA samples and in het-
erogenous samples.
Figure 5(a) shows the 〈(∆T )
2〉
T 2
as a function of the wait
time tw at 329K for the T7 DNA. We define wait time
as the time elapsed from when the temperature reached
a stable value. This is a typical data set at the on-
set of the fluctuation. Initially the fluctuation is very
small. It increases with time, reaches a maximum and
then decreases again. The tw dependence of the fluctu-
ation is also clearly seen in the probability distribution
function (PDF) of the temperature jumps (∆T ) shown
in figure 5(b). The PDF is shown as relative probability
vs (∆T )2. The data are offset for clarity. For Gaussian
distribution these plots should be straight lines. We see
that at tw = 0 the plot is a straight line. With larger tw
there is deviation from straight line. This deviation in-
creases with tw, reaches a maximum and then decreases
and finally the PDF again becomes Gaussian. For a given
tw the data are shown both for the positive and negative
∆T . We note that for large ∆T a small yet definite asym-
metry develops in the distribution function [12].
During the denaturation process the observed tem-
perature fluctuation 〈(∆T )2〉/T 2 is much larger than
what one would expect from the equilibrium fluctua-
tion. For a microcanonical ensemble at temperature T
and heat capacity C the temperature fluctuation is given
by 〈(∆T )
2〉
T 2eq
= kB
C
. For the calorimeter at 300K the esti-
mated relative fluctuation ≈ 4.5× 10−22. This is several
orders less than the observed fluctuation.
We would like to suggest that the observed large fluctu-
ation is a result of coexisting phases that are in dynamical
equilibrium. The transition between two phases has en-
ergetics associated with it because it involves making and
breaking of bonds leading to exchange of energy with the
calorimeter. The observed slow dynamics suggests that
the transition between the two phases involves thermal
activation across barriers. The co-existing phases can
arise from a number of sources like co-existence of loops
(denaturated) and bound segments or due to the sys-
tem being trapped in mismatched configuration. At this
time we cannot definitely identify what leads to these co-
existing phases observed in the experiment. We can get
an estimate of the average activation energy ∆E from
the wait time (tw) dependence of the fluctuation using
τ = τ0exp(|∆E|/kBT ). Here τ0 ≃ 10
−7 s is the micro-
scopic time for a basepair to move together or apart (in
the absence of tension or base pairing interactions) [10].
We find that ∆E ≃ 25− 30kBT0 where T0 = 300K. The
value of ∆E is similar to the energy at the critical force
of unzipping when the DNA is separated using force [11].
We also note that our observation is distinct from what
one expects from co-existing phases in a first order tran-
sition. The observation of co-existing phases and the
resulting fluctuation is metastable because it dies down
after a long wait time. Here the system appears to be
trapped for a long time with co-existing phases before it
reaches thermal equilibrium.
To summarize, we have made a direct measurement of
temperature fluctuations during thermal denaturation of
dsDNA. The fluctuation has a significant low frequency
component and it peaks in the temperature region of
denaturation. It is absent both in the fully closed and
fully denaturated state. The fluctuation also has a wait
time dependence and decays to zero after a sufficient wait
time. We suggest that the fluctuation arises due to co-
existing phases in dynamical equilibrium.
II. ACKNOWLEDGMENT
AKR and DC acknowledge financial support from DBT
(Government of India) for a sponsored project and Na-
gapriya acknowledges CSIR for support.
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(1985)
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(2004)
[4] M. Barbi, S. Lepri, M. Peyrard, and N. Theodorakopou-
los Phys. Rev. E 68, 061909 (2003)
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55 132, (2001)
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(2003).
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chaudhuri arXiv:cond-mat/0402130 v1 4 Feb 2004. J.
H. Scoffield, Rev. Sci. Instr. 58, 985 (1987).
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Ratliff, J. Mol. Biol. 143, 49 (1980)
[9] The response of the calorimeter to the bath temper-
ature fluctuations is that of a low pass thermal filter
with roll off at f∗ = 1
2piτbs
where τbs = RthCbath is
the time constant of bath to DNA-substrate system. The
contribution of the temperature fluctuation of the bath
to the power spectral density (PSD) can be given by
SBath(f) =
〈(∆Tbath)
2〉τbs
1+4pi2τ2
bs
f2
.
[10] S. Cocco, J. F. Marko and R. Monasson, Eur. Phys. J E
10, 153 (2003)
[11] Claudia Danilowicz, Vincent W. Coljee, Cedric
Bouzigues, David K. Lubensky, David R. Nelson
and Mara Prentiss, Proc. Natl. Sci. Acad., 100, 1694
(2003)
[12] The finite asymmetry in the PDF is a signature of non-
equilibrium nature of the system. As the system moves
towards equilibrium by absorbing heat from the sub-
strate, there are more cooling jumps than heating jumps.


Direct observation of large temperature fluctuations during DNA thermal denaturation

In this paper we report direct measurement of large low frequency temperature fluctuations in double stranded (ds) DNA when it undergoes thermal denaturation transition. The fluctuation, which occurs only in the temperature range where the denaturation occurs, is several orders more than the expected equilibrium fluctuation. It is absent in single stranded (ss) DNA of the same sequence. The fluctuation at a given temperature also depends on the wait time and vanishes in a scale of few hours. It is suggested that the large fluctuation occurs due to coexisting denaturated and closed base pairs that are in dynamic equilibrium due to transition through a potential barrier in the scale of $25 − 30k_BT_0(T_0 = 300K)$

Nagapriya, KS

Raychaudhuri, AK

Name not available

K. S.  Nagapriya

A. K. Raychaudhuri

Dipankar Chatterji

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Direct Observation of Large Temperature Fluctuations during DNA Thermal Denaturation

Direct observation of large temperature fluctuations during DNA thermal
  denaturation

Direct observation of large temperature fluctuations during DNA thermal denaturation

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