See discussions, stats, and author profiles for this publication at: https://www.researchgate.

net/publication/301262949

DNA and RNA, Biophysical Aspects

Chapter · December 2016

DOI: 10.1016/B978-0-12-803581-8.00981-4

CITATIONS READS
0 539

1 author:

Maxim Frank-Kamenetskii
Boston University
228 PUBLICATIONS   10,259 CITATIONS   

SEE PROFILE

All content following this page was uploaded by Maxim Frank-Kamenetskii on 17 October 2017.

The user has requested enhancement of the downloaded file.

978-0-08-054776-3

DNA and RNA, Biophysical Aspects

M.D. Frank-Kamenetskii
Boston University, Boston, MA, USA

87.15

Introduction
DNA and RNA together are known as nucleic acids. Their full names are
deoxyribonucleic acid and ribonucleic acid, respectively. They play a crucial role in all
living organisms because they are the key molecules responsible for storage,
duplication, and realization of genetic information. They are both heteropolymeric
molecules consisting of residues (nucleotides) of four types. Four RNA nucleotides are
shown in Figure 1. They consist of the phosphate group, sugar (called ribose) (these
two elements are identical for all four nucleotides), and nitrous bases, which determine
the type of the nucleotide. DNA nucleotides are very similar to RNA nucleotides. The
main difference is that the right-handed OH group in sugar is replaced with just H
(making deoxyribose). Three bases (A, G, and C) are the same for DNA and RNA. Only
the fourth base is different: instead of uracil (U), DNA carries thymine (T) (see Figure 2).
The DNA chain is shown in Figure 3.
 Figure
1. Chemical formulas of residues of RNA, i.e., of nucleotides. At the top are the
pyrimidine nucleotides (U and C), and below, the purine nucleotides (A and G).
Nucleotides within DNA differ in that, instead of the right-hand lower OH group, they
simply have H. In addition, DNA, instead of the uridine nucleotide, includes the
thymidine nucleotide whose top C–H group in the ring is replaced by the C–CH3 group.
 Figure 2. Thymidine monophosphate is a thymine
nucleotide that is part of DNA. The remaining three DNA nucleotides have similar
structure, but each has a nitrous base of its own (the top group). These three bases
(adenine, guanine, and cytosine) are identical in DNA and RNA (see Figure 1).

Figure 3. (a) The DNA

single strand and (b) the Watson–Crick complementary base pairs.

In living nature, as is observed today, DNA plays the most important role because
genetic information is stored and duplicated in the form of DNA in all living cells and
organisms without any exceptions. Only in some viruses, which are not living creatures
because they cannot reproduce themselves outside cells, the genetic information may
be carried in the form of RNA molecules. A notable class of such viruses is retroviruses,
which include many cancer-inducing viruses as well as HIV, the AIDS virus.
A genetic message is “written down” in the form of a continuous text consisting of four
letters (DNA nucleotides A, G, T, and C). This continuous text, however, is subdivided,
in its biological meaning, into sections. The most significant sections are genes, parts of
DNA, which carry information about the amino acid sequence of proteins. Whereas
DNA stores and duplicates genetic information, RNA plays a key role in its realization,
that is, in the process of synthesis of a protein molecule in accordance with the
nucleotide sequence of the corresponding gene.
This process consists of two major steps. First an RNA copy of the gene is made with
the help of a special enzyme, RNA polymerase. The process is called transcription and
the RNA copy of the gene is called messenger RNA (mRNA). The mRNA is an exact
copy of the gene, in which all thymines (T) are replaced with uracils (U). In the second
step, called translation, mRNA is used as a template for protein synthesis in a special
cell machinery, the ribosome. Ribosome is a complex aggregate of special ribosomal
RNA (rRNA) and a number of proteins. It translates the nucleic acid text into amino acid
language. In so doing, it uses a special dictionary, the genetic code. In the process of
translation, a very important class of additional small RNA molecules plays a crucial
role. These RNA molecules consist of about hundred nucleotides and are called
transfer RNA (tRNA).
In this article, an overview of the present knowledge of physical structures of nucleic
acids is provided. The most important structural transitions, such as DNA melting and
B–Z transition, are explained. Special attention is paid to the topological properties of
DNA, which play a significant role in its functioning within the cell. Theoretical models,
which are most popular in the field of biophysics of DNA and RNA are also overviewed.
Recently emerged areas of DNA and RNA biophysics, such as single-molecule
experiments and DNA/RNA nanostructures are also considered.
Structures of DNA and RNA
Traditionally, the structural versatility of nucleic acids had been considered as much
narrower than that of proteins. This viewpoint fitted well “the division of power” between
nucleic acids and proteins in present-day living creatures. The major function of nucleic
acids is to store and reproduce genetic information while proteins perform an
innumerable variety of reactions within the cell and are also its main construction
blocks. The discovery of ribozymes (RNA molecules capable of catalytic functions) and
of the remarkable versatility of the RNA structure completely changed the attitude
toward the pivotal question of which type of major biopolymers, proteins or nucleic
acids, had been the prebiotic molecule, forefather of the living cell. Earlier, everybody
believed that only protein could fulfill this function. Now, the common view is that this
should be the RNA molecule (the RNA World concept).

Major Helical Structures of DNA

In spite of enormous versatility of living creatures, and, accordingly, variability of genetic
texts which DNA molecules in different organisms carry, they all have virtually an
identical physical spatial structure: the double-helical B form discovered by Watson and
Crick in 1953. Sequences of the two strands of the double helix obey the
complementary principle. This principle is the most important law in the field of nucleic
acids, and, probably, the most important law of living nature. It declares that in the
double helix, A always opposes T and vice versa, whereas G always opposes C and
vice versa.
B-DNA
It (see Figure 4a) consists of two helically twisted sugar-phosphate backbones stuffed
with base pairs of two types, AT and GC. The helix is right-handed with 10 bp per turn.
The base pairs are isomorphous (see Figure 3): the distances between glycosidic
bonds, which attach bases to sugar, are virtually identical for AT and GC pairs. Due to
this isomorphism, the regular double helix is formed for an arbitrary sequence of
nucleotides and the fact that DNA should form a double helix imposes no limitations on
DNA texts. The surface of the double helix is by no means cylindrical. It has two very
distinct grooves: the major groove and the minor groove. These grooves are extremely
important for DNA functioning because in the cell, numerous proteins recognize specific
sites on the DNA via binding with the grooves.
Figure 4. Schematics of (a) B-DNA and some unusual structures of DNA: (b) Z-DNA,
(c) intermolecular triplex, (d) cruciform, (e) H-DNA, (f) G-quadruplex and its various
folding modes.

Each nucleotide has direction: if one treats sugar as a ring lying in the plane, then the
CH2 group will be above the plane (see Figure 1). This carbon is designated as 5′
whereas the carbon atom connecting the sugar to the next nucleotide in the
polynucleotide chain is designated as 3′. In the DNA double helix, the two strands have
opposite directions.
In B-DNA, base pairs are planar and perpendicular to the axis of the double helix.
Under normal conditions in solution, often referred to as “physiological” (neutral pH,
room temperature, ∼200 mM NaCl), DNA adopts the B form. All available data indicate
that the same is true for the totality of DNA within the cell. It does not exclude, however,
the possibility that separate stretches of DNA carrying special nucleotide sequences
would adopt other conformations.
B′-DNA
Up to now only one such conformation has been demonstrated, beyond any doubts, to
exist under physiological conditions. When three or more A residues in one strand (and,
accordingly, T's in the other DNA strand) are met, they adopt the B′ form. In many
respects, the B′ form is similar to the classical B form. There are two main differences:
base pairs in B′-DNA are not planar (they form a kind of propeller with the propeller
twist of 20°) and the minor groove in B′-DNA is twice as narrow as in B-DNA.
A-DNA
Similar to B-DNA, the A form can be adopted by an arbitrary sequence of nucleotides.
As in B-DNA, the two complementary strands in A-DNA are antiparallel and form right-
handed helices. Normal DNA undergoes transition from the B to A form under drying. In
A-DNA, the base pairs are planar but their planes form a considerable angle with the
axis of the double helix. In so doing, the base pairs shift from the center of the duplex
forming a channel in the center.
Z-DNA
It presents the most striking example of how different from the B form the DNA double
helix can be (Figure 4b). Although in Z-DNA the complementary strands are antiparallel
as in B-DNA, unlike in B-DNA they form left-handed, rather than right-handed, helices.
There are many other dramatic differences between Z- and B-DNA.
Not any sequence can adopt the Z form. To adopt the Z form, the regular alternation of
purines (A or G) and pyrimidines (T or C) along one strand is strongly preferred.
However, even this is not enough for Z-DNA to be formed under physiological
conditions. Nevertheless, Z-DNA can be adopted by DNA stretches in cell due to DNA
supercoiling (see below). The biological significance of Z-DNA, however, remains to be
elucidated.
ps-DNA
The complementary strands in DNA duplex can be parallel. Such parallel-stranded (ps)
DNA is formed most readily if both strands carry only adenines and thymines and their
sequence excludes formation of the ordinary antiparallel duplex. If these requirements
are met, the parallel duplex is formed under quite normal conditions. It is right-handed
but the AT pairs are not regular Watson–Crick ones, but rather so-called reverse
Watson–Crick.
Some other sequences also can adopt parallel duplexes. For instance, at acidic
conditions two strands carrying only C residues form parallel duplex consisting of
hemiprotonated CC+ base pairs (see the section “Quadruplexes”). However, any
possible biological role of psDNA remains obscure.
RNA Structure and Function
Quite naturally, similarity between DNA and RNA in their chemical nature entails
significant similarity in structures they adopt. RNA can also form the double helix with
complementary base pairs AU and GC. However, the major RNA duplex conformation
remains A-form rather than B-form.
In general, due to bulkier OH group in the sugar ring, the versatility of RNA duplexes is
rather narrower than those of DNA.
In a cell, different types of RNA molecules (mRNA, rRNA, tRNA, etc.) exist as single
strands. Of course, these strands are not unfolded, but fold into complex spatial
structures. Mutually complementary stretches of the same molecules form numerous
short duplexes, which are a major structural motif of RNA molecules. Single-stranded
regions form loops of different types. Sometimes very complex folding patterns, called
pseudoknots, are met.
Spatial structure plays an important role in RNA functioning. For instance, rRNA
organized in complex spatial structure forms a scaffolding to which numerous ribosomal
proteins attach to form the functional ribosome. The elucidation of the full 3D structure
of the ribosome by X-ray crystallography has been one of the major achievements of
biophysics and structural biology. Spatial structure at tRNA molecules are specially
designed to permit them to fulfill the central role in the realization of the genetic code.
One part of tRNA carries the anticodon, a trinucleotide complementary to a codon (a
trinucleotide corresponding to one amino acid in the genetic code), whereas the amino
acid, which corresponds to the codon in the genetic code, is attached to the 3’ terminus
of the molecule.
More we learn about the living cell, more RNA molecules of different kinds emerge,
which had been overlooked before and which proved to be extremely important. A
totally new class of small RNAs was discovered at the turn of the century, which are
involved in the RNA interference (RNAi) pathway and participate in the gene expression
regulation on the level of mRNA. Most important of these small regulatory RNAs are
small interfering RNAs (siRNAs) and micro RNAs (miRNAs). The RNAi pathway is
present only in eukaryotes. Another groundbreaking discovery made already in 21st
century was so-called CRISPR mechanism of bacterial immunity against
bacteriophages. Here small ssRNA molecules, called CRISPR RNAs (crRNAs) or
guide RNAs (gRNAs), recruit CRISPR associate (cas) endonucleases and guide them
to the specific sites on dsDNA recognized by gRNAs via base pairing with one of two
DNA strands. As a result, the cas protein inflicts the double strand break into target
dsDNA. The CISPR-cas mechanism discovered in bacteria has very recently been
converted into the revolutionary CISPR-cas technology, which makes it possible to
perform in vivo genome editing in eukaryotes, including humans.
DNA Topology
DNA very often operates within the cell in the form of a closed circular molecule in
which both strands form closed circles (Figure 5). The physical properties and
physiological behavior of closed circular (cc) DNA are different in many respects from
those of linear DNA molecules. These differences stem from the fact that ccDNA
acquires, as compared to linear DNA, a new fundamental feature, topology. There are
two levels of DNA topology.

Figure 5. In a ccDNA, two complementary

strands form a linkage of a high order.

Knots of DNA
The double helix, as a whole, may form a simple circle (i.e., a trivial knot) or be knotted
(see Figure 6). Knotting of DNA may be conducted by random closure of linear
molecules with “cohesive” ends (mutually complementary single-stranded overhangs).
There are also different enzymes which do the job. The most important class of such
enzymes is known as DNA topoisomerases II. The type of knot is the topological
invariant, that is, it cannot be changed (converted to another type of knot) without
breakage of both DNA strands. As a result, identical ccDNA molecules belonging to
different knot types may be separated in gel.

Figure 6. Knots.

DNA Supercoiling
The two complementary strands in ccDNA are topologically linked with one another
(see Figure 5). The degree of linkage, which is designated as Lk, the DNA linking
number, is a topological invariant, which cannot be changed with any deformations of
the DNA strands without strand breaks. The Lk value is easily calculated as the number
of times one strand pierces the surface placed on the other strand. If N is the number of
base pairs in DNA and γo is the number of base pairs per one turn of the double helix
under given ambient conditions, then the difference:

[1].

is the number of superhelical turns in ccDNA under given conditions. If τ≠0, then ccDNA
cannot form a planar ring with the helical twist corresponding the γo value. Either the
helical twist should change or the DNA molecule as a whole should writhe in space.
Actually, with τ≠0 both things happen: the DNA adopts the writhe, and its twist changes.
The distribution of energy associated with DNA supercoiling (i.e., with τ≠0) between
twist and writhe is determined by the torsional and bending rigidities, which have been
measured with good accuracy. Supercoiling is also significantly affected by replication
and transcription. DNA topology plays an extremely important role in DNA functioning.
Structural Transitions and Unusual Structures
If negative supercoiling in ccDNA becomes too high, the bending and torsional degrees
of freedom may become insufficient to accommodate the superhelical energy. Under
these circumstances, the integrity of the DNA double helix breaks down at its most “
weak” sites. These sites, which have the potential to adopt structures significantly
different from B-DNA, can undergo structural transitions into unusual (non-B-DNA)
structures.
DNA Melting
On heating or under superhelical stress, the DNA complementary strands separate
forming single-stranded loops. In case of linear duplex molecules, the process ends up,
at a high temperature, with complete separation of the two strands. The process has
been studied comprehensively both experimentally and theoretically and is known as
DNA melting (the terms denaturation or helix-coil transition are also used in literature).
AT pairs have significantly lower stability than GC pairs.
With increasing temperature, long DNA sections melt out. Melting of each such section
is a cooperative, all-or-none phenomenon. However, melting of a long enough molecule
becomes a series of such cooperative processes, each occurring at its own
temperature (Figure 7). Roughly speaking, sections more enriched with GC pairs melt
out at higher temperatures. Thus, DNA melting is not a classical phase transition
because two different “phases,” helical and melted, coexist with each other in one and
the same molecule.
 Figure 7. Melting of DNA. This curve is also
often called the differential melting curve. The curve was obtained for DNA that has the
code name of ColE1 and contains 6646 base pairs.

When two mutually complementary single-stranded DNA molecules are mixed, the
process reverse to melting occurs. It is called renaturation, annealing or hybridization.
DNA melting is an exceptionally important phenomenon. It occurs in the cell when DNA
replicates and when DNA polymerase “reads” the mRNA copy of the gene. Cycles of
melting and annealing are utilized in the polymerase chain reaction (PCR) machines,
which belong to the most remarkable tools of the current biotechnology revolution.
B–Z Transition
Negative supercoiling favors the formation of Z-DNA most because, in this case, the
maximal release of superhelical stress per 1 bp adopting a non-B-DNA structure is
achieved. As a result, although under physiological conditions the Z form is
energetically very unfavorable as compared with B-DNA, it is easily adopted in
negatively supercoiled DNA by appropriate DNA sequences (with alternating purines
and pyrimidines).
Cruciforms
Another structure readily formed under negative supercoiling is cruciform, which
requires palindromic regions (see Figure 4d). To form cruciform, a palindromic region
should be long enough. For example, 6 bp long palindromes recognized by restriction
enzymes do not form cruciforms under any conditions.
Triplexes
Intramolecular triplex or H-DNA forms a special class of unusual structures, which are
adopted under superhelical stress by sequences carrying purines (A and G) in one
strand and pyrimidines (T and C) in the other, that is, homopurine–homopyrimidine
sequences. The major element of H-DNA is triplex formed by a half of the insert
adopting the H form and by one of two strands of the second half of the insert (Figure
4e). Two major classes of triplexes are known: pyrimidine–purine–pyrimidine (YRY) and
pyrimidine–purine–purine (YRR). Figure 8 shows the canonical base-triads entering
these triplexes.

Figure 8.
The structure of (a) pyrimidine (TAT and C+GC), and (b) purine (AAT and GGC) base
triads of which the DNA triple helix is made. In YRY triplexes, the Y strand lying in the
major groove of the duplex is parallel to the R strand of the Watson-Crick duplex and
forms with it Hoogsteen pairs. In RYR triplexes, two R strands are anti-parallel to each
other and are connected with each other via reverse Hoogsteen pairs.
Always two isomeric forms of H-DNA are possible, which are designated as H-y3, H-y5,
H-r3, and H-r5 depending on which kind of triplex is formed and which half of the insert
forms the triplex (see Figure 4e).
Discovery of H-DNA stimulated studies of intermolecular triplexes, which may be
formed between homopurine–homopyrimidine regions of duplex DNA and
corresponding pyrimidine or purine oligonucleotides (Figure 4c).
Quadruplexes
Of all nucleotides, guanines are most versatile in forming different structures. They may
form GG pairs but the most stable structure, which is formed in the presence of
monovalent cations (especially potassium), is G4 quadruplex (see Figure 4f). G-
quadruplexes may exist in a variety of modifications: all-parallel, all-antiparallel, and
others. As a result, G-quadruplexes are easily formed both inter- and intramolecularly,
again with a variety of modifications. A remarkable variety of quadruplex structure was
discovered for protonated cytosines. This structure, called i-motif, consists of two pairs
of parallel stranded duplexes consisting of hemiprotonated CC+ base pairs. In the final
structure, two duplexes are mutually antiparallel and CC+ base pairs from one ps
duplex alternate with CC+ base pairs from the other ps duplex. The structure is stable
only at acidic pH because protonation is necessary.
Bent DNA
For an arbitrary sequence, the minimum energy conformation of the DNA double helix
corresponds to the straight DNA axis. However, there is a notable exception to this rule.
If three or more A nucleotides are located in a row in one of the DNA strands, the
corresponding regions adopt the B′ structure. As a result, the DNA axis experiences a
bend of 20° in such a region. DNA bending plays an important role in DNA functioning.
RNA Unusual Structures
Most DNA unusual structures have their analogs in the RNA world. Specifically,
formation of triplexes was first demonstrated for artificial RNA chains. Solitary RNA
base-triads are often met in tRNA structures. Triplexes are formed by mixed DNA–RNA
hybrids and some of them are rather stable.
However, in general, studies of RNA unusual structures lag behind corresponding DNA
structures because methods to study unusual structures are much better developed in
the case of DNA than in the case of RNA.
Nanostructures and Nanodevices from DNA and RNA
One of the most rapidly developing areas in DNA and RNA biophysics consists in using
the remarkable ability of nucleic acid to self-assembly for creation of nanostructures
and nanodevices. In so doing, virtually all unusual structures described above are
extensively used: triplexes, quadruplexes, Z-DNA, etc., as well as the duplex.
Specifically, a family of topological and pseudotopological nanostuctures has been
assembled as is shown in Figures 9a–9c. An example of a nanodevice (nanoactuator)
is shown in Figure 9d. By adding specially designed single-stranded DNA chains, the
nanoactuator is transformed from the relaxed form shown in Figure 9d to a straightened
form in which the A strand is extended into a straight double helix.

Figure 9. Examples of DNA nanostructures:

(a) padlock probe (pseudororaxane), (b) sliding clamp (pseudororaxane), (c) earring
probe (pseudocatenane), and (d) nanoactuator.

A very ingenious method for making sophisticated DNA nanostructures has been
invented, which makes it possible to create so-called DNA origami. Using special
computer programs, DNA oligonucleotides are designed, which will bind to a long DNA
molecule with the known sequence and fold it into the desired 3D structure. By this
approach a huge variety of nanostructures are being created.
A special class of short ssRNA molecules, called aptamers, has been developed.
These molecules are produced via special in vitro selection process, called SELEX, and
they are selected on their ability to bind strongly to particular proteins. Aptamers find
more and more applications.

Biophysical Methods to Study DNA and RNA

The whole arsenal of methods, which is traditionally used to study molecular structure,
is applied to DNA and RNA. A leading position is occupied by X-ray crystallography,
which provided us with a knowledge of details of the atomic structure of DNA and RNA.
X-ray crystallography made it possible to solve the structure of the nucleosome, the
main building block of chromosomes consisting of DNA and hystone proteins, and of a
major cellular machinery, ribosome, consisting of RNA and many proteins. The next
method is proton NMR, which is especially valuable when biological molecules resist
crystallization, a not uncommon problem with nucleic acids. An enormous body of data
on the structure of DNA triplexes, quadruplexes, and various ribozymes was delivered
by NMR. Electron microscopy (EM), cryo-EM and atomic force microscopy (AFM) have
become indispensable in studying the DNA and its complexes with proteins. Most
recently, a dramatic progress in single particle analysis of crio-EM images has made
this approach a method of choice in elucidation of structure of large nucleoprotein
assemblies, like ribosomes. All kinds of spectroscopy methods, UV, IR, Raman, and
CD are very useful in studying conformational transitions in DNA and RNA. A special
role is played by various fluorescence methods, which find more and more applications
not only in biophysical studies, but also in biotechnology. Below, specific methods,
which have been specially developed in the field of DNA and RNA biophysics are
discussed.
Theoretical Models
As in the study of any important physical object, a number of simplified theoretical
models of nucleic acids exist, different models being used to analyze different
properties. Figure 10 presents schematics of some of these models.

Figure 10. Theoretical models of nucleic

acids: (a) elastic-rod model, (b) helix-coil model, (c) polyelectrolyte model, and (d)
model of RNA folding.

The DNA double helix may be treated as an isotropic elastic rod (Figure 10a). In the
framework of this model, the DNA molecule is described by only three parameters:
bending, torsional rigidities, and the diameter. The model has proved to be extremely
useful for analyzing hydrodynamics and other properties of linear DNA, when it
behaves as a usual polymeric molecule. It has also provided a comprehensive
theoretical treatment of DNA topology of both levels: knotting and supercoiling. More
recently, the model has been extensively used for quantitative analysis of the force-
extension curves for DNA in single-molecule experiments (see below).
A quite different, but also very successful, model treats the DNA double helix as
consisting of base pairs of two types: closed and open (Figure 10b). This is the helix-
coil model, which explains all major features of DNA melting quantitatively.
The polyelectrolyte model (Figure 10c) treats DNA itself just as a charged cylinder but
allows for mobile counter-ions surrounding the double helix.
To predict the RNA structure, a simplified model of RNA folding is widely used (Figure
10d).
Gel Electrophoresis
Gel electrophoresis is a simple technique, introduced in the early 1970s, which truly
revolutionized the biophysical studies of DNA and RNA and, subsequently, the whole
field of molecular biology. All developments in this field in the past 40 years are
connected, directly or indirectly, with the gel electrophoresis method. Gel
electrophoresis has pushed aside ultracentrifugation as the method to separate nucleic
acids.
Gel electrophoresis differs from electrophoresis in solution only in the nature of the
medium in which molecules are separated in the electric field. In case of gel
electrophoresis the medium is the gel, a polymer network. The most popular in the field
of nucleic acids are gels made of polyacrylamide or agarose. Originally, the great
advantage of gels in the separation of nucleic acids was discovered purely empirically.
The understanding came later after some ideas of P-J De Grennes were borrowed from
polymer physics, namely the notion of reptation of polymer molecules.
Single-Molecule Experiments with DNA and RNA
In recent years, remarkable progress in the application of the single-molecule
techniques to DNA and RNA studies has been achieved. There are many different
formats for single-molecule experiments. For example, a DNA molecule consisting of
about 50 kbp is attached via one terminus to a pipette tip equipped with a streptavidin-
covered polymer bead. Streptavidin is a protein, which binds very strongly to a small
molecule, biotin. The DNA terminus is covalently tagged with biotin to be attached to
the streptavidin-covered bead. The other terminus is also attached to the polymer bead,
but the bead is not fixed. Then, optical tweezers are used to drag the free bead with the
DNA attached to it. As a result, a single DNA molecule can be stretched in a fully
controllable manner and the force created in the process can be accurately measured
(see Figure 11).
 Figure 11. Stretching a single DNA
molecule with optical tweezers.

These experiments have allowed, for the first time, measurement of the force–extension
curves of ds and ss DNAs and comparison of the curves with theoretical predictions.
One of the important directions of these studies include isothermal melting of DNA and
RNA duplexes under the external force. The influence of the force on the performance
of major enzymes working on DNA and RNA (DNA and RNA polymerases) has also
been studied. A very important feature of single-molecule experiments consists in the
fact that they introduce a new variable on which DNA and RNA structure critically
depend, the external force.
See also:
Biomolecules, Scanning Probe Microscopy of; Protein Folding, Engineering of.
Further Reading
Bates AD and Maxwell A (2005) DNA Topology. Oxford, UK: Oxford University Press.
Bloomfield VA, Crothers DM and Tinoco I (2000) Nucleic Acids Structures, Properties,
and Functions. Sausalito, CA: University Science Books.
Frank-Kamenetskii MD (1997) Unraveling DNA. Cambridge, MA: Perseus Publishing.
Sinden RR (1994) DNA Structure and Function. San Diego, CA: Academic Press.
Vologodskii A (2015) Biophysics of DNA. Cambridge, UK: Cambridge University Press.

View publication stats