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The Mathematics of DNA Sturcture, Mechanics, and Dynamics

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DOI: 10.1007/978-1-4419-0670-0_14

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 THE MATHEMATICS OF DNA STRUCTURE,
MECHANICS, AND DYNAMICS
DAVID SWIGON∗

Abstract. A brief review is given of the main concepts, ideas, and results in the
fields of DNA topology, elasticity, mechanics and statistical mechanics. Discussion in-
cludes the notions of the linking number, writhe, and twist of closed DNA, elastic rod
models, sequence-dependent base-pair level models, statistical models such as helical
worm-like chain and freely jointed chain, and dynamical simulation procedures. Experi-
mental methods that lead to the development of the models and the implications of the
models are also discussed. Emphasis is placed on illustrating the breadth of approaches
and the latest developments in the field, rather than the depth and completeness of
exposition.

Key words. DNA topology, elasticity, mechanics, statistical mechanics, stretching.

1. Introduction. The discovery of DNA structure 55 years ago

marked the beginning of a process that has transformed the foundations
of biology and medicine, and accelerated the development of new fields,
such as molecular biology or genetic engineering. Today, we know much
about DNA, its properties, and function. We can determine the struc-
ture of short DNA fragments with picometer precision, find majority of
the genes encoded in DNA, and we can manipulate, stretch and twist in-
dividual DNA molecules. We can utilize our knowledge of gene regulatory
apparatus encoded in DNA to produce new microorganisms with unex-
pected properties. Yet, there are aspects of DNA function that defy our
understanding, mostly because the molecule is just one, albeit essential,
component of a complex cellular machinery.
From the very beginning, abstraction and modeling played a significant
role in research on DNA, since the molecule could not be visualized by any
available experimental methods. These models gave rise to mathematical
concepts and techniques for study of DNA configurations at the macro-
scopic and mesoscopic levels, which are the subject of this short review.
The paper begins with a brief description of DNA atomic-level structure,
followed by a discussion of topological properties of DNA such as knot-
ting, catenation, and the definitions of linking number and supercoiling. It
continues with an outline of continuum and discrete models of DNA elas-
ticity, focusing on local energy contributions and analysis of equilibrium
states. Modeling of long range electrostatic interactions is described next,
followed by the treatment of thermal fluctuations and statistical mechan-
ics. The paper concludes with an outline of dynamical models of DNA, and

∗ Department of Mathematics, University of Pittsburgh, 301 Thackeray Hall, Pitts-

burgh, PA 15260 ([email protected]). The work was supported by Institute for Math-
ematics and its Applications (IMA), Alfred P SLoan Fellowship and NSF Grant DMS
0516646.
293

C.J. Benham et al. (eds.), Mathematics of DNA Structure, Function and Interactions,
The IMA Volumes in Mathematics and its Applications 150,
DOI 10.1007/978-1-4419-0670-0_14, © Springer Science+Business Media, LLC 2009
294 DAVID SWIGON

Fig. 1. Side view (left) and a view along the axis (right) of DNA double helix in
atomic level detail, showing the two DNA backbones (blue and red) and the base pairs
(yellow).

a discussion of future directions in DNA research. The analysis of DNA

sequences, or modeling of the atomic-level structure and dynamics of DNA
are not covered here.
2. Background. DNA is made up of two polymeric strands composed
of monomers that include a nitrogenous base (A-adenine, C-cytosine, G-
guanine, and T-thymine), deoxyribose sugar, and a phosphate group. The
sugar and phosphate groups, which form the backbone of each strand,
are located on the surface of DNA while the bases are on the inside of the
structure (see Fig. 1). Weak hydrogen bonds between complementary bases
of each strand (i.e., between A and T and between C and G) give rise to
pairing of bases that holds the two strands together. The base pairs (bp)
are flat and stack on top of each other like dominoes with centers separated
by approximately 0.34 nm. In normal conditions each base pair is rotated
relative to its predecessor by approximately 34◦ , giving rise to the familiar
right-handed Watson-Crick double helix.
The chemical nature of the backbone gives each strand an orientation
- one end is called the 5′ -end and the other the 3′ -end. In duplex DNA
the two strands run antiparallel to each other. A closed DNA (also called
a plasmid or ring) is formed when the ends of each strand are joined by
a covalent bond. A prokaryotic organism, e.g., a bacterium, lacks nuclear
structures and its entire genome is in the form of a single closed duplex
DNA. Genomic DNA of a eukaryotic cell is contained within a nucleus and
it is divided into a number of chromosomes.
 THE MATHEMATICS OF DNA 295

The DNA of any organism must be folded and packed in a complicated

fashion in order to fit inside a cell.1 This is complicated by the fact that
DNA resists bending and twisting deformations and also has a tendency
to repel itself electrostatically. In addition to being compacted, portions
of DNA must be accessible at various moments during the lifetime of the
cell, so that the genes encoded in the DNA can be expressed and proteins
produced when necessary. The effort to understand how DNA is packed and
unpacked in cells, and how its mechanical properties influence the processes
of transcription, replication and recombination, is one of the driving forces
behind the development of mathematical models of DNA.

3. Topology. When Watson and Crick first proposed the double he-
lical model for DNA [147], they remarked:
“Since the two chains in our model are intertwined, it
is essential for them to untwist if they are to separate.
Although it is difficult at the moment to see how these
processes occur without everything getting tangled, we do
not feel that this objection would be insuperable.”
The entanglement of DNA and Nature’s ways of coping with it is the subject
of DNA topology.
In the first approximation, a closed DNA molecule can be treated as
a single closed curve in space. (The resistance of DNA to bending implies
that this curve is rather smooth.) Because during regular deformation the
bonds in DNA strands do not break, it is natural to consider the problems
of DNA knotting and catenation.2
DNA plasmids can become catenated during DNA replication, a pro-
cess in which the two strands of DNA are separated, each strand is com-
plemented by one newly formed strand, and instead of a single plasmid
one obtains two plasmids that are catenated in the same way the strands
were linked in the original plasmid. Of course, it is crucial that during
replication the catenation of the plasmids is removed so that they can be
separated and placed one in each of the daughter cells. The enzymes that
preform decatenation are called type II topoisomerases [146]. They operate
by a strand passage mechanism in which two DNA segments are brought
to a close contact, one of the segments is severed in such a way that both
backbone chains of the molecule are broken, the second segment of DNA is
passed through the gap in the first segment, and finally the severed segment
is resealed.

1 For example the DNA of E. coli is a closed DNA of circumference 1.58 mm that

must fit inside a cell of diameter 1 µm. Human genome has more that 3 billion bp, i.e.,
a linear length of 1 m. Two copies of the genome must be packed inside every cell of
human body, which range in size between 3 and 35 µm.
2 As is customary in DNA research we here use the term catenation for linking of

two DNA molecules and reserve the term linking for topological relation between two
DNA strands.
296 DAVID SWIGON

DNA knotting rarely occurs naturally, but it has been achieved in a

laboratory using the aforementioned topoisomerases and also DNA recom-
binases, enzymes that cut two DNA molecules at specific recognition sites
and then switch and reconnect the ends. Because a given recombinase only
forms knots of certain types, knot theory, and in particular tangle analysis,
has been applied to the problem of determining the structure and function
of these enzymes [55, 47, 141]. The changes in knot type resulting from
strand passages have been classified and the probabilities of such passages
have been estimated [46, 70]. Knotting also occurs in DNA closure experi-
ments in which open (linear) DNA segments spontaneously cyclize to form
closed DNAs. Since DNA thermally fluctuates, the probability of forming
a knot can be related to the probability that a random configuration of a
phantom DNA (i.e., a DNA allowed to pass through itself) has the topology
of a knot (see Section 6). It was shown that in the limit of length going
to infinity a randomly cyclized polygon will be knotted with probability
1 [48].
A closed DNA molecule can also be viewed as a collection of two
continuous curves - the DNA strands. This is because the biochemical
nature of the strands guarantees that during closure ceach strand of the
DNA can only bind to itself. The axial curve of a closed DNA, which can
be thought of as the curve passing through the centroids of the base pairs,
is also a closed curve.
For any two closed curves C1 and C2 one can define a quantity, called
the linking number Lk, that characterizes how the curves are interwound
with each other. The linking number can be found by examining a generic
projection of the two curves on a plane (a projection in which every crossing
of one curve with the other is transversal). First, orientation is assigned
to each curve and a sign to each crossing of one curve over the other, in
accord with the convention shown in Fig. 2A.
The linking number Lk is then taken to be one half the sum of all signed
crossings (see Fig. 2B and C); it is a topological invariant of the two curves,
i.e., a number independent of homotopic deformations of the curves that do
not pass one curve through the another. In DNA research it is customary
to take C1 to be the axial curve of the molecule and C2 one of the backbone
chains.
For differentiable curves, a formula for linking number in terms of a
double integral was found by Gauss [42]

1 t1 (s1 ) × t2 (s2 ) · [x1 (s1 ) − x2 (s2 )]

I I
Lk(C1 , C2 ) = ds2 ds1 , (3.1)
4π C1 C2 |x1 (s1 ) − x2 (s2 )|3

where Ci is defined by giving its position xi (s) in space as a function of the

arc-length s, and ti (s) = x′i (s) = dxi (s)/ds .
There are two geometric properties of curves that are intimately re-
lated to the linking number. The first property, called the writhe W r,
 THE MATHEMATICS OF DNA 297

+ –

B C +
+ + +
+ +
+ + +
+ Lk = 8
+
+ +
– +
Lk = 1
+ +
+ +
+

Fig. 2. The linking number of two curves. A: A sign convention for crossings.
B and C: Examples of calculation of Lk for two curves.

Wr ~ 1

– –

Wr ~ –2
Wr = 0 for any planar
non-intersecting curve + –

Wr ~ 0

Fig. 3. The writhe of a curve.

characterizes the amount of chiral deformation of a single curve. To find

W r, one assigns orientation to the curve and computes the sum of signed
crossings in a planar projection along every direction; W r is equal to the
average of such sums over all projections. Examples of curves with various
values of W r are shown in Fig. 3. For a closed differentiable curve C a
formula for W r analogous to (3.1) exists:
1 t(s1 ) × t(s2 ) · [x(s1 ) − x(s2 )]
I I
W r(C) = ds2 ds1 . (3.2)
4π C C |x(s1 ) − x(s2 )|3
Alternative formulae relating W r to the area swept by the vector x(s1 ) −
x(s2 ) on a unit sphere when traversing C, or the difference in writhe of two
closed curves can be found in [57, 1].
298 DAVID SWIGON

The second property, called the twist T w, measures the winding of

one curve about the other. The most familiar definition requires that the
curves under consideration be differentiable; the twist of C2 about C1 is
then
1
I
T w(C2 , C1 ) = [t1 (s) × d(s)] · d′ (s)ds (3.3)
2π C1
where d(s) = x2 (σ(s)) − x2 (s) is taken to be perpendicular to t1 (s).
Neither the writhe nor the twist are topological invariants. However,
it follows from the results of Calugareanu [29] and White [149] that the
linking number of two closed curves is the sum of the writhe of one curve
and the twist of the second curve about the first:
Lk(C1 , C2 ) = W r(C1 ) + T w(C2 , C1 ). (3.4)
This relation has important implications for a closed DNA molecule. Since
in a closed duplex DNA Lk is invariant, any change in T w, which may
come about as a result of binding of DNA to proteins (such as histones)
or intercalating molecules, will induce a corresponding opposite change in
W r. Alternatively, DNA mechanics tells us that if Lk is changed by cutting
and resealing of DNA strands, that change will be partitioned into a change
in T w and a change in W r of equal signs. In DNA research an increase
in the magnitude of writhe, accompanied by an increase in the number of
crossings of the molecule, is called supercoiling, and a molecule with high
|W r| is known as supercoiled DNA.
Supercoiling is a characteristic deformation of a closed DNA that
can be observed and quantified experimentally. Supercoiling can be ei-
ther detrimental or beneficial to a cell, depending on its magnitude and
circumstances. Each cell contains enzymes topoisomerases that regulate
DNA supercoiling by constantly adjusting the linking number. Since the
linking number of a closed DNA molecule remains constant during any de-
formation of the molecule that preserves chemical bonding, it can therefore
be changed only by mechanisms in which chemical bonds are disrupted.
There are two such mechanisms: (i) a relaxation, in which a bond in one of
the backbone chains is broken, one end of the broken backbone is rotated
about the other backbone by 360◦ and the broken bond is repaired, or (ii)
a strand passage, described earlier, in which one segment of DNA is passed
through a gap created in the second segment. Type I DNA topoisomerases
use the first mechanism and hence change Lk by by ±1, while type II
topoisomerases use the second mechanism and change Lk by ±2.
Natural questions arise, such as what is the configuration of super-
coiled DNA with prescribed Lk, what is the probability of occurence of
topoisomers or knot types, or how much time does it take for a segment
of DNA to form a closed molecule. These questions can be answered with
the help of theories of DNA elasticity, statistical mechanics and dynamics,
described in subsequent sections.
 THE MATHEMATICS OF DNA 299

A B C
t
d

Fig. 4. Schematic representations of DNA. A: a wireframe representation of the

atomic level structure. B: continuum elastic rod. C: base-pair level description

4. Elasticity. The elasticity of DNA is governed by interactions be-

tween the atoms of the molecule and by interactions of the molecule with
the surrounding solvent. The primary interaction responsible for DNA
bending stiffness is base stacking, a tendency of the flat hydrophobic nu-
cleotides to aggregate in such a way as to minimize water accessible sur-
face [115]. Such a stacking occurs even in the absence of backbone con-
nections. The twisting rigidity of the molecule is due to the presence of
two backbone polymeric chains. The elastic properties are signigficantly
affected by electrostatic interaction between negatively charged phosphate
groups in the backbone, which are strongly modulated by ionic properties
of the surrounding solvent.
Continuum models. The simplest model of DNA deformability
treats DNA as an ideal elastic rod, i.e., thin elastic body that is inextensi-
ble, intrinsically straight, transversely isotropic and homogeneous [12, 13].
The configuration of DNA is described by giving the position x(s) of its
axial curve in space and its twist density Ω(s) as functions of the arc-length
s, where Ω(s) = [t1 (s) × d(s)] · d′ (s) with d(s) a vector pointing from the
axial curve to one of the backbones (see Figure 4A and Eq. (3.3)). The
elastic energy of the rod is given by
L
1
Z

2
Ψ= Aκ(s)2 + C Ω(s) − Ω̄(s) ds (4.1)
2 0

where κ(s) = |t′ (s)| is the curvature of the axial curve and Ω̄(s) is the twist
density in a stress free state. The bending modulus A and the twisting mod-
300 DAVID SWIGON

ulus C characterize the elastic properties of DNA. The accepted “average”

value of A for B-DNA under standard conditions is 50 kT ·nm [66, 23] and
C is between 25 kT ·nm and 100 kT ·nm [69, 121, 131], (here kT , an widely
used unit of energy in molecular biology, is the product of Boltzmann con-
stant k and absolute temperature T ).
A rod with the energy (4.1) obeys the classical theory of Kirchhoff [75,
51], which implies that in equilibrium ∆Ω = Ω(s) − Ω̄(s) is constant and
t(s) obeys a differential equation,

A(t × t′′ ) + C∆Ωt′ = F × t (4.2)

with the constant F playing the role of a force. Solutions of (4.2) have
been obtained in a closed form in terms of elliptic functions and integrals
[82, 139].
Although each solution of (4.2) corresponds to an equilibrium config-
uration of the rod, from a practical point of view it is important to know
which of these solutions are locally stable in the sense that any small per-
turbation of the configuration compatible with the boundary conditions
leads to an increase in elastic energy. Stability theory for closed Kirchhoff
elastic rods has been developed by a number of researchers using the frame-
work of calculus of variations; necessary conditions (the slope of the graph
of Lk versus W r for a family of equilibrium configurations [88, 140, 41]),
suficient conditions (the absence of conjugate points [96, 67]), or general
observations about stability of rod configurations [84].
Bifurcation theory of straight rods subject to tension and twist is a
classical subject [92, 3, 136, 105] and bifurcations of a closed rod with a
given linking number have also been analyzed [155, 87, 49]. The general
conclusion is that the straight or circular solution of (4.2) is stable for Lk
smaller than a critical value, while other solutions of (4.2) can be stable
only if |W r| is small and C/A is larger than a critical value that depends
on the boundary conditions.3 Experiments with steel wires, which have
C/A < 1, confirm this result [137]. Consequently, the solutions of (4.2)
cannot represent minimum energy configurations of supercoiled DNA with
high |W r|, because such configurations show self-contact, i.e., a contact
between the surfaces of two distinct subsegments of the rod.
In any theory of rod configurations with self-contact, the forces exerted
on the surface of DNA can be accounted for as external forces in the balance
equations. The existence of a globally minimizing configuration for general
nonlinearly elastic rods with self-contact has been demonstrated [62, 120].
In the case of an ideal elastic rod, segments of the rod between points of
contact can be treated using Kirchhoff’s theory, and by putting together
explicit expressions for contact-free segments and balance equations for
forces at the contact points one obtains a system of algebraic equations

3 This critical value is 11/8 for closed rods subject to twisting.

 THE MATHEMATICS OF DNA 301

that can be solved to obtain a configuration of DNA plasmid with self-

contact [88, 74, 49, 39]. The ideal rod model with self-contact has been
applied to the study of DNA supercoiling [41, 39], configurations of straight
DNA subject to stretching and twisting [132], and configurations of DNA
loops in mononucleosomes [133].
The ability to account for self-contact is critical if one intends to study
equilibrium configurations of knotted DNA, for it has been shown that
knotted contact-free equilibrium configurations of closed DNA have the
topology of torus knots and are all unstable [84]; examples of such config-
urations can be found in [88, 49, 129]. Thus any stable configuration of
a DNA knot shows self-contact; minimum energy configuration of a DNA
plasmid with the topology of a trefoil knot as a function of Lk has been
found [40].
Departures from ideality, such as intrinsic curvature, bending aniso-
tropy, shearing, or coupling between modes of deformation can be treated
using special Cosserat theory of rods (see, e.g., [2]). In that theory the
configuration of the rod is described by giving, as functions of the arc-
length s, its axial curve x(s) and an orthonormal triad (d1 (s), d2 (s), d3 (s)),
which is embedded in the cross-section of the rod in such a way that d3 is
normal to the cross-section. The vector d3 (s) need not be parallel to x′ (s)
and hence the theory can describe rods with shear. The elastic energy is
expressed in terms of the variables (κ1 , κ2 , κ3 , ν1 , ν2 , ν3 ) describing local
deformation of the rod, i.e.,
Z L
Ψ= W (κ κ, ν − ν¯)ds
κ − κ̄ (4.3)
0

where

d′i (s) = κ (s) × di (s) (4.4)

νi (s) = x′i (s) · di (s). (4.5)

When this theory is applied to DNA research [93, 6, 58], it is usually

assumed that DNA is inextensible and unshearable (i.e., d3 (s) = x′ (s) ),
and shows no coupling; consequently the energy density is given by

2W (κ κ) = K1 (κ1 − κ̄1 )2 + K2 (κ2 − κ̄2 )2 + K3 (κ3 − κ̄3 )2 .

κ − κ̄ (4.6)

Variational equations in the Cosserat theory are identical to the bal-

ance equations in the Kirchhoff theory:

F′ + f = 0 (4.7)
M′ + x′ × F + m = 0. (4.8)

These equations cannot be solved explicitly and therefore are usually inte-
grated numerically. Accurate numerical schemes employ a parametrization
302 DAVID SWIGON

A B

Tilt T Roll T Twist T

Shift U Slide U Rise U

Fig. 5. Parameters characterizing the base-pair step.

for (d1 , d2 , d3 ) using Euler angles or Euler parameters and reformulate the
problem as a set of differential equations for these parameters [49]. The
practical problem of computing DNA configurations using the Cosserat
model requires one to determine the unstressed values κ̄ κ and elastic moduli
K1 , K2 , K3 for a given DNA sequence, which can be done, for example,
by comparing computed equilibria with the results of a cyclization exper-
iment [95]. Cosserat theory has been employed to show that intrinsically
curved DNA circles and DNA segments with fixed ends can have multiple
stable contact-free equilibrium configurations [58, 142, 68], and was also
used to compute the structure of protein-induced DNA loops [7, 65].
Discrete models. Discrete models have been developed to model
sequence-dependent elasticity of DNA in a way that closely resembles de-
tailed DNA structure. The most common discrete models treat DNA as a
collection of rigid subunits representing the base-pairs (see Figure 4C). This
description has long been used by chemists to characterize DNA crystal
structures [28, 107]. The DNA configuration is specified by giving, for each
base pair, numbered by index n, its location xn in space and its orientation
described by an embedded orthonormal frame (dn1 , dn2 , dn3 ). The relative
orientation and position of the base pair and its predecessor are specified by
six kinematical variables (θ1n , θ2n , θ3n , ρn1 , ρn2 , ρn3 ), termed, respectively, tilt,
roll, twist, shift, slide, and rise (see Fig. 5). In the simplest, so-called dinu-
cleotide models, the elastic energy Ψ is taken to be the sum of the base-pair
step energies ψ n , each of which is a function of the kinematical variables,
i.e.,

N
X −1
Ψ= ψ n (θ1n , θ2n , θ3n , ρn1 , ρn2 , ρn3 ) (4.9)
n=1
 THE MATHEMATICS OF DNA 303

Table 1
Sequence-dependent variability of DNA elastic properties.

Quantity Range Units

Intrinsic bending 0.4 < θ̄2 < 5.1 deg
Bending anisotropy 1.3 < F11 /F22 < 3.0
Twisting/bending ratio 0.7 < F33 /F22 < 2.7
Twist-roll coupling 0.1 < F23 /F22 < 0.6
Twist-stretch coupling −0.8 < G33 < −0.25 kT /(deg · Å)
Shearing anisotropy 0.7 < H22 /H11 < 2.8

where the function ψ n depends on the base-pair composition of the nth

step, and is commonly assumed to be a quadratic function
3 3
1 X X XY n n
ψn = F ∆θi ∆θj + GXY n n XY n n
ij ∆θi ∆ρj + Hij ∆ρi ∆ρj . (4.10)
2 i=1 j=1 ij

Here XY is the nucleotide sequence (in the direction of the coding strand)
of the nth base pair step, ∆θin = θin − θ̄iXY , ∆ρni = ρni − ρ̄XY i are the
deviations of variables from their intrinsic values θ̄iXY , ρ̄XY
i , and FijXY ,
XY XY
Gij , Hij are the elastic moduli. A discrete version of the ideal elastic
model can be obtained by taking
     
0 0 A 0 0
θ̄XY =  0  , ρ̄XY =  0  nm, F XY =  0 A 0  , (4.11)
34◦ 0.34 0 0 C
GXY = 0, H XY → ∞. (4.12)

Empirical estimates of intrinsic values and elastic moduli have been

deduced from the averages and fluctuations of base-pair step parameters in
high-resolution DNA protein complexes [108] after normalization so that
the persistence length of mixed-sequence DNA matches observed values
(circa 500Å). Departures from ideal behavior found by Olson and collabo-
rators [108] and listed in Table 1 include intrinsic bending (in the roll vari-
able), bending anisotropy, inhomogeneity in twisting to bending stiffness
ratio, twist-roll coupling, twist-stretch coupling, and shearing anisotropy.
Analysis of X-ray crystal structures and NMR experiments yields the most
detailed information to date about DNA structure and flexibility. Other
experimental methods, such as cyclization [43, 8], fluorescence resonance
energy transfer (FRET) [111], gel mobility [20], or single-molecule stretch-
ing [27, 23] and twisting [24, 130], have been used to examine elastic behav-
ior of longer segments in which the effects of individual base-pair steps are
304 DAVID SWIGON

averaged over. The sequence-dependent nature of DNA deformability has

been independently confirmed by research aimed to deduce DNA elastic
properties from molecular dynamics simulations [17, 52].
For the dinucleotide model with energy (4.9) variational equations
have been derived [38] and equilibrium configurations for plasmids of vari-
ous compositions and end conditions have been found [38, 109], including
(i) multiple equilibria of ligand-free DNA o-rings (plasmids that are cir-
cular when stress-free), (ii) minimum configuration of DNA o-rings with
bound intercalating agents (iii) optimal distribution of intercalating agents
that minimizes elastic energy of DNA o-rings, (iv) collapsed configurations
of DNA o-rings subject to local overtwisting, (v) minimum energy configu-
rations of intrinsically straight DNA plasmids with various distributions of
twist-roll coupling, (vi) minimum energy of S-shaped DNA subject to local
overtwisting. The theory has been extended to account for electrostatic
repulsion and thermal fluctuations and applied to the study of minimum
energy configurations and looping free energies of LacR-mediated DNA
loops [134], and minimum energy configurations of free segments of pro-
moter DNA bound to Class I and Class II CAP dependent transcription-
activation complexes [86].
There have been suggestions that the local energy of DNA deforma-
tions may depend on the composition, or even the deformation, of more
than just the immediate base-pair neighbors, for example
N
X −1
Ψ= ψ n (θn , ρn , . . . , θn+k , ρn+k ). (4.13)
n=1

Trinucleotide and tetranucleotide models have been proposed to account

for some DNA structural features [110], and they also seem to better rep-
resent averaged DNA properties extracted from molecular dynamics sim-
ulations [17, 52]; the mechanical theory of such models has not yet been
constructed.
5. Electrostatics. DNA has a net negative charge that resides pri-
marily at the phosphate groups on the DNA backbone (see Figure 6).
Electrostatic interaction is an integral component of DNA response to
deformations but its role in DNA is not completely understood, mainly
because it is difficult to decouple such an effect from purely elastic local
contributions. The effect of electrostatics is modulated by the ionic con-
ditions of the solvent, such as its dielectric properties and the valence of
counterions. The two most important effects of electrostatic repulsion ap-
pear to be the increase in DNA effective diameter [144, 118] and increase
in DNA bending stiffness [10].
In accord with the classical theory of electrostatics, in the absence of
counterions (charged particles in the solution) the electrostatic energy of
DNA with M charged sites would be given by
 THE MATHEMATICS OF DNA 305

Fig. 6. Negative charge on DNA is located at the phosphate groups (red).

M−1 M
(2δ)2 X X 1
Φ= mn
(5.1)
4πǫ m=1 n=m+1 |r |

where rmn = xm − xn is the position vector connecting the charges m and

n, δ is the elementary charge, and ǫ is the permittivity of water at 300K.
In the presence of counterions this long-range electrostatic interaction
will be screened. Two main theories have been proposed to describe the
effect of screening by monovalent counterions. The Poisson-Boltzmann
theory replaces counterions by a continuous charge density and assumes
that the this density is proportional to the Boltzmann factor of the elec-
trostatic potential φ, which, after substituting in the classical equation of
electrostatics, obeys the equation
 qφ(x)

∇(ǫ(x)∇φ(x)) = −4π ρ(x) + qe− kT (5.2)

where ǫ is the dielectric, ρ is the charge density of DNA, q is the charge

of counterions, and kT is Boltzmann constant times temperature. The
electrostatic energy of DNA is then
M
δ X
Φ= φ(xm ). (5.3)
2 m=1

It was shown by Kirkwood [76] that the PB equation ignores the distinc-
tion between two different types of averages of the potential, which causes
serious errors in the theory of strong electrolytes. Nonetheless, PB theory
remains popular in studies of DNA at the atomic scale level [59, 19, 21, 138].
Alternative theory, proposed by Manning [94] and called the coun-
terion condensation theory, separates the counterion distribution around
306 DAVID SWIGON

DNA into two parts: some counterions condense on the DNA and becomes
immobile in all but one direction (along the DNA), the rest of the coun-
terions remain mobile. The condensed portion of counterions neutralizes
DNA charge to 24% of the original value, independent of the ionic strength.
The weakened DNA charge can now be treated using Debye-Huckel the-
ory (a linearized version of Poisson-Boltzmann theory) and yields, in place
of (5.1) or (5.3), the following expression for DNA electrostatic energy:
M−1 M mn
(2δ)2 X X e−κ|r |
Φ= (5.4)
4πǫ m=1 n=m+1 |rmn |

where δ is now the net effective charge of 0.24e− and κ is the Debye screen-
ing parameter, which, for monovalent salt such as NaCl, depends on the
√ −1
molar salt concentration c as κ = 0.329 cÅ .
The counterion condensation theory has been included in some cal-
culations of minimum energy configurations of DNA using continuum and
discrete elastic models. The electrostatic energy gives rise to an additional
term in the balance equation for forces, accounting for the force of repulsion
between a DNA base pair and the rest of the molecule. For simplicity, the
charges are usually assumed to be located in the centers of base-pairs, as
opposed to the phosphate groups. The singularity in (5.4) makes it difficult
to account for electostatics by a continuous charge density and hence, even
in continuum models, the charges are generally assumed to be discrete and
the resulting equations are solved numerically. The cases studied to date
include superoiled configrations of DNA plasmids [148], the effect of elec-
trostatics on LacR-induced DNA loops [6, 7], and the straghtening effect
of electrostatics on intrinsically curved DNA segments [18].
Vologodskii and Cozzarelli have employed an alternative method to ac-
count for electrostatic repulsion of DNA, the so called hard-core repulsion
model in which no energy is added to the elastic energy of DNA but con-
figurations with intersegmental distance smaller than some effective DNA
radius R are inadmissible [144]. They found that such a model yields ac-
curate results in Monte Carlo simulations of the dependence of knotting
probability on on ionic strength, in the sense that R can be calibrated for
each ionic strength and with this calbibrated value their statistical model
of DNA was able to predict correctly knotting probability for various types
of experiments.
The effects of multivalent counterions are much more difficult to treat
because such ions have the ability to interact with more than one charged
phosphate group. They have been hypothesized to bridge DNA segments
in DNA condensation or to participate in charge-neutralization induced
DNA bending [72, 80].
6. Statistical mechanics. A long molecule of DNA in solution is
subject to thermal fluctuations that perturb its shape away from the mini-
mum energy configuration. Statistical mechanical theories of DNA account
 THE MATHEMATICS OF DNA 307

for fluctuations by assuming that each attainable configuration has a proba-

bility of occurence proportional to the Boltzmann factor of its total energy.
Depending on the length and level of detail one seeks to describe, a fluc-
tuating DNA can be treated using one of several polymer chain models:
a freely-jointed chain, a worm-like chain, or a helical worm-like chain. In
each of these models a DNA molecule is represented by a chain with ver-
tices xn N
n=1 . The models are characterized by the dependence on N of the
mean square end-to-end distance < R2 >=< |xN − x1 |2 > , end-to-end
(or radial) probability distribution function ρ(R), or the closure (looping)
probability P (R = 0, t1 = tN ).
The freely-jointed chain represents DNA as a chain of N rigid segments
of length l, referred to as the Kuhn length, with uncorrelated orientations,
i.e., |xn+1 − xn | = l, < (xn+1 − xn ) · (xn − xn−1 ) >= 0 . (It corresponds
to an unbiased random walk of equidistant steps in 3-space.) In the limit
as N → ∞, one finds that [53]:
3/2 
3R2
 
2 2 3
< R >→ N l , ρ(R) → exp − (6.1)
2πN l2 2N l2
provided that the orientation of the first segment is random, which implies
that the root mean squared end-to-end distance scales with the square root
of the length of the chain.
The worm-like chain accounts for bending rigidity of DNA. It can be
derived in two ways - as a Kratky-Porod limit of a freely rotating chain
with fixed angles between neighboring segments [81], or using Landau and
Lifshitz method of averaging of configurations of an elastic rod with bending
energy but no twisting energy (i.e., with C = 0 in (4.1)) [83]. In both cases
one obtains the following expression:
  L2 (1−L/3P ) for L << P
2
< R >= 2P L−P (1−e −L/P
) ∼= (6.2)
2P (L−P ) for L >> P
where the persistence length P is a constant characterizing the stiffness of
DNA; it is related to the bending rigidity A as A = P kT . The two limits
of < R2 > in expression (6.2) tell us that a DNA that is much shorter than
P behaves essentially as a stiff rod, while a DNA that is much larger than
P behaves as a freely jointed chain with segments of length l = 2P .
The helical worm-like chain (HWLC) generalizes the worm-like chain
model by accounting for the twisting deformation of DNA [123]. The par-
tition function for HWLC is given by the path integral
Z
Z(d(L), t(L), x(L)|d(0), t(0), x(0)) = exp(−Ψ/kT )Dx(.)Dd(.) (6.3)
S

with Ψ as in equation (4.1) and integration taken over the set S of all con-
figurations (x(.), d(.)) with the specified end-conditions. For closed DNA
plasmids these end-conditions are:
308 DAVID SWIGON

d(L) = d(0), t(L) = t(0), x(L) = x(0) (6.4)

and an additional constraint of prescibed Lk is imposed on the contigura-

tions in S which yields Z = Z(Lk). This path integral cannot be evaluated
explicitly but in various cases of interest approximate solutions have been
obtained by asymptotic expansion [123, 99], Metropolis Monte-Carlo sam-
pling [56, 90, 60], saddle-point expansion about the minimum energy con-
figuration [156], or numerical integration on Euler motion group [34]. The
integral (6.3) can also be evaluated using techniques developed for solving
the Schrödinger equation [103, 22].
The HWLC theory has been employed in the study of DNA super-
coiling and topoisomer distribution. Experimental results indicate that
when DNA plasmids are reacted with type I topoisomerase [69], or are ran-
domly formed by cyclization [125], one obtains a distribution of plasmid
topoisomers that are identical apart from a difference in Lk. The resulting
distribution of Lk is approximately Gaussian

P (Lk) ∼
= exp(−G(Lk)/kT ), G(Lk) = K(N )(Lk − N/h)2 , (6.5)

where N is the plasmid size (in bp) and h is the helical repeat length
( 10.5 bp/turn). Theoretical predictions of this distribution [89] and the
dependence of K on N by HWLC theory [79] were found to be in excellent
agreement with experimental results. The shape of supercoiled configura-
tions corresponding to high values of excess link ∆Lk = |Lk − N/h| was
found to be of plectonemic nature with multiple terminal loops [119, 98].
The DNA cyclization experiment is one of the most sensitive methods
for measuring DNA structural and elastic properties in solution [126, 43].
In the experiment identical linear DNA molecules with complementary free
ends are reacted with an enzyme ligase that connects the free ends. The
molecules can connect in two ways: (i) the two ends of a single molecule
can join to form a cyclized molecule, or (ii) the ends of two molecules can
dimerize to form a linear DNA segment of twice the length. The rates of
cyclization and dimerization can be measured and their ratio, called the
Jacobson-Stockmayer factor (or the J factor), can be plotted as a function
of N to obtain the characteristic J curve [126, 124, 43, 8]. The J factor has
been shown to be proportional to the probability of cyclization, which is an
equilibrium quantity that can be computed using a HWLC model. Thus,
material properties of DNA can be estimated by fitting the measured data
with a computed J curve [123, 156, 90].
During a closure experiment DNA molecules may become knot-
ted [122]. The probability of DNA knotting can be estimated using HWLC
model [113], and the results are sensitive to DNA electrostatic repulsion,
both in the magnitude of the screening and the treatment of electrostatic
interaction [144]. DNA knotting is also produced by the action of topoiso-
merases of type II and type I (on nicked DNA), which has been used to elu-
cidate the function of those enzymes. An important issue related to type II
 THE MATHEMATICS OF DNA 309

topoisomerases is that they are very efficient in removing knots, cate-

nations, and supercoils well below the thermodynamic equilibrium [114],
which is made possible by the fact that they utilize ATP, a source of energy,
during their action. A definite mechanism of how a small enzyme manages
to recognize a global property of DNA as a knot type has not yet been found
although several hypotheses have been proposed [145, 152, 25]. DNA knot-
ting probability within the confined volume of bacteriophage head has also
been studied using FJC model [5, 101].
Another area of DNA research that has greatly benefitted from and
stimulated the development of statistical modeling is the area of single-
molecule DNA manipulation experiments. Single-molecule DNA stretching
and twisting experiments represent breakthroughs in the study of DNA
properties because they allow researchers to track time-dependent behavior
of individual molecules as opposed to ensemble averaged quantities. In
these experiments one end of DNA is attached to a fixed object, for example
the microscope slide or a bead that is held by a pipette, while the other end
is attached to a bead that is captured and manipulated by an optical or
magnetic trap. By varying the distance between the beads experimenters
can stretch the captured molecule, and by rotating the magnetic bead they
can twist the molecule.
Results of DNA stretching experiments [128, 26] are in excellent accord
with theoretical predictions using WLC and HWLC models in ranges of
loading that preserve the duplex DNA structure. The dependence of force
on extension for a torsionally relaxed molecule of length L is fitted very
accurately by the formula [99]

FP 1 x −2 1 x
= 1− − + (6.6)
kT 4 L 4 L

where P is the persistence length. DNA twisting experiments [131, 30] have
also been found in close agreement with HWLC predictions [103, 102, 22].
When large forces and/or twist is imposed on DNA, the molecule changes
its secondary structure into alternative structures - overstretched DNA
[127, 97], melted duplex with separated strands [131], or Pauli structure
with backbone on the inside and bases on the outside [130] - none of which
are governed by the HWLC theory.
The HWLC theory is built on the simplest, ideal model of DNA elas-
ticity. An equivalent statistical mechanical theory has been developed also
for sequence-dependent base-pair level DNA model [61]. Various cases of
interest for DNA with sequence dependent properties have been analyzed,
such the statistics of polymer chains with intrinsic bends or elastic inhomo-
geneity [112], the looping free energy of LacR-mediated DNA loops [134, 6],
the free energy of LacR loops in the presence of CAP [135], the effect of
intrinsic curvature, anisotropy, or twist-roll coupling on ring closure prob-
ability [44].
310 DAVID SWIGON

7. Dynamics. Dynamical models of DNA have been constructed to

help us uncover time-dependent features of DNA behavior, such as pertur-
bation relaxation times, rates of transition between configurational states,
rates of closure and loop formation, etc. The primary interactions control-
ing DNA dynamics are hydrodynamic resistance and thermal fluctuations.
Dynamical models of DNA can be divided into two groups - those based
on theories of elastic rods and those based on theories of polymer dynamics.
Dynamical theories of rods can be formulated within both Kirchhoff and
special Cosserrat theories (see, e.g., [2]). Suppose that the rod is described
by giving, as functions of the arc-length s and time t, its axial curve x(s, t)
and an orthonormal triad (d1 (s, t), d2 (s, t), d3 (s, t)) embedded in the cross-
section. The equations of motion are given by
Ṗ = F′ + f (7.1)
′ ′
Ṙ = M + x × F + m (7.2)
where dot stands for the time derivative, P and R are the linear and
angular momentum of the cross-section, F and M are the contact forces
and moments applied on the cross-section at s by material with arc-length
greater than s, and f and m are the external forces and moments. The
precise form of P and R and the constitutive equations for F and M depend
on the type of rod under consideration and the approximations taken. The
terms f and m account for hydrodynamic resistance.
When f = m = 0, exact solutions of (7.1)–(7.2) can be obtained for
special motions, called traveling waves, in which the shape of the axial curve
remains invariant and its apex is moving with constant velocity along the
rod [4, 37, 50]. Other results include perturbation analysis of looping and
ring collapse transitions [63, 64]. Hydrodynamic resistance was accounted
for in numerical analyses of the formation of supercoiled states of over-
twisted rings plasmids [77, 91]. Some researchers have used the solution
of dynamical equations as a method for finding stable equilibrium config-
urations of DNA [6, 65]. With the exception of [6], the studies of DNA
dynamics using continuum models published to date ignore thermal fluctu-
ations but, nonetheless, yield useful information about the transition from
circular to supercoiled DNA configurations.
In polymer dynamics models, a DNA molecule is replaced by a collec-
tion of rigid spheres of radius R with centers at {xn }N
n=1 that are connected
by elastic linkages simulating the bending and twisting rigidity of DNA. The
total energy E of the chain is composed of stretching, bending, twisting,
and electrostatic energy components. Because of high hydrodynamics re-
sistance of the solvent, the molecule is assumed to move by diffusion which
results in a Brownian type dynamics. At each time step ∆t the positions
of the beads change in accord with the following formula
∆t X mn
xn (t + ∆t) = xn (t) − D (t)∇xn E + Rn (t) (7.3)
kT m
 THE MATHEMATICS OF DNA 311

where the Rotne-Prager diffusion tensor Dmn accounts for hydrody-

namic coupling between beads m and n, and the random displacements
Rn (t) obey

< Rn (t) >= 0, < Rn (t)Rn (t)T >= 2∆tDmn (t). (7.4)

Brownian dynamics has been employed in the study of DNA tumbling

and twisting, where computed results were compared with data coming
from fluorescence depolarization experiments [91]. It has also been used to
study the dynamics of DNA supercoiling [31, 78], and the dependence of site
juxtaposition in DNA on the distance between sites [73, 71] and supercoiling
density [32]. It was found, for example, that at low salt juxtaposition times
are accelerated by a factor of 10 or more due to supercoiling [73]. DNA
supercoiling was found [32] to occur on the timescale of 3–6 µs starting
from a planar closed molecule, with an initial phase of 1–2 µs during which
toroidal supercoiling appeared, followed by a conversion into a plectonemic
supercoiling. The effect of intrinsic curvature on DNA supercoiling [33]
and looping [100] has also been studied
8. Conclusion. This survey outlines the main mathematical results
and models used by researchers to discuss DNA deformability and structure
at the macroscopic level, covering a whole range of topological, geometrical,
mechanical, electrostatic, statistical and dynamical models. There are few
important topics in DNA research that do not naturally fit under the head-
ings above, and one of them is the connection between DNA denaturation
and supercoiling. It is known that although DNA molecule is stable under
the conditions mimicking the intracellular environment, the base-pairing
interaction can be disrupted, in a process called denaturation, as a result
of a high temperature or mechanical deformation such as large untwisting,
stretching, or bending. The energy required for DNA denaturation de-
pends on base-pair composition and have been determined very accurately
in calorimetric experiments. Craig Benham has used this information to
develop a theory of stress-induced duplex destabilization [14, 15], which
he used to compute the sites in a genome that would be most prone to
denaturation due to supercoiling, and found that such sites coincide with
transcription initiation regions [16].
The response of DNA to large deformations is still not well under-
stood. Extensive stretching or twisting can induce the transition of DNA
to alternative conformations with disrupted base-pairing (see Section 6),
but it is not known whether such conformations play any biological role.
DNA kinking - a higher order response to bending associated with dis-
ruption of base-stacking - has been proposed [154, 151, 116, 85, 54] as an
explanation for unusually large cyclization probabilities of certain special
DNA sequences [35, 36]. Furthermore, in addition to the well known B-
DNA form there are other, alternative forms of DNA - A-DNA, C-DNA,
Z-DNA, - which are induced by special experimental conditions (ethanol,
312 DAVID SWIGON

high salt), and for which mechanical properties have not been explored,
nor mechanical theories of transitions between these forms have been
formulated.
A large area of DNA research is concerned with protein-DNA inter-
actions. We are still far from complete understanding the principles of
protein-DNA binding affinity and specificity, and the role of DNA defor-
mations that many proteins impose on DNA. This problem requires the
use of local atomic level description of DNA and proteins and is beyond
the scope of this essay.
The modeling efforts described above have focused on the understand-
ing of DNA physical properties. The ultimate goal of DNA modeling,
however, is to address important biological problems such as the prob-
lem of DNA compaction, chromatin formation and remodeling, and the
problem of the role of DNA deformability in replication, recombination,
or regulation of transcription. The first steps in this direction are pro-
vided by methods that utilize current information about protein-DNA in-
teraction (X-ray crystal data, binding affinity measurements, DNA foot-
printing, etc.) to compute the structures of complex multi-protein DNA
assemblies [6, 142, 65, 134, 7, 86, 135, 45].
A new direction in simulation of DNA dynamics and mechanics is to
move away from models tailored to the conditions in vitro (i.e., in the test
tube) to models of DNA in vivo (i.e., inside of a living cell). One important
difference here is that the DNA in vivo is subject to random interactions
with a large number of DNA binding proteins, both sequence specific and
non-specific, that bend and twist the molecule. The first examples of a
reserch concerned with intracellular DNA modeling include the analysis of
DNA stretching in the presence of randomly binding bending or stiffen-
ing agents [153], and the study of DNA cyclization in the presence of a
nonspecifically binding bending protein HU [45].
Although this overview of various areas of DNA modeling is under-
standably sketchy and incomplete, it gives the reader an idea about the
variety of areas of DNA research that benefit from the use of mathemat-
ics. Further information about specific areas can be found in numerous
survey papers and books, e.g., DNA topology [9, 150], base-pair level
DNA structure [28], detail DNA structure [104], DNA mechanics [11, 65],
single-molecule DNA stretching [26] and twisting [130], DNA supercoil-
ing [106, 117, 143], or DNA topoisomerase action [146]. Additional mate-
rial is available online, and includes two lectures given by the author at the
tutorial “Mathematics of Nucleic Acids” which has taken place at the IMA
on September 15, 2007. The slides and videorecordings of these lectures
can be found on the IMA website (www.ima.umn.edu).

Acknowledgements. The author wishes to express his thanks to

Zuzana Swigonova for careful proofreading of the manuscript and numer-
ous suggestions. Much of this work was written during a stimulating one-
 THE MATHEMATICS OF DNA 313

semester visit at the Institute for Mathematics and its Applications, Uni-
versity of Minnesota. Support by A.P. Sloan Fellowship and NSF grant
DMS-05-16646 is also acknowledged.

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