Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions
specifying the biological development of all cellular forms of life (and many viruses).
DNA is often referred to as the molecule of heredity, as it is responsible for the
genetic propagation of most inherited traits. During reproduction, DNA is replicated
and transmitted to the offspring.
Basically what the description above says is that DNA is a basic building block of life
and that it contains all the information that living things need to function correctly.
For example, in humans this can range from your hair colour to the ability to roll your
tongue and to any herditary diseases.
Your DNA is composed of genes inherited from both your mother and father. DNA
from both of your parents was combined to form the genome of a fertilized egg (that's
you), then that egg divided many times, copying the DNA before every division, until
all the cells of your body were formed. As a result, each cell in your body contains
copies of the DNA from your parents (except red blood cells, which lose their
chromosomal DNA but cannot divide).
Contents
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• 1 DNA in brief
• 2 DNA in practice
o 2.1 DNA in crime
o 2.2 DNA in computation
• 3 Overview of molecular structure
• 4 The role of the sequence
• 5 DNA replication
• 6 Mechanical properties relevant to biology
o 6.1 Strands association and dissociation
o 6.2 Circular DNA
o 6.3 Great length versus tiny breadth
o 6.4 Different helix geometries
6.4.1 Supercoiled DNA
6.4.2 Conditions for formation of
A and Z helices
6.4.3 Table of comparison of the
properties of different helical
forms
o 6.5 Non-helical forms
• 7 Direction of DNA strands
o 7.1 Chemical nomenclature (5' and 3')
o 7.2 Sense and antisense
o 7.3 An exception: viruses
o 7.4 As viewed by topologists
• 8 Single-stranded DNA (ssDNA) and repair of
mutations
• 9 The history of DNA research
o 9.1 First isolation of DNA
o 9.2 Establishing a link between heritable
traits and chromosomes
o 9.3 Discovery of the structure of DNA
9.3.1 Discovery that DNA is
helical
9.3.2 Discovery that
complementary nucleotides occur
in equal proportions
9.3.3 Watson and Crick's model
9.3.4 Publishing of the "Central
Dogma"
• 10 Bibliography
• 11 External links
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DNA in brief
Unsolved problems in biology: Do all organisms link together to a primary source? Given a DNA
sequence, what shape will the protein fold into? Given a particular desired shape, what DNA sequence
will produce it? What are all the functions of the DNA? The building block of life may be a precursor
to a generation of electronic devices and computers, but what are the electronic properties of DNA? Is
junk DNA only molecular garbage?
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DNA in practice
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DNA in crime
Forensic scientists can use DNA located in blood, semen, or hair left at the scene of a
crime to identify a possible suspect, a process called DNA profiling or genetic
fingerprinting. In DNA profiling the relative lengths of sections of repetitive DNA,
such as short tandem repeats and minisatellites, are compared. DNA profiling was
developed in 1984 by English geneticist Alec Jeffreys, and was first used in 1986 in
the Enderby murders case in Leicestershire, England. Many jurisdictions require
convicts of certain types of crimes to provide a sample of DNA for inclusion in a
computerized database. This has helped investigators solve old cases where the
perpetrator was unknown and only a DNA sample was obtained from the scene
(particularly in rape cases between strangers). This method is one of the most reliable
techniques for identifying a criminal, but is not always perfect, for example if no
DNA can be retrieved, or if the scene is contaminated with the DNA of several
possible suspects.
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DNA in computation
Despite its biological origins, DNA plays an important role in computer science, both
as a motivating research problem and as a method of computation in itself, called
DNA computing.
Databases have also been strongly motivated by DNA research, which requires special
tools for storing and manipulating DNA sequences. Databases specialized for this
purpose are called genomic databases, and have a number of unique technical
challenges associated with the operations of approximate matching, sequence
comparison, finding repeating patterns, and homology searching.
In 1994, Leonard Adleman of the University of Southern California made headlines
when he discovered a way of solving the directed Hamiltonian path problem, an NP-
complete problem, using tools from molecular biology, in particular DNA. The new
approach, dubbed DNA computing, has practical advantages over traditional
computers in power use, space use, and efficiency, due to its ability to highly
parallelize the computation (see parallel computing). A number of other problems,
including simulation of various abstract machines, the boolean satisfiability problem,
and the bounded version of the Post correspondence problem, have since been tackled
using DNA computing.
Due to its compactness, DNA also has an important role in cryptography, where in
particular it allows unbreakable one-time pads to be efficiently constructed and
used.[1]
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Schematic representation of the DNA which illustrates its double helix structure
The diversity of the bases means that there are four kinds of nucleotides, which are
commonly referred to by the identity of their bases. These are adenine (A), thymine
(T), cytosine (C), and guanine (G).
In a DNA double helix, two polynucleotide strands can associate through the
hydrophobic effect and pi stacking. Specificity of which strands stay associated is
determined by complementary pairing. Each base forms hydrogen bonds readily to
only one other -- A to T and C to G -- so that the identity of the base on one strand
dictates the strength of the association; the more complementary bases exist, the
stronger and longer-lasting the association.
The cell's machinery is capable of melting or disassociating a DNA double helix, and
using each DNA strand as a template for synthesizing a new strand which is nearly
identical to the previous strand. Errors that occur in the synthesis are known as
mutations. The process known as PCR mimics this process in vitro in a nonliving
system.
Because pairing causes the nucleotide bases to face the helical axis, the sugar and
phosphate groups of the nucleotides run along the outside; the two chains they form
are sometimes called the "backbones" of the helix. In fact, it is chemical bonds
between the phosphates and the sugars that link one nucleotide to the next in the DNA
strand.
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In many species, only a small fraction of the total sequence of the genome appears to
encode protein. For example, only about 1.5% of the human genome consists of
protein-coding exons. The function of the rest is a matter of speculation. It is known
that certain nucleotide sequences specify affinity for DNA binding proteins, which
play a wide variety of vital roles, in particular through control of replication and
transcription. These sequences are frequently called regulatory sequences, and
researchers assume that so far they have identified only a tiny fraction of the total that
exist. "Junk DNA" represents sequences that do not yet appear to contain genes or to
have a function. The reasons for the presence of so much non-coding DNA in
eukaryotic genomes and the extraordinary differences in genome size ("C-value")
among species represent a long-standing puzzle in DNA research known as the "C-
value enigma".
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DNA replication
Main article: DNA replication
DNA replication
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The hydrogen bonds between the strands of the double helix are weak enough that
they can be easily separated by enzymes. Enzymes known as helicases unwind the
strands to facilitate the advance of sequence-reading enzymes such as DNA
polymerase. The unwinding requires that helicases chemically cleave the phosphate
backbone of one of the strands so that it can swivel around the other. The strands can
also be separated by gentle heating, as used in PCR, provided they have fewer than
about 10,000 base pairs (10 kilobase pairs, or 10 kbp). The intertwining of the DNA
strands makes long segments difficult to separate.
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Circular DNA
When the ends of a piece of double-helical DNA are joined so that it forms a circle, as
in plasmid DNA, the strands are topologically knotted. This means they cannot be
separated by gentle heating or by any process that does not involve breaking a strand.
The task of unknotting topologically linked strands of DNA falls to enzymes known
as topoisomerases. Some of these enzymes unknot circular DNA by cleaving two
strands so that another double-stranded segment can pass through. Unknotting is
required for the replication of circular DNA as well as for various types of
recombination in linear DNA.
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The narrow breadth of the double helix makes it impossible to detect by conventional
electron microscopy, except by heavy staining. At the same time, the DNA found in
many cells can be macroscopic in length -- approximately 5 centimetres long for
strands in a human chromosome. Consequently, cells must compact or "package"
DNA to carry it within them. This is one of the functions of the chromosomes, which
contain spool-like proteins known as histones, around which DNA winds.
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The DNA helix can assume one of three slightly different geometries, of which the
"B" form described by James D. Watson and Francis Crick is believed to predominate
in cells. It is 2 nanometres wide and extends 3.4 nanometres per 10 bp of sequence.
This is also the approximate length of sequence in which the double helix makes one
complete turn about its axis. This frequency of twist (known as the helical pitch)
depends largely on stacking forces that each base exerts on its neighbors in the chain.
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Supercoiled DNA
The B form of the DNA helix twists 360° per 10.6 bp in the absence of strain. But
many molecular biological processes can induce strain. A DNA segment with excess
or insufficient helical twisting is referred to, respectively, as positively or negatively
"supercoiled". DNA in vivo is typically negatively supercoiled, which facilitates the
unwinding of the double-helix required for RNA transcription.
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The two other known double-helical forms of DNA, called A and Z, differ modestly in
their geometry and dimensions. The A form appears likely to occur only in dehydrated
samples of DNA, such as those used in crystallographic experiments, and possibly in
hybrid pairings of DNA and RNA strands. Segments of DNA that cells have
methylated for regulatory purposes may adopt the Z geometry, in which the strands
turn about the helical axis like a mirror image of the B form.
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Non-helical forms
Other, including non-helical, forms of DNA have been described, for example a side-
by-side (SBS) configuration. Indeed, it is far from certain that the B-form double
helix is the dominant form in living cells.
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Direction of DNA strands
The asymmetric shape and linkage of nucleotides means that a DNA strand always
has a discernible orientation or directionality. Because of this directionality, close
inspection of a double helix reveals that nucleotides are heading one way along one
strand (the "ascending strand"), and the other way along the other strand (the
"descending strand"). This arrangement of the strands is called antiparallel.
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For reasons of chemical nomenclature, people who work with DNA refer to the
asymmetric ends of each strand as the 5' and 3' ends (pronounced "five prime" and
"three prime"). DNA workers and enzymes alike always read nucleotide sequences in
the "5' to 3' direction". In a vertically oriented double helix, the 3' strand is said to be
ascending while the 5' strand is said to be descending.
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An exception: viruses
Some viruses blur the distinction between sense and antisense, because certain
sequences of their genomes do double duty, encoding one protein when read 5' to 3'
along one strand, and a second protein when read in the opposite direction along the
other strand. As a result, the genomes of these viruses are unusually compact for the
number of genes they contain, which biologists view as an adaptation.
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As viewed by topologists
Topologists like to note that the juxtaposition of the 3′ end of one DNA strand beside
the 5′ end of the other at both ends of a double-helical segment makes the
arrangement a "crab canon".
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Single-stranded DNA (ssDNA) and repair of
mutations
In some viruses DNA appears in a non-helical, single-stranded form. Because many of
the DNA repair mechanisms of cells work only on paired bases, viruses that carry
single-stranded DNA genomes mutate more frequently than they would otherwise. As
a result, such species may adapt more rapidly to avoid extinction. The result would
not be so favorable in more complicated and more slowly replicating organisms,
however, which may explain why only viruses carry single-stranded DNA. These
viruses presumably also benefit from the lower cost of replicating one strand versus
two.
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The discovery that DNA was the carrier of genetic information was a process that
required many earlier discoveries. The existence of DNA was discovered in the mid
19th century. However, it was only in the early 20th century that researchers began
suggesting that it might store genetic information. This was only accepted after the
structure of DNA was elucidated by Watson and Crick in their 1953 Nature
publication. Watson and Crick proposed the central dogma of molecular biology in
1957, describing the process whereby proteins are produced from nucleic DNA.
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Working in the 19th century, biochemists initially isolated DNA and RNA (mixed
together) from cell nuclei. They were relatively quick to appreciate the polymeric
nature of their "nucleic acid" isolates, but realized only later that nucleotides were of
two types--one containing ribose and the other deoxyribose. It was this subsequent
discovery that led to the identification and naming of DNA as a substance distinct
from RNA.
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Just how the presence of specific features in the molecular structure of chromosomes
could produce traits and behaviors in living organisms was unimaginable at the time.
Because chemical dissection of DNA samples always yielded the same four
nucleotides, the chemical composition of DNA appeared simple, perhaps even
uniform. Organisms, on the other hand, are fantastically complex individually and
widely diverse collectively. Geneticists did not speak of genes as conveyors of
"information" in such words, but if they had, they would not have hesitated to
quantify the amount of information that genes need to convey as vast. The idea that
information might reside in a chemical in the same way that it exists in text--as a
finite alphabet of letters arranged in a sequence of unlimited length--had not yet been
conceived. It would emerge upon the discovery of DNA's structure, but few
researchers imagined that DNA's structure had much to say about genetics.
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In the 1950s, only a few groups made it their goal to determine the structure of DNA.
These included an American group led by Linus Pauling, and two groups in Britain.
At the University of Cambridge, Crick and Watson were building physical models
using metal rods and balls, in which they incorporated the known chemical structures
of the nucleotides, as well as the known position of the linkages joining one
nucleotide to the next along the polymer. At King's College, London, Maurice Wilkins
and Rosalind Franklin were examining X-ray diffraction patterns of DNA fibers. Of
the three groups, only the London group was able to produce good quality diffraction
patterns and thus produce sufficient quantitative data about the structure
The chemical structure of DNA
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A key inspiration in the work of all of these teams was the discovery in 1948 by
Pauling that many proteins included helical (see alpha helix) shapes. Pauling had
deduced this structure from X-ray patterns. Even in the initial diffraction data from
DNA by Maurice Wilkins, it was evident that the structure involved helices. But this
insight was only a beginning. There remained the questions of how many strands
came together, whether this number was the same for every helix, whether the bases
pointed toward the helical axis or away, and ultimately what were the explicit angles
and coordinates of all the bonds and atoms. Such questions motivated the modeling
efforts of Watson and Crick.
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In their modeling, Watson and Crick restricted themselves to what they saw as
chemically and biologically reasonable. Still, the breadth of possibilities was very
wide. A breakthrough occurred in 1952, when Erwin Chargaff visited Cambridge and
inspired Crick with a description of experiments Chargaff had published in 1947.
Chargaff had observed that the proportions of the four nucleotides vary between one
DNA sample and the next, but that for particular pairs of nucleotides -- adenine and
thymine, guanine and cytosine -- the two nucleotides are always present in equal
proportions.
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Watson and Crick had begun to contemplate double helical arrangements, but they
lacked information about the amount of twist (pitch) and the distance between the two
strands. Fortunately Rosalind Franklin had to disclose some of her findings for the
Medical Research Council and Crick saw this material through MaxPerutz's links to
the MRC. Franklin's work confirmed a double helix that was on the outside of the
molecule and also gave an insight into its symmetry, in particular that the two helical
strands ran in opposite directions.
Watson and Crick were again greatly assisted by more of Franklin's data. This is
controversial because Franklin's critical X-ray pattern was shown to Watson and Crick
without Franklin's knowledge or permission. Wilkins showed the famous Photo 51 to
Watson at his lab immediately after Watson had been unsucessful in asking Franklin
to collaborate to beat Pauling in finding the structure.
From the data in photograph 51 Watson and Crick were able to discern that not only
was the distance between the two strands was constant, but also to measure its exact
value of 2 nanometres. The same photograph also gave them the 3.4 nanometre-per-
10 bp "pitch" of the helix.
The final insight came when Crick and Watson saw that a complementary pairing of
the bases could provide an explanation for Chargaff's puzzling finding. However the
structure of the bases had been incorrectly guessed in the textbooks as the enol
tautomer when they were more likely to be in the keto form. When Jerry Donohue
pointed this fallacy out to Watson, Watson quickly realised that the pairs of adenine
and thymine, and guanine and cytosine were almost identical in shape and so would
provide equally sized 'rungs' between the two strands. With the base-pairing, the
Watson and Crick quickly converged upon a model, which they announced before
Franklin herself had published any of her work.
Franklin was two steps away from the solution. She had not guessed the base-pairing
and had not appreciated the implications of the symmetry that she had described.
However she had been working almost alone and did not have regular contact with a
partner like Crick and Watson, and with other experts such as Jerry Donohoe. Her
notebooks show that she was aware both of Jerry Donohue's work concerning
tautomeric forms of bases (she used the keto forms for three of the bases) and of
Chargaff's work.
The disclosure of Franklin's data to Watson has angered some people who believe
Franklin did not receive the credit due to her at the time and that she might have
discovered the structure on her own before Crick and Watson. In Crick and Watson's
famous paper in Nature in 1953, they said that their work had been stimulated by the
work of Wilkins and Franklin, whereas it had been the basis of their work. However
they had agreed with Wilkins and Franklin that they all should publish papers in the
same issue of Nature in support of the proposed structure.
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Watson and Crick's model attracted great interest immediately upon its presentation.
Arriving at their conclusion on February 21, 1953, Watson and Crick made their first
announcement on February 28. Their paper 'A Structure for Deoxyribose Nucleic
Acid' was published on April 25. In an influential presentation in 1957, Crick laid out
the "Central Dogma", which foretold the relationship between DNA, RNA, and
proteins, and articulated the "sequence hypothesis." A critical confirmation of the
replication mechanism that was implied by the double-helical structure followed in
1958 in the form of the Meselson-Stahl experiment. Work by Crick and coworkers
showed that the genetic code was based on non-overlapping triplets of codons, and
Har Gobind Khorana and others deciphered the genetic code not long afterward.
These findings represent the birth of molecular biology.
Watson, Crick, and Wilkins were awarded the 1962 Nobel Prize for Medicine for
discovering the molecular structure of DNA, by which time Franklin had died. Nobel
prizes are not awarded posthumously.
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Bibliography
• DNA: The Secret of Life, by James D. Watson. ISBN 0-375-41546-7
• The Double Helix: A Personal Account of the Discovery of the Structure of
DNA (Norton Critical Editions), by James D. Watson. ISBN 0393950751
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External links
• Defending Franklin's Legacy
• 17 April, 2003, BBC News: Most ancient DNA ever?
• DNA Interactive (requires Macromedia Flash)
• Free DNA Images
• DNA: PDB molecule of the month
• DNA under electron microscope
• My First Book About DNA Designed for children to learn more about DNA.
• Nucleic Acids at the Open Directory Project
• Rotten Library Article on DNA
• Watson, James, and Francis Crick, "Molecular structure of nucleic acids, A
structure for Deoxyribose Nucleic Acid". April 2, 1953. (paper on the structure
of DNA)
Nucleotides: AMP - m5UMP - UMP - GMP - CMP - ADP - m5UDP - UDP - GDP - CDP - ATP -
m5UTP - UTP - GTP - CTP - cAMP - cGMP
Deoxynucleotides: dAMP - dTMP - dUMP - dGMP - dCMP - dADP - dTDP - dUDP - dGDP - dCDP -
dATP - dTTP - dUTP - dGTP - dCTP
Nucleic acids: DNA - RNA - LNA - PNA - mRNA - ncRNA - miRNA - rRNA - shRNA - siRNA -
tRNA - mtDNA - Oligonucleotide