Deoxyribonucleic acid (/diˈɒksiˌraɪboʊnjʊˈkliːɪk,
-ˈkleɪ.ɪk/ ( listen); DNA) is a thread-like chain of
nucleotides carrying the genetic instructions used in the growth,
development, functioning and reproduction of all known living
organisms and many viruses.
DNA and ribonucleic acid (RNA) are nucleic
acids; alongside proteins, lipids and complex carbohydrates
(polysaccharides), they are one of the four major types of
macromolecules that are essential for all known forms of life. Most
DNA molecules consist of two biopolymer strands coiled around each
other to form a double helix.
DNA strands are called polynucleotides since they are composed
of simpler monomer units called nucleotides. Each nucleotide is
composed of one of four nitrogen-containing nucleobases (cytosine [C],
guanine [G], adenine [A] or thymine [T]), a sugar called deoxyribose,
and a phosphate group. The nucleotides are joined to one another in a
chain by covalent bonds between the sugar of one nucleotide and the
phosphate of the next, resulting in an alternating sugar-phosphate
backbone. The nitrogenous bases of the two separate polynucleotide
strands are bound together, according to base pairing rules (A with T
and C with G), with hydrogen bonds to make double-stranded DNA.
The complementary nitrogenous bases are divided into two groups,
pyrimidines and purines. In a
DNA molecule, the pyrimidines are
thymine and cytosine, the purines are adenine and guanine.
DNA stores biological information. The
DNA backbone is resistant to
cleavage, and both strands of the double-stranded structure store the
same biological information. This information is replicated as and
when the two strands separate. A large part of
DNA (more than 98% for
humans) is non-coding, meaning that these sections do not serve as
patterns for protein sequences.
The two strands of
DNA run in opposite directions to each other and
are thus antiparallel. Attached to each sugar is one of four types of
nucleobases (informally, bases). It is the sequence of these four
nucleobases along the backbone that encodes biological information.
RNA strands are created using
DNA strands as a template in a process
called transcription. Under the genetic code, these
RNA strands are
translated to specify the sequence of amino acids within proteins in a
process called translation.
Within eukaryotic cells
DNA is organized into long structures called
chromosomes. During cell division these chromosomes are duplicated in
the process of
DNA replication, providing each cell its own complete
set of chromosomes. Eukaryotic organisms (animals, plants, fungi and
protists) store most of their
DNA inside the cell nucleus and some of
DNA in organelles, such as mitochondria or chloroplasts. In
contrast prokaryotes (bacteria and archaea) store their
DNA only in
the cytoplasm. Within the eukaryotic chromosomes, chromatin proteins
such as histones compact and organize DNA. These compact structures
guide the interactions between
DNA and other proteins, helping control
which parts of the
DNA are transcribed.
DNA was first isolated by
Friedrich Miescher in 1869. Its molecular
structure was first identified by
James Watson and
Francis Crick at
Cavendish Laboratory within the
University of Cambridge
University of Cambridge in 1953,
whose model-building efforts were guided by
X-ray diffraction data
acquired by Raymond Gosling, who was a post-graduate student of
DNA is used by researchers as a molecular tool to
explore physical laws and theories, such as the ergodic theorem and
the theory of elasticity. The unique material properties of
made it an attractive molecule for material scientists and engineers
interested in micro- and nano-fabrication. Among notable advances in
this field are
DNA origami and DNA-based hybrid materials.
1.2 Non canonical bases
1.3 Listing of non canonical bases found in DNA
1.5 Base pairing
1.6 Sense and antisense
1.10 Quadruplex structures
1.11 Branched DNA
2 Chemical modifications and altered
2.1 Base modifications and
3 Biological functions
3.1 Genes and genomes
3.2 Transcription and translation
3.4 Extracellular nucleic acids
4 Interactions with proteins
4.1 DNA-binding proteins
4.2 DNA-modifying enzymes
4.2.1 Nucleases and ligases
4.2.2 Topoisomerases and helicases
5 Genetic recombination
7 Uses in technology
7.1 Genetic engineering
DNA enzymes or catalytic DNA
7.6 History and anthropology
8 History of
9 See also
11 Further reading
12 External links
Chemical structure of DNA; hydrogen bonds shown as dotted lines
DNA is a long polymer made from repeating units called
nucleotides. The structure of
DNA is dynamic along its length,
being capable of coiling into tight loops, and other shapes. In all
species it is composed of two helical chains, bound to each other by
hydrogen bonds. Both chains are coiled round the same axis, and have
the same pitch of 34 ångströms (3.4 nanometres). The pair
of chains has a radius of 10 ångströms (1.0 nanometre).
According to another study, when measured in a different solution, the
DNA chain measured 22 to 26 ångströms wide (2.2 to
2.6 nanometres), and one nucleotide unit measured 3.3 Å
(0.33 nm) long. Although each individual nucleotide repeating
unit is very small,
DNA polymers can be very large molecules
containing millions to hundreds of millions of nucleotides. For
DNA in the largest human chromosome, chromosome number
1, consists of approximately 220 million base pairs and would be
85 mm long if straightened.
In living organisms,
DNA does not usually exist as a single molecule,
but instead as a pair of molecules that are held tightly
together. These two long strands entwine like vines, in the
shape of a double helix. The nucleotide contains both a segment of the
backbone of the molecule (which holds the chain together) and a
nucleobase (which interacts with the other
DNA strand in the helix). A
nucleobase linked to a sugar is called a nucleoside and a base linked
to a sugar and one or more phosphate groups is called a nucleotide. A
polymer comprising multiple linked nucleotides (as in DNA) is called a
The backbone of the
DNA strand is made from alternating phosphate and
sugar residues. The sugar in
DNA is 2-deoxyribose, which is a
pentose (five-carbon) sugar. The sugars are joined together by
phosphate groups that form phosphodiester bonds between the third and
fifth carbon atoms of adjacent sugar rings. These asymmetric bonds
mean a strand of
DNA has a direction. In a double helix, the direction
of the nucleotides in one strand is opposite to their direction in the
other strand: the strands are antiparallel. The asymmetric ends of DNA
strands are said to have a directionality of five prime (5′) and
three prime (3′), with the 5′ end having a terminal phosphate
group and the 3′ end a terminal hydroxyl group. One major difference
RNA is the sugar, with the 2-deoxyribose in
replaced by the alternative pentose sugar ribose in RNA.
A section of DNA. The bases lie horizontally between the two spiraling
strands. (animated version).
DNA double helix is stabilized primarily by two forces: hydrogen
bonds between nucleotides and base-stacking interactions among
aromatic nucleobases. In the aqueous environment of the cell, the
conjugated π bonds of nucleotide bases align perpendicular to the
axis of the
DNA molecule, minimizing their interaction with the
solvation shell. The four bases found in
DNA are adenine (A), cytosine
(C), guanine (G) and thymine (T). These four bases are attached to the
sugar-phosphate to form the complete nucleotide, as shown for
Adenine pairs with thymine and guanine pairs
with cytosine. It was represented by A-T base pairs and G-C base
The nucleobases are classified into two types: the purines, A and G,
being fused five- and six-membered heterocyclic compounds, and the
pyrimidines, the six-membered rings C and T. A fifth pyrimidine
nucleobase, uracil (U), usually takes the place of thymine in
differs from thymine by lacking a methyl group on its ring. In
RNA and DNA, many artificial nucleic acid analogues have
been created to study the properties of nucleic acids, or for use in
Non canonical bases
Uracil is not usually found in DNA, occurring only as a breakdown
product of cytosine. However, in several bacteriophages, Bacillus
subtilis bacteriophages PBS1 and PBS2 and Yersinia bacteriophage
piR1-37, thymine has been replaced by uracil. Another phage -
Staphylococcal phage S6 - has been identified with a genome where
thymine has been replaced by uracil.
5-hydroxymethyldeoxyuracil (hm5dU) is also known to replace thymidine
in several genomes including the Bacillus phages SPO1, ϕe, SP8, H1,
2C and SP82. Another modified uracil - 5-dihydroxypentauracil – has
also been described.
Base J (beta-d-glucopyranosyloxymethyluracil), a modified form of
uracil, is also found in several organisms: the flagellates Diplonema
and Euglena, and all the kinetoplastid genera.
Biosynthesis of J
occurs in two steps: in the first step, a specific thymidine in
converted into hydroxymethyldeoxyuridine; in the second, HOMedU is
glycosylated to form J. Proteins that bind specifically to this
base have been identified. These proteins appear to be
distant relatives of the Tet1 oncogene that is involved in the
pathogenesis of acute myeloid leukemia. J appears to act as a
termination signal for
RNA polymerase II.
In 1976 a bacteriophage - S-2L - which infects species of the genus
Synechocystis was found to have all the adenosine bases within its
genome replaced by 2,6-diaminopurine. In 2016 deoxyarchaeosine was
found to be present in the genomes of several bacteria and the
Escherichia phage 9g.
Modified bases also occur in DNA. The first of these recognised was
5-methylcytosine which was found in the genome of Mycobacterium
tuberculosis in 1925. The complete replacement of cytosine by
5-glycosylhydroxymethylcytosine in T even phages (T2, T4 and T6) was
observed in 1953 In the genomes of Xanthomonas oryzae
bacteriophage Xp12 and halovirus FH the full complement of cystosine
has been replaced by 5-methylcytosine. 6N-methyadenine was
discovered to be present in
DNA in 1955.
N6-carbamoyl-methyladenine was described in 1975. 7-methylguanine
was described in 1976.
DNA was described in
1983. In 1985 5-hydroxycytosine was found in the genomes of the
Rhizobium phages RL38JI and N17. α-putrescinylthymine occurs in
both the genomes of the Delftia phage ΦW-14 and the Bacillus phage
SP10. α-glutamythymidine is found in the Bacillus phage SP01 and
5-dihydroxypentyluracil is found in the Bacillus phage SP15.
The reason for the presence of these non canonical bases in
DNA is not
known. It seems likely that at least part of the reason for their
presence in bacterial viruses (phages) is to avoid the restriction
enzymes present in bacteria. This enzyme system acts at least in part
as a molecular immune system protecting bacteria from infection by
This does not appear to be the entire story. Four modifications to the
cytosine residues in human
DNA have been reported. These
modifications are the addition of methyl (CH3)-, hydroxymethyl
(CH2OH)-, formyl (CHO)- and carboxyl (COOH)- groups. These
modifications are thought to have regulatory functions.
Listing of non canonical bases found in DNA
Seventeen non canonical bases are known to occur in DNA. Most of these
are modifications of the canonical bases plus uracil.
Uracil and modifications
DNA major and minor grooves. The latter is a binding site for the
Hoechst stain dye 33258.
Twin helical strands form the
DNA backbone. Another double helix may
be found tracing the spaces, or grooves, between the strands. These
voids are adjacent to the base pairs and may provide a binding site.
As the strands are not symmetrically located with respect to each
other, the grooves are unequally sized. One groove, the major groove,
is 22 Å wide and the other, the minor groove, is 12 Å
wide. The width of the major groove means that the edges of the
bases are more accessible in the major groove than in the minor
groove. As a result, proteins such as transcription factors that can
bind to specific sequences in double-stranded
DNA usually make contact
with the sides of the bases exposed in the major groove. This
situation varies in unusual conformations of
DNA within the cell (see
below), but the major and minor grooves are always named to reflect
the differences in size that would be seen if the
DNA is twisted back
into the ordinary B form.
Further information: Base pair
DNA double helix, each type of nucleobase on one strand bonds
with just one type of nucleobase on the other strand. This is called
complementary base pairing. Here, purines form hydrogen bonds to
pyrimidines, with adenine bonding only to thymine in two hydrogen
bonds, and cytosine bonding only to guanine in three hydrogen bonds.
This arrangement of two nucleotides binding together across the double
helix is called a Watson-Crick base pair. Another type of base pairing
is Hoogsteen base pairing where two hydrogen bonds form between
guanine and cytosine. As hydrogen bonds are not covalent, they can
be broken and rejoined relatively easily. The two strands of
DNA in a
double helix can thus be pulled apart like a zipper, either by a
mechanical force or high temperature. As a result of this base
pair complementarity, all the information in the double-stranded
sequence of a
DNA helix is duplicated on each strand, which is vital
DNA replication. This reversible and specific interaction between
complementary base pairs is critical for all the functions of
Top, a GC base pair with three hydrogen bonds. Bottom, an AT base pair
with two hydrogen bonds. Non-covalent hydrogen bonds between the pairs
are shown as dashed lines.
The two types of base pairs form different numbers of hydrogen bonds,
AT forming two hydrogen bonds, and GC forming three hydrogen bonds
(see figures, right).
DNA with high
GC-content is more stable than DNA
with low GC-content.
As noted above, most
DNA molecules are actually two polymer strands,
bound together in a helical fashion by noncovalent bonds; this
double-stranded (dsDNA) structure is maintained largely by the
intrastrand base stacking interactions, which are strongest for G,C
stacks. The two strands can come apart – a process known as
melting – to form two single-stranded
DNA (ssDNA) molecules.
Melting occurs at high temperature, low salt and high pH (low pH also
melts DNA, but since
DNA is unstable due to acid depurination, low pH
is rarely used).
The stability of the ds
DNA form depends not only on the
G,C basepairs) but also on sequence (since stacking is sequence
specific) and also length (longer molecules are more stable). The
stability can be measured in various ways; a common way is the
"melting temperature", which is the temperature at which 50% of the ds
molecules are converted to ss molecules; melting temperature is
dependent on ionic strength and the concentration of DNA. As a result,
it is both the percentage of GC base pairs and the overall length of a
DNA double helix that determines the strength of the association
between the two strands of DNA. Long
DNA helices with a high
GC-content have stronger-interacting strands, while short helices with
high AT content have weaker-interacting strands. In biology, parts
DNA double helix that need to separate easily, such as the
Pribnow box in some promoters, tend to have a high AT content,
making the strands easier to pull apart.
In the laboratory, the strength of this interaction can be measured by
finding the temperature necessary to break the hydrogen bonds, their
melting temperature (also called Tm value). When all the base pairs in
DNA double helix melt, the strands separate and exist in solution as
two entirely independent molecules. These single-stranded DNA
molecules have no single common shape, but some conformations are more
stable than others.
Sense and antisense
Further information: Sense (molecular biology)
DNA sequence is called "sense" if its sequence is the same as that
of a messenger
RNA copy that is translated into protein. The
sequence on the opposite strand is called the "antisense" sequence.
Both sense and antisense sequences can exist on different parts of the
same strand of
DNA (i.e. both strands can contain both sense and
antisense sequences). In both prokaryotes and eukaryotes, antisense
RNA sequences are produced, but the functions of these RNAs are not
entirely clear. One proposal is that antisense RNAs are involved
in regulating gene expression through RNA-
RNA base pairing.
DNA sequences in prokaryotes and eukaryotes, and more in
plasmids and viruses, blur the distinction between sense and antisense
strands by having overlapping genes. In these cases, some DNA
sequences do double duty, encoding one protein when read along one
strand, and a second protein when read in the opposite direction along
the other strand. In bacteria, this overlap may be involved in the
regulation of gene transcription, while in viruses, overlapping
genes increase the amount of information that can be encoded within
the small viral genome.
DNA can be twisted like a rope in a process called
DNA in its "relaxed" state, a strand usually circles the axis of
the double helix once every 10.4 base pairs, but if the
DNA is twisted
the strands become more tightly or more loosely wound. If the DNA
is twisted in the direction of the helix, this is positive
supercoiling, and the bases are held more tightly together. If they
are twisted in the opposite direction, this is negative supercoiling,
and the bases come apart more easily. In nature, most
DNA has slight
negative supercoiling that is introduced by enzymes called
topoisomerases. These enzymes are also needed to relieve the
twisting stresses introduced into
DNA strands during processes such as
From left to right, the structures of A, B and Z DNA
Further information: Molecular Structure of Nucleic Acids: A Structure
Deoxyribose Nucleic Acid, Molecular models of DNA, and DNA
DNA exists in many possible conformations that include A-DNA, B-DNA,
Z-DNA forms, although, only B-
Z-DNA have been directly
observed in functional organisms. The conformation that
depends on the hydration level,
DNA sequence, the amount and direction
of supercoiling, chemical modifications of the bases, the type and
concentration of metal ions, and the presence of polyamines in
The first published reports of
X-ray diffraction patterns—and
also B-DNA—used analyses based on Patterson transforms that provided
only a limited amount of structural information for oriented fibers of
DNA. An alternative analysis was then proposed by Wilkins et
al., in 1953, for the in vivo B-
patterns of highly hydrated
DNA fibers in terms of squares of Bessel
functions. In the same journal,
James Watson and Francis Crick
presented their molecular modeling analysis of the
diffraction patterns to suggest that the structure was a
Although the B-
DNA form is most common under the conditions found in
cells, it is not a well-defined conformation but a family of
DNA conformations that occur at the high hydration levels
present in living cells. Their corresponding
X-ray diffraction and
scattering patterns are characteristic of molecular paracrystals with
a significant degree of disorder.
Compared to B-DNA, the
A-DNA form is a wider right-handed spiral, with
a shallow, wide minor groove and a narrower, deeper major groove. The
A form occurs under non-physiological conditions in partly dehydrated
samples of DNA, while in the cell it may be produced in hybrid
RNA strands, and in enzyme-
DNA where the bases have been chemically modified by
methylation may undergo a larger change in conformation and adopt the
Z form. Here, the strands turn about the helical axis in a left-handed
spiral, the opposite of the more common B form. These unusual
structures can be recognized by specific
Z-DNA binding proteins and
may be involved in the regulation of transcription.
For many years exobiologists have proposed the existence of a shadow
biosphere, a postulated microbial biosphere of Earth that uses
radically different biochemical and molecular processes than currently
known life. One of the proposals was the existence of lifeforms that
use arsenic instead of phosphorus in DNA. A report in 2010 of the
possibility in the bacterium GFAJ-1, was announced, though
the research was disputed, and evidence suggests the bacterium
actively prevents the incorporation of arsenic into the
and other biomolecules.
Further information: G-quadruplex
At the ends of the linear chromosomes are specialized regions of DNA
called telomeres. The main function of these regions is to allow the
cell to replicate chromosome ends using the enzyme telomerase, as the
enzymes that normally replicate
DNA cannot copy the extreme 3′ ends
of chromosomes. These specialized chromosome caps also help
DNA ends, and stop the
DNA repair systems in the cell from
treating them as damage to be corrected. In human cells, telomeres
are usually lengths of single-stranded
DNA containing several thousand
repeats of a simple TTAGGG sequence.
DNA quadruplex formed by telomere repeats. The looped conformation of
DNA backbone is very different from the typical
DNA helix. The
green spheres in the center represent potassium ions.
These guanine-rich sequences may stabilize chromosome ends by forming
structures of stacked sets of four-base units, rather than the usual
base pairs found in other
DNA molecules. Here, four guanine bases form
a flat plate and these flat four-base units then stack on top of each
other, to form a stable
G-quadruplex structure. These structures
are stabilized by hydrogen bonding between the edges of the bases and
chelation of a metal ion in the centre of each four-base unit.
Other structures can also be formed, with the central set of four
bases coming from either a single strand folded around the bases, or
several different parallel strands, each contributing one base to the
In addition to these stacked structures, telomeres also form large
loop structures called telomere loops, or T-loops. Here, the
DNA curls around in a long circle stabilized by
telomere-binding proteins. At the very end of the T-loop, the
DNA is held onto a region of double-stranded
DNA by the telomere strand disrupting the double-helical
DNA and base
pairing to one of the two strands. This triple-stranded structure is
called a displacement loop or D-loop.
Branched DNA can form networks containing multiple branches.
Branched DNA and
In DNA, fraying occurs when non-complementary regions exist at the end
of an otherwise complementary double-strand of DNA. However, branched
DNA can occur if a third strand of
DNA is introduced and contains
adjoining regions able to hybridize with the frayed regions of the
pre-existing double-strand. Although the simplest example of branched
DNA involves only three strands of DNA, complexes involving additional
strands and multiple branches are also possible.
Branched DNA can
be used in nanotechnology to construct geometric shapes, see the
section on uses in technology below.
Chemical modifications and altered
Structure of cytosine with and without the 5-methyl group. Deamination
converts 5-methylcytosine into thymine.
Base modifications and
DNA methylation and
The expression of genes is influenced by how the
DNA is packaged in
chromosomes, in a structure called chromatin. Base modifications can
be involved in packaging, with regions that have low or no gene
expression usually containing high levels of methylation of cytosine
DNA packaging and its influence on gene expression can also
occur by covalent modifications of the histone protein core around
DNA is wrapped in the chromatin structure or else by remodeling
carried out by chromatin remodeling complexes (see Chromatin
remodeling). There is, further, crosstalk between
DNA methylation and
histone modification, so they can coordinately affect chromatin and
For one example, cytosine methylation produces 5-methylcytosine, which
is important for
X-inactivation of chromosomes. The average level
of methylation varies between organisms – the worm
Caenorhabditis elegans lacks cytosine methylation, while vertebrates
have higher levels, with up to 1% of their
5-methylcytosine. Despite the importance of 5-methylcytosine, it
can deaminate to leave a thymine base, so methylated cytosines are
particularly prone to mutations. Other base modifications include
adenine methylation in bacteria, the presence of
5-hydroxymethylcytosine in the brain, and the glycosylation of
uracil to produce the "J-base" in kinetoplastids.
DNA damage (naturally occurring), Mutation, and
DNA damage theory of aging
A covalent adduct between a metabolically activated form of
benzo[a]pyrene, the major mutagen in tobacco smoke, and DNA
DNA can be damaged by many sorts of mutagens, which change the DNA
sequence. Mutagens include oxidizing agents, alkylating agents and
also high-energy electromagnetic radiation such as ultraviolet light
and X-rays. The type of
DNA damage produced depends on the type of
mutagen. For example, UV light can damage
DNA by producing thymine
dimers, which are cross-links between pyrimidine bases. On the
other hand, oxidants such as free radicals or hydrogen peroxide
produce multiple forms of damage, including base modifications,
particularly of guanosine, and double-strand breaks. A typical
human cell contains about 150,000 bases that have suffered oxidative
damage. Of these oxidative lesions, the most dangerous are
double-strand breaks, as these are difficult to repair and can produce
point mutations, insertions, deletions from the
DNA sequence, and
chromosomal translocations. These mutations can cause cancer.
Because of inherent limits in the
DNA repair mechanisms, if humans
lived long enough, they would all eventually develop cancer.
DNA damages that are naturally occurring, due to normal cellular
processes that produce reactive oxygen species, the hydrolytic
activities of cellular water, etc., also occur frequently. Although
most of these damages are repaired, in any cell some
DNA damage may
remain despite the action of repair processes. These remaining DNA
damages accumulate with age in mammalian postmitotic tissues. This
accumulation appears to be an important underlying cause of
Many mutagens fit into the space between two adjacent base pairs, this
is called intercalation. Most intercalators are aromatic and planar
molecules; examples include ethidium bromide, acridines, daunomycin,
and doxorubicin. For an intercalator to fit between base pairs, the
bases must separate, distorting the
DNA strands by unwinding of the
double helix. This inhibits both transcription and
causing toxicity and mutations. As a result,
may be carcinogens, and in the case of thalidomide, a teratogen.
Others such as benzo[a]pyrene diol epoxide and aflatoxin form DNA
adducts that induce errors in replication. Nevertheless, due to
their ability to inhibit
DNA transcription and replication, other
similar toxins are also used in chemotherapy to inhibit rapidly
growing cancer cells.
Location of eukaryote nuclear
DNA within the chromosomes.
DNA usually occurs as linear chromosomes in eukaryotes, and circular
chromosomes in prokaryotes. The set of chromosomes in a cell makes up
its genome; the human genome has approximately 3 billion base pairs of
DNA arranged into 46 chromosomes. The information carried by DNA
is held in the sequence of pieces of
DNA called genes. Transmission of
genetic information in genes is achieved via complementary base
pairing. For example, in transcription, when a cell uses the
information in a gene, the
DNA sequence is copied into a complementary
RNA sequence through the attraction between the
DNA and the correct
RNA nucleotides. Usually, this
RNA copy is then used to make a
matching protein sequence in a process called translation, which
depends on the same interaction between
RNA nucleotides. In
alternative fashion, a cell may simply copy its genetic information in
a process called
DNA replication. The details of these functions are
covered in other articles; here the focus is on the interactions
DNA and other molecules that mediate the function of the
Genes and genomes
Further information: Cell nucleus, Chromatin, Chromosome, Gene, and
Genomic DNA is tightly and orderly packed in the process called DNA
condensation, to fit the small available volumes of the cell. In
DNA is located in the cell nucleus, with small amounts in
mitochondria and chloroplasts. In prokaryotes, the
DNA is held within
an irregularly shaped body in the cytoplasm called the nucleoid.
The genetic information in a genome is held within genes, and the
complete set of this information in an organism is called its
genotype. A gene is a unit of heredity and is a region of
influences a particular characteristic in an organism. Genes contain
an open reading frame that can be transcribed, and regulatory
sequences such as promoters and enhancers, which control transcription
of the open reading frame.
In many species, only a small fraction of the total sequence of the
genome encodes protein. For example, only about 1.5% of the human
genome consists of protein-coding exons, with over 50% of human DNA
consisting of non-coding repetitive sequences. The reasons for
the presence of so much noncoding
DNA in eukaryotic genomes and the
extraordinary differences in genome size, or C-value, among species,
represent a long-standing puzzle known as the "
DNA sequences that do not code protein may still encode
RNA molecules, which are involved in the
regulation of gene expression.
RNA polymerase (blue) producing an m
RNA (green) from a
DNA sequences play structural roles in chromosomes.
Telomeres and centromeres typically contain few genes but are
important for the function and stability of chromosomes. An
abundant form of noncoding
DNA in humans are pseudogenes, which are
copies of genes that have been disabled by mutation. These
sequences are usually just molecular fossils, although they can
occasionally serve as raw genetic material for the creation of new
genes through the process of gene duplication and divergence.
Transcription and translation
Further information: Genetic code, Transcription (genetics), and
A gene is a sequence of
DNA that contains genetic information and can
influence the phenotype of an organism. Within a gene, the sequence of
bases along a
DNA strand defines a messenger
RNA sequence, which then
defines one or more protein sequences. The relationship between the
nucleotide sequences of genes and the amino-acid sequences of proteins
is determined by the rules of translation, known collectively as the
genetic code. The genetic code consists of three-letter 'words' called
codons formed from a sequence of three nucleotides (e.g. ACT, CAG,
In transcription, the codons of a gene are copied into messenger RNA
RNA polymerase. This
RNA copy is then decoded by a ribosome that
RNA sequence by base-pairing the messenger
RNA to transfer
RNA, which carries amino acids. Since there are 4 bases in 3-letter
combinations, there are 64 possible codons (43 combinations).
These encode the twenty standard amino acids, giving most amino acids
more than one possible codon. There are also three 'stop' or
'nonsense' codons signifying the end of the coding region; these are
the TAA, TGA, and TAG codons.
DNA replication. The double helix is unwound by a helicase and
topoisomerase. Next, one
DNA polymerase produces the leading strand
DNA polymerase binds to the lagging strand. This enzyme
makes discontinuous segments (called Okazaki fragments) before DNA
ligase joins them together.
Cell division is essential for an organism to grow, but, when a cell
divides, it must replicate the
DNA in its genome so that the two
daughter cells have the same genetic information as their parent. The
double-stranded structure of
DNA provides a simple mechanism for DNA
replication. Here, the two strands are separated and then each
DNA sequence is recreated by an enzyme called
DNA polymerase. This enzyme makes the complementary strand by finding
the correct base through complementary base pairing and bonding it
onto the original strand. As
DNA polymerases can only extend a DNA
strand in a 5′ to 3′ direction, different mechanisms are used to
copy the antiparallel strands of the double helix. In this way,
the base on the old strand dictates which base appears on the new
strand, and the cell ends up with a perfect copy of its DNA.
Extracellular nucleic acids
DNA (eDNA), most of it released by cell death, is
nearly ubiquitous in the environment. Its concentration in soil may be
as high as 2 μg/L, and its concentration in natural aquatic
environments may be as high at 88 μg/L. Various possible
functions have been proposed for eDNA: it may be involved in
horizontal gene transfer; it may provide nutrients; and it
may act as a buffer to recruit or titrate ions or antibiotics.
DNA acts as a functional extracellular matrix component
in the biofilms of several bacterial species. It may act as a
recognition factor to regulate the attachment and dispersal of
specific cell types in the biofilm; it may contribute to biofilm
formation; and it may contribute to the biofilm's physical
strength and resistance to biological stress.
Cell-free fetal DNA
Cell-free fetal DNA is found in the blood of the mother, and can be
sequenced to determine a great deal of information about the
Interactions with proteins
All the functions of
DNA depend on interactions with proteins. These
protein interactions can be non-specific, or the protein can bind
specifically to a single
DNA sequence. Enzymes can also bind to DNA
and of these, the polymerases that copy the
DNA base sequence in
DNA replication are particularly important.
Further information: DNA-binding protein
DNA (in orange) with histones (in blue). These
proteins' basic amino acids bind to the acidic phosphate groups on
Structural proteins that bind
DNA are well-understood examples of
non-specific DNA-protein interactions. Within chromosomes,
DNA is held
in complexes with structural proteins. These proteins organize the DNA
into a compact structure called chromatin. In eukaryotes, this
DNA binding to a complex of small basic proteins
called histones, while in prokaryotes multiple types of proteins are
involved. The histones form a disk-shaped complex called a
nucleosome, which contains two complete turns of double-stranded DNA
wrapped around its surface. These non-specific interactions are formed
through basic residues in the histones, making ionic bonds to the
acidic sugar-phosphate backbone of the DNA, and are thus largely
independent of the base sequence. Chemical modifications of these
basic amino acid residues include methylation, phosphorylation, and
acetylation. These chemical changes alter the strength of the
interaction between the
DNA and the histones, making the
DNA more or
less accessible to transcription factors and changing the rate of
transcription. Other non-specific DNA-binding proteins in
chromatin include the high-mobility group proteins, which bind to bent
or distorted DNA. These proteins are important in bending arrays
of nucleosomes and arranging them into the larger structures that make
A distinct group of DNA-binding proteins is the DNA-binding proteins
that specifically bind single-stranded DNA. In humans, replication
protein A is the best-understood member of this family and is used in
processes where the double helix is separated, including DNA
replication, recombination, and
DNA repair. These binding
proteins seem to stabilize single-stranded
DNA and protect it from
forming stem-loops or being degraded by nucleases.
The lambda repressor helix-turn-helix transcription factor bound to
In contrast, other proteins have evolved to bind to particular DNA
sequences. The most intensively studied of these are the various
transcription factors, which are proteins that regulate transcription.
Each transcription factor binds to one particular set of
and activates or inhibits the transcription of genes that have these
sequences close to their promoters. The transcription factors do this
in two ways. Firstly, they can bind the
RNA polymerase responsible for
transcription, either directly or through other mediator proteins;
this locates the polymerase at the promoter and allows it to begin
transcription. Alternatively, transcription factors can bind
enzymes that modify the histones at the promoter. This changes the
accessibility of the
DNA template to the polymerase.
DNA targets can occur throughout an organism's genome,
changes in the activity of one type of transcription factor can affect
thousands of genes. Consequently, these proteins are often the
targets of the signal transduction processes that control responses to
environmental changes or cellular differentiation and development. The
specificity of these transcription factors' interactions with
from the proteins making multiple contacts to the edges of the DNA
bases, allowing them to "read" the
DNA sequence. Most of these
base-interactions are made in the major groove, where the bases are
The restriction enzyme
EcoRV (green) in a complex with its substrate
Nucleases and ligases
Nucleases are enzymes that cut
DNA strands by catalyzing the
hydrolysis of the phosphodiester bonds. Nucleases that hydrolyse
nucleotides from the ends of
DNA strands are called exonucleases,
while endonucleases cut within strands. The most frequently used
nucleases in molecular biology are the restriction endonucleases,
DNA at specific sequences. For instance, the
shown to the left recognizes the 6-base sequence 5′-GATATC-3′ and
makes a cut at the horizontal line. In nature, these enzymes protect
bacteria against phage infection by digesting the phage
DNA when it
enters the bacterial cell, acting as part of the restriction
modification system. In technology, these sequence-specific
nucleases are used in molecular cloning and
DNA ligases can rejoin cut or broken
Ligases are particularly important in lagging strand
as they join together the short segments of
DNA produced at the
replication fork into a complete copy of the
DNA template. They are
also used in
DNA repair and genetic recombination.
Topoisomerases and helicases
Topoisomerases are enzymes with both nuclease and ligase activity.
These proteins change the amount of supercoiling in DNA. Some of these
enzymes work by cutting the
DNA helix and allowing one section to
rotate, thereby reducing its level of supercoiling; the enzyme then
DNA break. Other types of these enzymes are capable of
DNA helix and then passing a second strand of
this break, before rejoining the helix. Topoisomerases are
required for many processes involving DNA, such as
DNA replication and
Helicases are proteins that are a type of molecular motor. They use
the chemical energy in nucleoside triphosphates, predominantly
adenosine triphosphate (ATP), to break hydrogen bonds between bases
and unwind the
DNA double helix into single strands. These
enzymes are essential for most processes where enzymes need to access
Polymerases are enzymes that synthesize polynucleotide chains from
nucleoside triphosphates. The sequence of their products is created
based on existing polynucleotide chains—which are called templates.
These enzymes function by repeatedly adding a nucleotide to the 3′
hydroxyl group at the end of the growing polynucleotide chain. As a
consequence, all polymerases work in a 5′ to 3′ direction. In
the active site of these enzymes, the incoming nucleoside triphosphate
base-pairs to the template: this allows polymerases to accurately
synthesize the complementary strand of their template. Polymerases are
classified according to the type of template that they use.
DNA replication, DNA-dependent
DNA polymerases make copies of DNA
polynucleotide chains. To preserve biological information, it is
essential that the sequence of bases in each copy are precisely
complementary to the sequence of bases in the template strand. Many
DNA polymerases have a proofreading activity. Here, the polymerase
recognizes the occasional mistakes in the synthesis reaction by the
lack of base pairing between the mismatched nucleotides. If a mismatch
is detected, a 3′ to 5′ exonuclease activity is activated and the
incorrect base removed. In most organisms,
function in a large complex called the replisome that contains
multiple accessory subunits, such as the
DNA clamp or helicases.
DNA polymerases are a specialized class of polymerases
that copy the sequence of an
RNA strand into DNA. They include reverse
transcriptase, which is a viral enzyme involved in the infection of
cells by retroviruses, and telomerase, which is required for the
replication of telomeres. For example, HIV reverse
transcriptase is an enzyme for AIDS virus replication. Telomerase
is an unusual polymerase because it contains its own
RNA template as
part of its structure. It synthesizes telomeres at the ends of
Telomeres prevent fusion of the ends of neighboring
chromosomes and protect chromosome ends from damage.
Transcription is carried out by a DNA-dependent
RNA polymerase that
copies the sequence of a
DNA strand into RNA. To begin transcribing a
RNA polymerase binds to a sequence of
DNA called a promoter
and separates the
DNA strands. It then copies the gene sequence into a
RNA transcript until it reaches a region of
DNA called the
terminator, where it halts and detaches from the DNA. As with human
RNA polymerase II, the enzyme that
transcribes most of the genes in the human genome, operates as part of
a large protein complex with multiple regulatory and accessory
Structure of the
Holliday junction intermediate in genetic
recombination. The four separate
DNA strands are coloured red, blue,
green and yellow.
Further information: Genetic recombination
Recombination involves the breaking and rejoining of two chromosomes
(M and F) to produce two rearranged chromosomes (C1 and C2).
DNA helix usually does not interact with other segments of DNA, and
in human cells, the different chromosomes even occupy separate areas
in the nucleus called "chromosome territories". This physical
separation of different chromosomes is important for the ability of
DNA to function as a stable repository for information, as one of the
few times chromosomes interact is in chromosomal crossover which
occurs during sexual reproduction, when genetic recombination occurs.
Chromosomal crossover is when two
DNA helices break, swap a section
and then rejoin.
Recombination allows chromosomes to exchange genetic information and
produces new combinations of genes, which increases the efficiency of
natural selection and can be important in the rapid evolution of new
Genetic recombination can also be involved in DNA
repair, particularly in the cell's response to double-strand
The most common form of chromosomal crossover is homologous
recombination, where the two chromosomes involved share very similar
sequences. Non-homologous recombination can be damaging to cells, as
it can produce chromosomal translocations and genetic abnormalities.
The recombination reaction is catalyzed by enzymes known as
recombinases, such as RAD51. The first step in recombination is a
double-stranded break caused by either an endonuclease or damage to
the DNA. A series of steps catalyzed in part by the recombinase
then leads to joining of the two helices by at least one Holliday
junction, in which a segment of a single strand in each helix is
annealed to the complementary strand in the other helix. The Holliday
junction is a tetrahedral junction structure that can be moved along
the pair of chromosomes, swapping one strand for another. The
recombination reaction is then halted by cleavage of the junction and
re-ligation of the released DNA. Only strands of like polarity
DNA during recombination. There are two types of cleavage:
east-west cleavage and north-south cleavage. The north-south cleavage
nicks both strands of DNA, while the east-west cleavage has one strand
DNA intact. The formation of a
Holliday junction during
recombination makes it possible for genetic diversity, genes to
exchange on chromosomes, and expression of wild-type viral genomes.
RNA world hypothesis
DNA contains the genetic information that allows all modern living
things to function, grow and reproduce. However, it is unclear how
long in the 4-billion-year history of life
DNA has performed this
function, as it has been proposed that the earliest forms of life may
RNA as their genetic material.
RNA may have acted
as the central part of early cell metabolism as it can both transmit
genetic information and carry out catalysis as part of ribozymes.
RNA world where nucleic acid would have been used for
both catalysis and genetics may have influenced the evolution of the
current genetic code based on four nucleotide bases. This would occur,
since the number of different bases in such an organism is a trade-off
between a small number of bases increasing replication accuracy and a
large number of bases increasing the catalytic efficiency of
ribozymes. However, there is no direct evidence of ancient
genetic systems, as recovery of
DNA from most fossils is impossible
DNA survives in the environment for less than one million
years, and slowly degrades into short fragments in solution.
Claims for older
DNA have been made, most notably a report of the
isolation of a viable bacterium from a salt crystal 250 million years
old, but these claims are controversial.
Building blocks of
DNA (adenine, guanine, and related organic
molecules) may have been formed extraterrestrially in outer
RNA organic compounds of life,
including uracil, cytosine, and thymine, have also been formed in the
laboratory under conditions mimicking those found in outer space,
using starting chemicals, such as pyrimidine, found in meteorites.
Pyrimidine, like polycyclic aromatic hydrocarbons (PAHs), the most
carbon-rich chemical found in the universe, may have been formed in
red giants or in interstellar cosmic dust and gas clouds.
Uses in technology
Further information: Molecular biology,
Nucleic acid methods, and
Methods have been developed to purify
DNA from organisms, such as
phenol-chloroform extraction, and to manipulate it in the laboratory,
such as restriction digests and the polymerase chain reaction. Modern
biology and biochemistry make intensive use of these techniques in
Recombinant DNA is a man-made
that has been assembled from other
DNA sequences. They can be
transformed into organisms in the form of plasmids or in the
appropriate format, by using a viral vector. The genetically
modified organisms produced can be used to produce products such as
recombinant proteins, used in medical research, or be grown in
Forensic scientists can use
DNA in blood, semen, skin, saliva or hair
found at a crime scene to identify a matching
DNA of an individual,
such as a perpetrator. This process is formally termed DNA
profiling, but may also be called "genetic fingerprinting". In DNA
profiling, the lengths of variable sections of repetitive DNA, such as
short tandem repeats and minisatellites, are compared between people.
This method is usually an extremely reliable technique for identifying
a matching DNA. However, identification can be complicated if the
scene is contaminated with
DNA from several people.
was developed in 1984 by British geneticist Sir Alec Jeffreys,
and first used in forensic science to convict
Colin Pitchfork in the
1988 Enderby murders case.
The development of forensic science and the ability to now obtain
genetic matching on minute samples of blood, skin, saliva, or hair has
led to re-examining many cases. Evidence can now be uncovered that was
scientifically impossible at the time of the original examination.
Combined with the removal of the double jeopardy law in some places,
this can allow cases to be reopened where prior trials have failed to
produce sufficient evidence to convince a jury. People charged with
serious crimes may be required to provide a sample of
DNA for matching
purposes. The most obvious defense to
DNA matches obtained
forensically is to claim that cross-contamination of evidence has
occurred. This has resulted in meticulous strict handling procedures
with new cases of serious crime.
DNA profiling is also used
successfully to positively identify victims of mass casualty
incidents, bodies or body parts in serious accidents, and
individual victims in mass war graves, via matching to family members.
DNA profiling is also used in
DNA paternity testing
DNA paternity testing to determine if
someone is the biological parent or grandparent of a child with the
probability of parentage is typically 99.99% when the alleged parent
is biologically related to the child. Normal
DNA sequencing methods
happen after birth, but there are new methods to test paternity while
a mother is still pregnant.
DNA enzymes or catalytic DNA
Further information: Deoxyribozyme
Deoxyribozymes, also called DNAzymes or catalytic DNA, are first
discovered in 1994. They are mostly single stranded
isolated from a large pool of random
DNA sequences through a
combinatorial approach called in vitro selection or systematic
evolution of ligands by exponential enrichment (SELEX). DNAzymes
catalyze variety of chemical reactions including RN
A-DNA ligation, amino acids phosphorylation-dephosphorylation,
carbon-carbon bond formation, and etc. DNAzymes can enhance catalytic
rate of chemical reactions up to 100,000,000,000-fold over the
uncatalyzed reaction. The most extensively studied class of
DNAzymes is RNA-cleaving types which have been used to detect
different metal ions and designing therapeutic agents. Several
metal-specific DNAzymes have been reported including the GR-5 DNAzyme
(lead-specific), the CA1-3 DNAzymes (copper-specific), the
39E DNAzyme (uranyl-specific) and the NaA43 DNAzyme
(sodium-specific). The NaA43 DNAzyme, which is reported to be
more than 10,000-fold selective for sodium over other metal ions, was
used to make a real-time sodium sensor in living cells.
Further information: Bioinformatics
Bioinformatics involves the development of techniques to store, data
mine, search and manipulate biological data, including
acid sequence data. These have led to widely applied advances in
computer science, especially string searching algorithms, machine
learning, and database theory. String searching or matching
algorithms, which find an occurrence of a sequence of letters inside a
larger sequence of letters, were developed to search for specific
sequences of nucleotides. The
DNA sequence may be aligned with
DNA sequences to identify homologous sequences and locate the
specific mutations that make them distinct. These techniques,
especially multiple sequence alignment, are used in studying
phylogenetic relationships and protein function. Data sets
representing entire genomes' worth of
DNA sequences, such as those
produced by the Human
Genome Project, are difficult to use without the
annotations that identify the locations of genes and regulatory
elements on each chromosome. Regions of
DNA sequence that have the
characteristic patterns associated with protein- or RNA-coding genes
can be identified by gene finding algorithms, which allow researchers
to predict the presence of particular gene products and their possible
functions in an organism even before they have been isolated
experimentally. Entire genomes may also be compared, which can
shed light on the evolutionary history of particular organism and
permit the examination of complex evolutionary events.
DNA structure at left (schematic shown) will self-assemble into
the structure visualized by atomic force microscopy at right. DNA
nanotechnology is the field that seeks to design nanoscale structures
using the molecular recognition properties of
DNA molecules. Image
from Strong, 2004.
DNA nanotechnology uses the unique molecular recognition properties of
DNA and other nucleic acids to create self-assembling branched DNA
complexes with useful properties.
DNA is thus used as a
structural material rather than as a carrier of biological
information. This has led to the creation of two-dimensional periodic
lattices (both tile-based and using the
DNA origami method) and
three-dimensional structures in the shapes of polyhedra.
Nanomechanical devices and algorithmic self-assembly have also been
demonstrated, and these
DNA structures have been used to template
the arrangement of other molecules such as gold nanoparticles and
History and anthropology
Phylogenetics and Genetic genealogy
DNA collects mutations over time, which are then inherited, it
contains historical information, and, by comparing
geneticists can infer the evolutionary history of organisms, their
phylogeny. This field of phylogenetics is a powerful tool in
evolutionary biology. If
DNA sequences within a species are compared,
population geneticists can learn the history of particular
populations. This can be used in studies ranging from ecological
genetics to anthropology; For example,
DNA evidence is being used to
try to identify the
Ten Lost Tribes
Ten Lost Tribes of Israel.
DNA digital data storage
In a paper published in Nature in January 2013, scientists from the
Bioinformatics Institute and
Agilent Technologies proposed a
mechanism to use DNA's ability to code information as a means of
digital data storage. The group was able to encode 739 kilobytes of
DNA code, synthesize the actual DNA, then sequence the DNA
and decode the information back to its original form, with a reported
100% accuracy. The encoded information consisted of text files and
audio files. A prior experiment was published in August 2012. It was
conducted by researchers at Harvard University, where the text of a
54,000-word book was encoded in DNA.
Moreover, in living cells, the storage can be turned active by
enzymes. Light-gated protein domains fused to
DNA processing enzymes
are suitable for that task in vitro. Fluorescent
exonucleases can transmit the output according to the nucleotide they
Further information: History of molecular biology
James Watson and
Francis Crick (right), co-originators of the
double-helix model, with
Maclyn McCarty (left).
Pencil sketch of the
DNA double helix by
Francis Crick in 1953
DNA was first isolated by the Swiss physician
Friedrich Miescher who,
in 1869, discovered a microscopic substance in the pus of discarded
surgical bandages. As it resided in the nuclei of cells, he called it
"nuclein". In 1878,
Albrecht Kossel isolated the non-protein
component of "nuclein", nucleic acid, and later isolated its five
primary nucleobases. In 1919, Phoebus Levene identified the
base, sugar, and phosphate nucleotide unit. Levene suggested that
DNA consisted of a string of nucleotide units linked together through
the phosphate groups. Levene thought the chain was short and the bases
repeated in a fixed order. In 1937,
William Astbury produced the first
X-ray diffraction patterns that showed that
DNA had a regular
structure. In 1927,
Nikolai Koltsov proposed that inherited
traits would be inherited via a "giant hereditary molecule" made up of
"two mirror strands that would replicate in a semi-conservative
fashion using each strand as a template". In 1928, Frederick
Griffith in his experiment discovered that traits of the "smooth" form
of Pneumococcus could be transferred to the "rough" form of the same
bacteria by mixing killed "smooth" bacteria with the live "rough"
form. This system provided the first clear suggestion that
DNA carries genetic information—the Avery–MacLeod–McCarty
experiment—when Oswald Avery, along with coworkers Colin MacLeod and
Maclyn McCarty, identified
DNA as the transforming principle in
1943. DNA's role in heredity was confirmed in 1952 when Alfred
Martha Chase in the
Hershey–Chase experiment showed that
DNA is the genetic material of the T2 phage.
A blue plaque outside The Eagle pub commemorating Crick and Watson
Late in 1951,
Francis Crick started working with
James Watson at the
Cavendish Laboratory within the University of Cambridge. In 1953,
Watson and Crick suggested what is now accepted as the first correct
double-helix model of
DNA structure in the journal Nature. Their
double-helix, molecular model of
DNA was then based on one X-ray
diffraction image (labeled as "Photo 51") taken by Rosalind
Raymond Gosling in May 1952, and the information that the
DNA bases are paired. On 28 February 1953 Crick interrupted patrons'
lunchtime at The Eagle pub in Cambridge to announce that he and Watson
had "discovered the secret of life".
Experimental evidence supporting the Watson and Crick model was
published in a series of five articles in the same issue of
Nature. Of these, Franklin and Gosling's paper was the first
publication of their own
X-ray diffraction data and original analysis
method that partly supported the Watson and Crick model; this
issue also contained an article on
DNA structure by Maurice Wilkins
and two of his colleagues, whose analysis and in vivo B-
patterns also supported the presence in vivo of the double-helical DNA
configurations as proposed by Crick and Watson for their double-helix
molecular model of
DNA in the prior two pages of Nature. In 1962,
after Franklin's death, Watson, Crick, and Wilkins jointly received
the Nobel Prize in Physiology or Medicine. Nobel Prizes are
awarded only to living recipients. A debate continues about who should
receive credit for the discovery.
In an influential presentation in 1957, Crick laid out the central
dogma of molecular biology, which foretold the relationship between
DNA, RNA, and proteins, and articulated the "adaptor hypothesis".
Final confirmation of the replication mechanism that was implied by
the double-helical structure followed in 1958 through the
Meselson–Stahl experiment. Further work by Crick and coworkers
showed that the genetic code was based on non-overlapping triplets of
bases, called codons, allowing Har Gobind Khorana, Robert W. Holley,
Marshall Warren Nirenberg
Marshall Warren Nirenberg to decipher the genetic code. These
findings represent the birth of molecular biology.
DNA-encoded chemical library
Comparison of nucleic acid simulation software
Nucleic acid double helix
Nucleic acid notation
Nucleic acid sequence
X-ray scattering techniques
Xeno nucleic acid
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