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DNA repair
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DNA damage resulting in multiple broken chromosomes

DNA repair refers to a collection of processes by which a cell identifies and corrects damage to
the DNA molecules that encode its genome. In human cells, both normal metabolic activities and
environmental factors such as UV light and Radiation can cause DNA damage, resulting in as
many as 1 million individual molecular lesions per cell per day.[1] Many of these lesions cause
structural damage to the DNA molecule and can alter or eliminate the cell's ability to transcribe
the gene that the affected DNA encodes. Other lesions induce potentially harmful mutations in
the cell's genome, which affect the survival of its daughter cells after it undergoes mitosis.
Consequently, the DNA repair process is constantly active as it responds to damage in the DNA
structure.
The rate of DNA repair is dependent on many factors, including the cell type, the age of the cell,
and the extracellular environment. A cell that has accumulated a large amount of DNA damage,
or one that no longer effectively repairs damage incurred to its DNA, can enter one of three
possible states:
1. an irreversible state of dormancy, known as senescence
2. cell suicide, also known as apoptosis or programmed cell death
3. unregulated cell division, which can lead to the formation of a tumor that is cancerous
The DNA repair ability of a cell is vital to the integrity of its genome and thus to its normal
functioning and that of the organism. Many genes that were initially shown to influence lifespan
have turned out to be involved in DNA damage repair and protection.[2] Failure to correct
molecular lesions in cells that form gametes can introduce mutations into the genomes of the
offspring and thus influence the rate of evolution.

Contents
[hide]
• 1 DNA damage
○ 1.1 Sources of damage
○ 1.2 Types of damage
○ 1.3 Nuclear versus mitochondrial DNA damage
○ 1.4 Senescence and apoptosis
○ 1.5 DNA damage and mutation
• 2 DNA repair mechanisms
○ 2.1 Direct reversal
○ 2.2 Single strand damage
○ 2.3 Double-strand breaks
○ 2.4 Translesion synthesis
• 3 Global response to DNA damage
○ 3.1 DNA damage checkpoints
○ 3.2 The prokaryotic SOS response
○ 3.3 Eukaryotic transcriptional responses to DNA damage
• 4 DNA repair and aging
○ 4.1 Pathological effects of poor DNA repair
○ 4.2 Longevity and caloric restriction
• 5 Medicine and DNA repair modulation
○ 5.1 Hereditary DNA repair disorders
○ 5.2 DNA repair and cancer
• 6 DNA repair and evolution
○ 6.1 Rate of evolutionary change
• 7 See also
• 8 References
• 9 External links

[edit] DNA damage

DNA damage, due to environmental factors and normal metabolic processes inside the cell,
occurs at a rate of 1,000 to 1,000,000 molecular lesions per cell per day.[1] While this constitutes
only 0.000165% of the human genome's approximately 6 billion bases (3 billion base pairs),
unrepaired lesions in critical genes (such as tumor suppressor genes) can impede a cell's ability
to carry out its function and appreciably increase the likelihood of tumor formation.
The vast majority of DNA damage affects the primary structure of the double helix; that is, the
bases themselves are chemically modified. These modifications can in turn disrupt the molecules'
regular helical structure by introducing non-native chemical bonds or bulky adducts that do not
fit in the standard double helix. Unlike proteins and RNA, DNA usually lacks tertiary structure
and therefore damage or disturbance does not occur at that level. DNA is, however, supercoiled
and wound around "packaging" proteins called histones (in eukaryotes), and both superstructures
are vulnerable to the effects of DNA damage.
[edit] Sources of damage
DNA damage can be subdivided into two main types:
1. endogenous damage such as attack by reactive oxygen species produced from normal
metabolic byproducts (spontaneous mutation), especially the process of oxidative
deamination;
1. also includes replication errors
2. exogenous damage caused by external agents such as
1. ultraviolet [UV 200-300nm] radiation from the sun
2. other radiation frequencies, including x-rays and gamma rays
3. hydrolysis or thermal disruption
4. certain plant toxins
5. human-made mutagenic chemicals, especially aromatic compounds that act as
DNA intercalating agents
6. cancer chemotherapy and radiotherapy
7. viruses [3]
The replication of damaged DNA before cell division can lead to the incorporation of wrong
bases opposite damaged ones. Daughter cells that inherit these wrong bases carry mutations from
which the original DNA sequence is unrecoverable (except in the rare case of a back mutation,
for example, through gene conversion).
[edit] Types of damage
There are four main types of damage to DNA due to endogenous cellular processes:
1. oxidation of bases [e.g. 8-oxo-7,8-dihydroguanine (8-oxoG)] and generation of DNA
strand interruptions from reactive oxygen species,
2. alkylation of bases (usually methylation), such as formation of 7-methylguanine, 1-
methyladenine, O6 methylguanine
3. hydrolysis of bases, such as deamination, depurination and depyrimidination.
4. "bulky adduct formation" (i.e. benzo[a]pyrene diol epoxide-dG adduct)
5. mismatch of bases, due to errors in DNA replication, in which the wrong DNA base is
stitched into place in a newly forming DNA strand, or a DNA base is skipped over or
mistakenly inserted.
Damage caused by exogenous agents comes in many forms. Some examples are:
 1. UV-B light causes crosslinking between adjacent cytosine and thymine bases creating
pyrimidine dimers. This is called direct DNA damage.
2. UV-A light creates mostly free radicals. The damage caused by free radicals is called
indirect DNA damage.
3. Ionizing radiation such as that created by radioactive decay or in cosmic rays causes
breaks in DNA strands.
4. Thermal disruption at elevated temperature increases the rate of depurination (loss of
purine bases from the DNA backbone) and single strand breaks. For example, hydrolytic
depurination is seen in the thermophilic bacteria, which grow in hot springs at 85–250
°C.[4] The rate of depurination (300 purine residues per genome per generation) is too
high in these species to be repaired by normal repair machinery, hence a possibility of an
adaptive response cannot be ruled out.
5. Industrial chemicals such as vinyl chloride and hydrogen peroxide, and environmental
chemicals such as polycyclic hydrocarbons found in smoke, soot and tar create a huge
diversity of DNA adducts- ethenobases, oxidized bases, alkylated phosphotriesters and
Crosslinking of DNA just to name a few.
UV damage, alkylation/methylation, X-ray damage and oxidative damage are examples of
induced damage. Spontaneous damage can include the loss of a base, deamination, sugar ring
puckering and tautomeric shift. [5]
[edit] Nuclear versus mitochondrial DNA damage
In human cells, and eukaryotic cells in general, DNA is found in two cellular locations - inside
the nucleus and inside the mitochondria. Nuclear DNA (nDNA) exists as chromatin during non-
replicative stages of the cell cycle and is condensed into aggregate structures known as
chromosomes during cell division. In either state the DNA is highly compacted and wound up
around bead-like proteins called histones. Whenever a cell needs to express the genetic
information encoded in its nDNA the required chromosomal region is unravelled, genes located
therein are expressed, and then the region is condensed back to its resting conformation.
Mitochondrial DNA (mtDNA) is located inside mitochondria organelles, exists in multiple
copies, and is also tightly associated with a number of proteins to form a complex known as the
nucleoid. Inside mitochondria, reactive oxygen species (ROS), or free radicals, byproducts of the
constant production of adenosine triphosphate (ATP) via oxidative phosphorylation, create a
highly oxidative environment that is known to damage mtDNA. A critical enzyme in
counteracting the toxicity of these species is superoxide dismutase, which is present in both the
mitochondria and cytoplasm of eukaryotic cells.
[edit] Senescence and apoptosis
Senescence, an irreversible state in which the cell no longer divides, is a protective response to
the shortening of the chromosome ends. The telomeres are long regions of repetitive noncoding
DNA that cap chromosomes and undergo partial degradation each time a cell undergoes division
(see Hayflick limit).[6] In contrast, quiescence is a reversible state of cellular dormancy that is
unrelated to genome damage (see cell cycle). Senescence in cells may serve as a functional
alternative to apoptosis in cases where the physical presence of a cell for spatial reasons is
required by the organism,[7] which serves as a "last resort" mechanism to prevent a cell with
damaged DNA from replicating inappropriately in the absence of pro-growth cellular signaling.
Unregulated cell division can lead to the formation of a tumor (see cancer), which is potentially
lethal to an organism. Therefore the induction of senescence and apoptosis is considered to be
part of a strategy of protection against cancer.
[edit] DNA damage and mutation
It is important to distinguish between DNA damage and mutation, the two major types of error in
DNA. DNA damages and mutation are fundamentally different. Damages are physical
abnormalities in the DNA, such as single and double strand breaks, 8-hydroxydeoxyguanosine
residues and polycyclic aromatic hydrocarbon adducts. DNA damages can be recognized by
enzymes, and thus they can be correctly repaired if redundant information, such as the
undamaged sequence in the complementary DNA strand or in a homologous chromosome, is
available for copying. If a cell retains DNA damage, transcription of a gene can be prevented and
thus translation into a protein will also be blocked. Replication may also be blocked and/or the
cell may die.
In contrast to DNA damage, a mutation is a change in the base sequence of the DNA. A mutation
cannot be recognized by enzymes once the base change is present in both DNA strands, and thus
a mutation cannot be repaired. At the cellular level, mutations can cause alterations in protein
function and regulation. Mutations are replicated when the cell replicates. In a population of
cells, mutant cells will increase or decrease in frequency according to the effects of the mutation
on the ability of the cell to survive and reproduce. Although distinctly different from each other,
DNA damages and mutations are related because DNA damages often cause errors of DNA
synthesis during replication or repair and these errors are a major source of mutation.
Given these properties of DNA damage and mutation, it can be seen that DNA damages are a
special problem in non-dividing or slowly dividing cells, where unrepaired damages will tend to
accumulate over time. On the other hand, in rapidly dividing cells, unrepaired DNA damages that
do not kill the cell by blocking replication will tend to cause replication errors and thus mutation.
The great majority of mutations that are not neutral in their effect are deleterious to a cell’s
survival. Thus, in a population of cells comprising a tissue with replicating cells, mutant cells
will tend to be lost. However infrequent mutations that provide a survival advantage will tend to
clonally expand at the expense of neighboring cells in the tissue. This advantage to the cell is
disadvantageous to the whole organism, because such mutant cells can give rise to cancer. Thus
DNA damages in frequently dividing cells, because they give rise to mutations, are a prominent
cause of cancer. In contrast, DNA damages in infrequently dividing cells are likely a prominent
cause of aging.
[edit] DNA repair mechanisms
Single strand and double strand DNA damage
Cells cannot function if DNA damage corrupts the integrity and accessibility of essential
information in the genome (but cells remain superficially functional when so-called "non-
essential" genes are missing or damaged). Depending on the type of damage inflicted on the
DNA's double helical structure, a variety of repair strategies have evolved to restore lost
information. If possible, cells use the unmodified complementary strand of the DNA or the sister
chromatid as a template to losslessly recover the original information. Without access to a
template, cells use an error-prone recovery mechanism known as translesion synthesis as a last
resort.
Damage to DNA alters the spatial configuration of the helix and such alterations can be detected
by the cell. Once damage is localized, specific DNA repair molecules bind at or near the site of
damage, inducing other molecules to bind and form a complex that enables the actual repair to
take place. The types of molecules involved and the mechanism of repair that is mobilized
depend on the type of damage that has occurred and the phase of the cell cycle that the cell is in.
[edit] Direct reversal
Cells are known to eliminate three types of damage to their DNA by chemically reversing it.
These mechanisms do not require a template, since the types of damage they counteract can only
occur in one of the four bases. Such direct reversal mechanisms are specific to the type of
damage incurred and do not involve breakage of the phosphodiester backbone. The formation of
thymine dimers (a common type of cyclobutyl dimer) upon irradiation with UV light results in
an abnormal covalent bond between adjacent thymidine bases. The photoreactivation process
directly reverses this damage by the action of the enzyme photolyase, whose activation is
obligately dependent on energy absorbed from blue/UV light (300–500 nm wavelength) to
promote catalysis.[8] Another type of damage, methylation of guanine bases, is directly reversed
by the protein methyl guanine methyl transferase (MGMT), the bacterial equivalent of which is
called as ogt. This is an expensive process because each MGMT molecule can only be used once;
that is, the reaction is stoichiometric rather than catalytic.[9] A generalized response to
methylating agents in bacteria is known as the adaptive response and confers a level of resistance
to alkylating agents upon sustained exposure by upregulation of alkylation repair enzymes.[10]
The third type of DNA damage reversed by cells is certain methylation of the bases cytosine and
adenine.
[edit] Single strand damage

Structure of the base-excision repair enzyme uracil-DNA glycosylase. The uracil residue is
shown in yellow.
When only one of the two strands of a double helix has a defect, the other strand can be used as a
template to guide the correction of the damaged strand. In order to repair damage to one of the
two paired molecules of DNA, there exist a number of excision repair mechanisms that remove
the damaged nucleotide and replace it with an undamaged nucleotide complementary to that
found in the undamaged DNA strand.[9]
1. Base excision repair (BER), which repairs damage to a single base caused by oxidation,
alkylation, hydrolysis, or deamination. The damaged base is removed by a DNA
glycosylase, resynthesized by a DNA polymerase, and a DNA ligase performs the final
nick-sealing step.
2. Nucleotide excision repair (NER), which recognizes bulky, helix-distorting lesions such
as pyrimidine dimers and 6,4 photoproducts. A specialized form of NER known as
transcription-coupled repair deploys NER enzymes to genes that are being actively
transcribed.
3. Mismatch repair (MMR), which corrects errors of DNA replication and recombination
that result in mispaired (but undamaged) nucleotides.

[edit] Double-strand breaks

Double-strand breaks (DSBs), in which both strands in the double helix are severed, are
particularly hazardous to the cell because they can lead to genome rearrangements. Three
mechanisms exist to repair DSBs: non-homologous end joining (NHEJ), Microhomology-
mediated End Joining (MMEJ) and recombinational repair (also known as template-assisted
repair or homologous recombination repair).[9]

DNA ligase, shown above repairing chromosomal damage, is an enzyme that joins broken
nucleotides together by catalyzing the formation of an internucleotide ester bond between the
phosphate backbone and the deoxyribose nucleotides.
In NHEJ, DNA Ligase IV, a specialized DNA Ligase that forms a complex with the cofactor
XRCC4, directly joins the two ends.[11] To guide accurate repair, NHEJ relies on short
homologous sequences called microhomologies present on the single-stranded tails of the DNA
ends to be joined. If these overhangs are compatible, repair is usually accurate.[12][13][14][15] NHEJ
can also introduce mutations during repair. Loss of damaged nucleotides at the break site can
lead to deletions, and joining of nonmatching termini forms translocations. NHEJ is especially
important before the cell has replicated its DNA, since there is no template available for repair
by homologous recombination. There are "backup" NHEJ pathways in higher eukaryotes.[16]
Besides its role as a genome caretaker, NHEJ is required for joining hairpin-capped double-
strand breaks induced during V(D)J recombination, the process that generates diversity in B-cell
and T-cell receptors in the vertebrate immune system.[17]
Recombinational repair requires the presence of an identical or nearly identical sequence to be
used as a template for repair of the break. The enzymatic machinery responsible for this repair
process is nearly identical to the machinery responsible for chromosomal crossover during
meiosis. This pathway allows a damaged chromosome to be repaired using a sister chromatid
(available in G2 after DNA replication) or a homologous chromosome as a template. DSBs
caused by the replication machinery attempting to synthesize across a single-strand break or
unrepaired lesion cause collapse of the replication fork and are typically repaired by
recombination.
Topoisomerases introduce both single- and double-strand breaks in the course of changing the
DNA's state of supercoiling, which is especially common in regions near an open replication
fork. Such breaks are not considered DNA damage because they are a natural intermediate in the
topoisomerase biochemical mechanism and are immediately repaired by the enzymes that
created them.
A team of French researchers bombarded Deinococcus radiodurans to study the mechanism of
double-strand break DNA repair in that organism. At least two copies of the genome, with
random DNA breaks, can form DNA fragments through annealing. Partially overlapping
fragments are then used for synthesis of homologous regions through a moving D-loop that can
continue extension until they find complementary partner strands. In the final step there is
crossover by means of RecA-dependent homologous recombination.[18]
[edit] Translesion synthesis
Translesion synthesis is a DNA damage tolerance process that allows the DNA replication
machinery to replicate past DNA lesions such as thymine dimers or AP sites.[19] It involves
switching out regular DNA polymerases for specialized translesion polymerases (e.g. DNA
polymerase V), often with larger active sites that can facilitate the insertion of bases opposite
damaged nucleotides. The polymerase switching is thought to be mediated by, among other
factors, the post-translational modification of the replication processivity factor PCNA.
Translesion synthesis polymerases often have low fidelity (high propensity to insert wrong
bases) relative to regular polymerases. However, many are extremely efficient at inserting correct
bases opposite specific types of damage. For example, Pol η mediates error-free bypass of
lesions induced by UV irradiation, whereas Pol ζ introduces mutations at these sites. From a
cellular perspective, risking the introduction of point mutations during translesion synthesis may
be preferable to resorting to more drastic mechanisms of DNA repair, which may cause gross
chromosomal aberrations or cell death.
[edit] Global response to DNA damage
Cells exposed to ionizing radiation, ultraviolet light or chemicals are prone to acquire multiple
sites of bulky DNA lesions and double strand breaks. Moreover, DNA damaging agents can
damage other biomolecules such as proteins, carbohydrates, lipids and RNA. The accumulation
of damage, specifically double strand breaks or adducts stalling the replication forks, are among
known stimulation signals for a global response to DNA damage.[20] The global response to
damage is an act directed toward the cells' own preservation and triggers multiple pathways of
macromolecular repair, lesion bypass, tolerance or apoptosis. The common features of global
response are induction of multiple genes, cell cycle arrest, and inhibition of cell division.
[edit] DNA damage checkpoints
After DNA damage, cell cycle checkpoints are activated. Checkpoint activation pauses the cell
cycle and gives the cell time to repair the damage before continuing to divide. DNA damage
checkpoints occur at the G1/S and G2/M boundaries. An intra-S checkpoint also exists.
Checkpoint activation is controlled by two master kinases, ATM and ATR. ATM responds to
DNA double-strand breaks and disruptions in chromatin structure,[21] whereas ATR primarily
responds to stalled replication forks. These kinases phosphorylate downstream targets in a signal
transduction cascade, eventually leading to cell cycle arrest. A class of checkpoint mediator
proteins including BRCA1, MDC1, and 53BP1 has also been identified.[22] These proteins seem
to be required for transmitting the checkpoint activation signal to downstream proteins.
p53 is an important downstream target of ATM and ATR, as it is required for inducing apoptosis
following DNA damage.[23] At the G1/S checkpoint, p53 functions by deactivating the
CDK2/cyclin E complex. Similarly, p21 mediates the G2/M checkpoint by deactivating the
CDK1/cyclin B complex[citation needed].
[edit] The prokaryotic SOS response
The SOS response is the term used to describe changes in gene expression in Escherichia coli
and other bacteria in response to extensive DNA damage. The prokaryotic SOS system is
regulated by two key proteins: LexA and RecA. The LexA homodimer is a transcriptional
repressor that binds to operator sequences commonly referred to as SOS boxes. It is known that
LexA regulates transcription of approximately 48 genes including the lexA and recA genes.[24]
The most common cellular signals activating the SOS response are regions of single stranded
DNA (ssDNA), arising from stalled replication forks or double strand breaks, which are
processed by DNA helicase to separate the two DNA strands.[20] In the initiation step, RecA
protein binds to ssDNA in an ATP hydrolysis driven reaction creating RecA–ssDNA filaments.
RecA–ssDNA filaments activate LexA autoprotease activity which ultimately leads to cleavage
of LexA dimer and subsequent LexA degradation. The loss of LexA repressor induces
transcription of the SOS genes and allows for further signal induction, inhibition of cell division
and an increase in levels of proteins responsible for damage processing.
SOS boxes are 20-nucleotide long sequences near promoters with palindromic structure and a
high degree of sequence conservation. This distinction in promoter sequences causes differential
binding of LexA to different promoters and allows for timing of the SOS response. Logically, the
lesion repair genes are induced at the beginning of SOS response. The error prone translesion
polymerases, for example: UmuCD’2 (also called DNA polymerase V), are induced later on as a
last resort.[25] Once the DNA damage is repaired or bypassed using polymerases or through
recombination, the amount of single-stranded DNA in cells is decreased, lowering the amounts
of RecA filaments decreases cleavage activity of LexA homodimer which subsequently binds to
the SOS boxes near promoters and restores normal gene expression.
[edit] Eukaryotic transcriptional responses to DNA damage
Eukaryotic cells exposed to DNA damaging agents also activate important defensive pathways
by inducing multiple proteins involved in DNA repair, cell cycle checkpoint control, protein
trafficking and degradation. Such genome wide transcriptional response is very complex and
tightly regulated, thus allowing coordinated global response to damage. Exposure of yeast
Saccharomyces cerevisiae to DNA damaging agents results in overlapping but distinct
transcriptional profiles. Similarities to environmental shock response indicates that a general
global stress response pathway exist at the level of transcriptional activation. In contrast,
different human cell types respond to damage differently indicating an absence of a common
global response. The probable explanation for this difference between yeast and human cells may
be in the heterogeneity of mammalian cells. In an animal different types of cells are distributed
amongst different organs which have evolved different sensitivities to DNA damage.[25]
In general global response to DNA damage involves expression of multiple genes responsible for
postreplication repair, homologous recombination, nucleotide excision repair, DNA damage
checkpoint, global transcriptional activation, genes controlling mRNA decay and many others. A
large amount of damage to a cell leaves it with an important decision: undergo apoptosis and die,
or survive at the cost of living with a modified genome. An increase in tolerance to damage can
lead to an increased rate of survival which will allow a greater accumulation of mutations. Yeast
Rev1 and human polymerase η are members of [Y family translesion DNA polymerases present
during global response to DNA damage and are responsible for enhanced mutagenesis during a
global response to DNA damage in eukaryotes.[20]
[edit] DNA repair and aging
[edit] Pathological effects of poor DNA repair

DNA repair rate is an important determinant of cell pathology

Experimental animals with genetic deficiencies in DNA repair often show decreased lifespan and
increased cancer incidence. For example, mice deficient in the dominant NHEJ pathway and in
telomere maintenance mechanisms get lymphoma and infections more often, and consequently
have shorter lifespans than wild-type mice.[26] Similarly, mice deficient in a key repair and
transcription protein that unwinds DNA helices have premature onset of aging-related diseases
and consequent shortening of lifespan.[27] However, not every DNA repair deficiency creates
exactly the predicted effects; mice deficient in the NER pathway exhibited shortened lifespan
without correspondingly higher rates of mutation.[28]
If the rate of DNA damage exceeds the capacity of the cell to repair it, the accumulation of errors
can overwhelm the cell and result in early senescence, apoptosis or cancer. Inherited diseases
associated with faulty DNA repair functioning result in premature aging, increased sensitivity to
carcinogens, and correspondingly increased cancer risk (see below). On the other hand,
organisms with enhanced DNA repair systems, such as Deinococcus radiodurans, the most
radiation-resistant known organism, exhibit remarkable resistance to the double strand break-
inducing effects of radioactivity, likely due to enhanced efficiency of DNA repair and especially
NHEJ.[29]
[edit] Longevity and caloric restriction
Most lifespan influencing genes affect the rate of DNA damage
A number of individual genes have been identified as influencing variations in lifespan within a
population of organisms. The effects of these genes is strongly dependent on the environment,
particularly on the organism's diet. Caloric restriction reproducibly results in extended lifespan in
a variety of organisms, likely via nutrient sensing pathways and decreased metabolic rate. The
molecular mechanisms by which such restriction results in lengthened lifespan are as yet unclear
(see[30] for some discussion); however, the behavior of many genes known to be involved in DNA
repair is altered under conditions of caloric restriction.
For example, increasing the gene dosage of the gene SIR-2, which regulates DNA packaging in
the nematode worm Caenorhabditis elegans, can significantly extend lifespan.[31] The
mammalian homolog of SIR-2 is known to induce downstream DNA repair factors involved in
NHEJ, an activity that is especially promoted under conditions of caloric restriction.[32] Caloric
restriction has been closely linked to the rate of base excision repair in the nuclear DNA of
rodents,[33] although similar effects have not been observed in mitochondrial DNA.[34]
Interestingly, the C. elegans gene AGE-1, an upstream effector of DNA repair pathways, confers
dramatically extended lifespan under free-feeding conditions but leads to a decrease in
reproductive fitness under conditions of caloric restriction.[35] This observation supports the
pleiotropy theory of the biological origins of aging, which suggests that genes conferring a large
survival advantage early in life will be selected for even if they carry a corresponding
disadvantage late in life.
[edit] Medicine and DNA repair modulation
[edit] Hereditary DNA repair disorders
Defects in the NER mechanism are responsible for several genetic disorders, including:
• xeroderma pigmentosum: hypersensitivity to sunlight/UV, resulting in increased skin
cancer incidence and premature aging
• Cockayne syndrome: hypersensitivity to UV and chemical agents
• trichothiodystrophy: sensitive skin, brittle hair and nails
Mental retardation often accompanies the latter two disorders, suggesting increased vulnerability
of developmental neurons.
Other DNA repair disorders include:
• Werner's syndrome: premature aging and retarded growth
• Bloom's syndrome: sunlight hypersensitivity, high incidence of malignancies (especially
leukemias).
• ataxia telangiectasia: sensitivity to ionizing radiation and some chemical agents
All of the above diseases are often called "segmental progerias" ("accelerated aging diseases")
because their victims appear elderly and suffer from aging-related diseases at an abnormally
young age.
Other diseases associated with reduced DNA repair function include Fanconi's anemia,
hereditary breast cancer and hereditary colon cancer.
[edit] DNA repair and cancer
Inherited mutations that affect DNA repair genes are strongly associated with high cancer risks in
humans. Hereditary nonpolyposis colorectal cancer (HNPCC) is strongly associated with specific
mutations in the DNA mismatch repair pathway. BRCA1 and BRCA2, two famous mutations
conferring a hugely increased risk of breast cancer on carriers, are both associated with a large
number of DNA repair pathways, especially NHEJ and homologous recombination.
Cancer therapy procedures such as chemotherapy and radiotherapy work by overwhelming the
capacity of the cell to repair DNA damage, resulting in cell death. Cells that are most rapidly
dividing - most typically cancer cells - are preferentially affected. The side effect is that other
non-cancerous but rapidly dividing cells such as stem cells in the bone marrow are also affected.
Modern cancer treatments attempt to localize the DNA damage to cells and tissues only
associated with cancer, either by physical means (concentrating the therapeutic agent in the
region of the tumor) or by biochemical means (exploiting a feature unique to cancer cells in the
body).
[edit] DNA repair and evolution
The basic processes of DNA repair are highly conserved among both prokaryotes and eukaryotes
and even among bacteriophage (viruses that infect bacteria); however, more complex organisms
with more complex genomes have correspondingly more complex repair mechanisms.[36] The
ability of a large number of protein structural motifs to catalyze relevant chemical reactions has
played a significant role in the elaboration of repair mechanisms during evolution. For an
extremely detailed review of hypotheses relating to the evolution of DNA repair, see.[37]
The fossil record indicates that single celled life began to proliferate on the planet at some point
during the Precambrian period, although exactly when recognizably modern life first emerged is
unclear. Nucleic acids became the sole and universal means of encoding genetic information,
requiring DNA repair mechanisms that in their basic form have been inherited by all extant life
forms from their common ancestor. The emergence of Earth's oxygen-rich atmosphere (known as
the "oxygen catastrophe") due to photosynthetic organisms, as well as the presence of potentially
damaging free radicals in the cell due to oxidative phosphorylation, necessitated the evolution of
DNA repair mechanisms that act specifically to counter the types of damage induced by
oxidative stress.
[edit] Rate of evolutionary change
On some occasions, DNA damage is not repaired, or is repaired by an error-prone mechanism
which results in a change from the original sequence. When this occurs, mutations may
propagate into the genomes of the cell's progeny. Should such an event occur in a germ line cell
that will eventually produce a gamete, the mutation has the potential to be passed on to the
organism's offspring. The rate of evolution in a particular species (or, more narrowly, in a
particular gene) is a function of the rate of mutation. Consequently, the rate and accuracy of
DNA repair mechanisms have an influence over the process of evolutionary change.[38]
[edit] See also
• Direct DNA damage
• Indirect DNA damage
• DNA damage theory of aging
• Accelerated aging disease
• Aging DNA
• Cell cycle
• DNA replication
• Gene therapy
• Life extension
• Human mitochondrial genetics
• Progeria
• Senescence
• The scientific journal DNA Repair under Mutation Research

[edit] References
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(2004). Molecular Biology of the Cell, p963. WH Freeman: New York, NY. 5th ed.
2. ^ Browner WS, Kahn AJ, Ziv E, Reiner AP, Oshima J, Cawthon RM, Hsueh WC, Cummings SR.
(2004). The genetics of human longevity. Am J Med 117(11):851–60.
3. ^ Roulston A, Marcellus RC, Branton PE (1999). "Viruses and apoptosis". Annu. Rev. Microbiol.
53: 577–628. doi:10.1146/annurev.micro.53.1.577. PMID 10547702.
http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.micro.53.1.577?url_ver=Z39.88-
2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dncbi.nlm.nih.gov. Retrieved on 2008-12-
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4. ^ Toshihiro Ohta, Shin-ichi Tokishita, Kayo Mochizuki, Jun Kawase, Masahide Sakahira and
Hideo Yamagata, UV Sensitivity and Mutagenesis of the Extremely Thermophilic Eubacterium
Thermus thermophilus HB27, Genes and Environment Vol. 28 (2006), No. 2 p.56–61.
5. ^ DNA Lesions That Require Repair:
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• Roswell Park Cancer Institute DNA Repair Lectures
• DNA Repair - A summary of the primary mechanisms
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• DNA Repair
• DNA Damage and DNA Repair
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Index to this page

• Agents that Damage DNA
• Types of DNA Damage
• Repairing Damaged Bases
○ Direct Reversal of Base Damage
○ Base Excision Repair (BER)
○ Nucleotide Excision Repair (NER)
○ Xeroderma Pigmentosum (XP)
○ Transcription-coupled NER
○ Mismatch Repair (MMR)
• Repairing Strand Breaks
○ Single-Strand Breaks (SSBs)
○ Double-Strand Breaks (DSBs)
○ The Generation of Antibody Diversity
• Meiosis also involves DSBs
• Gene Conversion
 • Cancer Chemotherapy

DNA Repair
Importance
DNA in the living cell is subject to many chemical alterations (a fact often
forgotten in the excitement of being able to do DNA sequencing on dried
and/or frozen specimens [Link]). If the genetic information encoded in the
DNA is to remain uncorrupted, any chemical changes must be corrected.
A failure to repair DNA produces a mutation.
The recent publication of the human genome [Link] has already revealed 130 genes
whose products participate in DNA repair. More will probably be identified soon.

Agents that Damage DNA

• Certain wavelengths of radiation
○ ionizing radiation such as gamma rays and x-rays
○ ultraviolet rays, especially the UV-C rays (~260 nm) that are
absorbed strongly by DNA but also the longer-wavelength UV-B that
penetrates the ozone shield [Link].
• Highly-reactive oxygen radicals produced during normal cellular respiration
as well as by other biochemical pathways. [Link to further discussion.]
• Chemicals in the environment
○ many hydrocarbons, including some found in cigarette smoke
○ some plant and microbial products, e.g. the aflatoxins produced in
moldy peanuts
• Chemicals used in chemotherapy, especially chemotherapy of cancers
Link to description of a test measuring the mutations caused by the
hydrocarbon benzopyrene.
○ some plant and microbial products, e.g. the aflatoxins produced in
moldy peanuts
• Chemicals used in chemotherapy, especially chemotherapy of cancers

Types of DNA Damage

1. All four of the bases in DNA (A, T, C, G) can be covalently modified at various
positions.
○ One of the most frequent is the loss of an amino group ("deamination")
— resulting, for example, in a C being converted to a U.
 2. Mismatches of the normal bases because of a failure of proofreading during
DNA replication.
○ Common example: incorporation of the pyrimidine U (normally found
only in RNA) instead of T.
3. Breaks in the backbone.
○ Can be limited to one of the two strands (a single-stranded break, SSB)
or
○ on both strands (a double-stranded break (DSB).
○ Ionizing radiation is a frequent cause, but some chemicals produce
breaks as well.
4. Crosslinks Covalent linkages can be formed between bases
○ on the same DNA strand ("intrastrand") or
○ on the opposite strand ("interstrand").
Several chemotherapeutic drugs used against cancers crosslink DNA [Link].

Repairing Damaged Bases

Damaged or inappropriate bases can be repaired by several mechanisms:

• Direct chemical reversal of the damage

• Excision Repair, in which the damaged base or bases are removed and then
replaced with the correct ones in a localized burst of DNA synthesis. There
are three modes of excision repair, each of which employs specialized sets of
enzymes.
1. Base Excision Repair (BER)
2. Nucleotide Excision Repair (NER)
3. Mismatch Repair (MMR)
Direct Reversal of Base Damage
Perhaps the most frequent cause of point mutations in humans is the
spontaneous addition of a methyl group (CH3-) (an example of alkylation) to
Cs followed by deamination to a T. Fortunately, most of these changes are
repaired by enzymes, called glycosylases, that remove the mismatched T
restoring the correct C. This is done without the need to break the DNA
backbone (in contrast to the mechanisms of excision repair described
below).
Some of the drugs used in cancer chemotherapy ("chemo") also damage DNA by
alkylation. Some of the methyl groups can be removed by a protein encoded by our
MGMT gene. However, the protein can only do it once, so the removal of each
methyl group requires another molecule of protein.
This illustrates a problem with direct reversal mechanisms of DNA repair:
they are quite wasteful. Each of the myriad types of chemical alterations to
bases requires its own mechanism to correct. What the cell needs are more
general mechanisms capable of correcting all sorts of chemical damage with
a limited toolbox. This requirement is met by the mechanisms of excision
repair.
Base Excision Repair (BER)
The steps and some key players:

1. removal of the damaged base (estimated to occur some 20,000 times a day
in each cell in our body!) by a DNA glycosylase. We have at least 8 genes
encoding different DNA glycosylases each enzyme responsible for identifying
and removing a specific kind of base damage.
2. removal of its deoxyribose phosphate in the backbone, producing a gap. We
have two genes encoding enzymes with this function.
3. replacement with the correct nucleotide. This relies on DNA polymerase
beta, one of at least 11 DNA polymerases encoded by our genes.
4. ligation of the break in the strand. Two enzymes are known that can do this;
both require ATP to provide the needed energy.
Nucleotide Excision Repair (NER)
NER differs from BER in several ways.

• It uses different enzymes.

• Even though there may be only a single "bad" base to correct, its nucleotide
is removed along with many other adjacent nucleotides; that is, NER removes
a large "patch" around the damage.
The steps and some key players:
1. The damage is recognized by one or more protein factors that assemble at
the location.
2. The DNA is unwound producing a "bubble". The enzyme system that does this
is Transcription Factor IIH, TFIIH, (which also functions in normal
transcription).
3. Cuts are made on both the 3' side and the 5' side of the damaged area so the
tract containing the damage can be removed.
4. A fresh burst of DNA synthesis — using the intact (opposite) strand as a
template — fills in the correct nucleotides. The DNA polymerases responsible
are designated polymerase delta and epsilon.
5. A DNA ligase covalent binds the fresh piece into the backbone.

Xeroderma Pigmentosum (XP)

XP is a rare inherited disease of humans which, among other things, predisposes
the patient to
 • pigmented lesions on areas of the skin exposed to the sun and
• an elevated incidence of skin cancer.
It turns out that XP can be caused by mutations in any one of several genes — all of
which have roles to play in NER. Some of them:
• XPA, which encodes a protein that binds the damaged site and helps
assemble the other proteins needed for NER.
• XPB and XPD, which are part of TFIIH. Some mutations in XPB and XPD also
produce signs of premature aging. [Link]
• XPF, which cuts the backbone on the 5' side of the damage
• XPG, which cuts the backbone on the 3' side.

Transcription-Coupled NER
Nucleotide-excision repair proceeds most rapidly

• in cells whose genes are being actively transcribed

• on the DNA strand that is serving as the template for transcription.
This enhancement of NER involves XPB, XPD, and several other gene products. The
genes for two of them are designated CSA and CSB (mutations in them cause an
inherited disorder called Cockayne's syndrome).
The CSB product associates in the nucleus with RNA polymerase II, the
enzyme responsible for synthesizing messenger RNA (mRNA), providing a
molecular link between transcription and repair.
One plausible scenario: If RNA polymerase II, tracking along the template
(antisense) strand), encounters a damaged base, it can recruit other
proteins, e.g., the CSA and CSB proteins, to make a quick fix before it moves
on to complete transcription of the gene.
Mismatch Repair (MMR)
Mismatch repair deals with correcting mismatches of the normal bases; that is,
failures to maintain normal Watson-Crick base pairing (A•T, C•G)

It can enlist the aid of enzymes involved in both base-excision repair (BER)
and nucleotide-excision repair (NER) as well as using enzymes specialized
for this function.
• Recognition of a mismatch requires several different proteins including one
encoded by MSH2.
• Cutting the mismatch out also requires several proteins, including one
encoded by MLH1.
Mutations in either of these genes predisposes the person to an inherited
form of colon cancer. So these genes qualify as tumor suppressor genes.
Question: How does the MMR system know which is the incorrect nucleotide? In E.
coli, certain adenines become methylated shortly after the new strand of DNA has
been synthesized. The MMR system works more rapidly, and if it detects a mismatch,
it assumes that the nucleotide on the already-methylated (parental) strand is the
correct one and removes the nucleotide on the freshly-synthesized daughter strand.
How such recognition occurs in mammals is not yet known.

Synthesis of the repair patch is done by the same enzymes used in NER:
DNA polymerase delta and epsilon.
Cells also use the MMR system to enhance the fidelity of recombination; i.e., assure
that only homologous regions of two DNA molecules pair up to crossover and
recombine segments (e.g., in meiosis).

Repairing Strand Breaks

Ionizing radiation and certain chemicals can produce both single-strand breaks
(SSBs) and double-strand breaks (DSBs) in the DNA backbone.

Single-Strand Breaks (SSBs)

Breaks in a single strand of the DNA molecule are repaired using the same enzyme
systems that are used in Base-Excision Repair (BER).

Double-Strand Breaks (DSBs)

There are two mechanisms by which the cell attempts to repair a complete break in
a DNA molecule:

• Direct joining of the broken ends. This requires proteins that recognize and
bind to the exposed ends and bring them together for ligating. They would
prefer to see some complementary nucleotides but can proceed without them
so this type of joining is also called Nonhomologous End-Joining (NHEJ).
• Errors in direct joining may be a cause of the various translocations
that are associated with cancers.
• Examples:
○ Burkitt's lymphoma
○ the Philadelphia chromosome in chronic myelogenous leukemia (CML)
○ B-cell leukemia
A protein called Ku is essential for NHEJ. Ku is a heterodimer of the subunits
Ku70 and Ku80. In the 9 August 2001 issue of Nature, Walker, J. R., et al,
report the three-dimensional structure of Ku attached to DNA. Their structure
shows beautifully how the protein aligns the broken ends of DNA for rejoining.
 • Errors in direct joining may be a cause of the various translocations
that are associated with cancers.
• Examples:
○ Burkitt's lymphoma
○ the Philadelphia chromosome in chronic myelogenous leukemia (CML)
○ B-cell leukemia

The Generation of Antibody Diversity

Some of the same enzymes used to repair DSBs by direct joining are also
used to break and reassemble the gene segments used to make
○ antibody variable regions; that is, to accomplish V(D)J joining —
(mice whose Ku80 genes have been knocked out cannot do this);
○ different antibody classes; that is, to accomplish class
switching.

• Homologous Recombination. Here the broken ends are repaired using the
information on the intact
○ sister chromatid (available in G2 after chromosome duplication), or
on the
○ homologous chromosome (in G1; that is, before each chromosome
has been duplicated). This requires searching around in the nucleus for
the homolog — a task sufficiently uncertain that G1 cells usually prefer
to mend their DSBs by NHEJ. or on the
○ same chromosome if there are duplicate copies of the gene on the
chromosome oriented in opposite directions (head-to-head or back-to-
back). [Example]
Two of the proteins used in homologous recombination are encoded by
the genes BRCA1 and BRCA2. Inherited mutations in these genes
predispose women to breast and ovarian cancers.

Meiosis also involves DSBs

Recombination between homologous chromosomes in meiosis I also involves
the formation of DSBs and their repair. So it is not surprising that this
process uses the same enzymes. [Link to a discussion with diagrams
showing how this may work.]
Meiosis I with the alignment of homologous sequences provides a
mechanism for repairing damaged DNA; that is, mutations. in fact, many
biologists feel that the main function of sex is to provide this mechanism for
maintaining the integrity of the genome. [More]
However, most of the genes on the human Y chromosome have no
counterpart on the X chromosome, and thus cannot benefit from this repair
mechanism. They seem to solve this problem by having multiple copies of
the same gene — oriented in opposite directions. Looping the intervening
DNA brings the duplicates together and allowing repair by homologous
recombination.

Gene Conversion
If the sequence used as a template for repairing a gene by homologous
recombination differs slightly from the gene needing repair; that is, is an
allele, the repaired gene will acquire the donor sequence. This
nonreciprocal transfer of genetic information is called gene conversion.
The donor of the new gene sequence may by:

• the homologous chromosome (during meiosis)

• the sister chromatid (also during meiosis)
• a duplicate of the gene on the same chromosome (during mitosis) [More]
Gene conversion during meiosis alters the normal mendelian ratios. Normally,
meiosis in a heterozygous (A,a) parent will produce gametes or spores in a 1:1
ratio; e.g., 50% A; 50% a. However, if gene conversion has occurred, other ratios
will appear. If, for example, an A allele donates its sequence as it repairs a damaged
a allele, the repaired gene will become A, and the ratio will be 75% A; 25% a.

Cancer Chemotherapy
• The hallmark of all cancers is continuous cell division.
• Each division requires both
○ the replication of the cell's DNA (in S phase) and
○ transcription and translation of many genes needed for continued
growth.
• So, any chemical that damages DNA has the potential to inhibit the spread of
a cancer.
• Many (but not all) drugs used for cancer therapy do their work by damaging
DNA.
The table lists (by trade name as well as generic name) some of the
anticancer drugs that specifically target DNA.
Cyclophospham
Cytoxan®
ide
Melphalan Alkeran®
Busulfan Myleran® alkylating agents; form interstrand
Chlorambucil Leukeran® and/or intrastrand crosslinks
Mutamycin
Mitomycin
®

Cisplatin Platinol® forms crosslinks

Blenoxane cuts DNA strands between GT or
Bleomycin
® GC
Camptosar inhibit the proper functioning of
Irinotecan
® enzymes (topoisomerases)
Novantron needed to unwind DNA for
Mitoxantrone
e® replication and transcription
Cosmegen inserts into the double helix
Dactinomycin
® preventing its unwinding

Sadly,
• the cancer patient has many other cell types that are also proliferating
rapidly, e.g., cells of the
○ intestinal endothelium
○ bone marrow
○ hair follicles
and anticancer drugs also damage these — producing many of the
unpleasant side effects of "chemo".
• Agents that damage DNA are themselves carcinogenic, and chemotherapy
poses a significant risk of creating a new cancer, often a leukemia.
Welcome&Next
Search

15 February 2007New Mechanism Discovered For DNA

Recombination And Repair
ScienceDaily (Sep. 12, 2007) — A biochemistry research team led by Dr.
Andrew H.-J. Wang and Dr. Ting-Fang Wang at the Institute of Biological
Chemistry, Academia Sinica(IBCAS), has discovered that the RecA family
recombinases function as a new type of rotary motor proteins to repair DNA
damages.
See also:

Plants & Animals

1. Cell Biology
2. Biochemistry Research
3. Molecular Biology
4. Biology
5. Developmental Biology
6. Biotechnology
Reference
1. Genetic recombination
2. Chromosomal crossover
3. DNA repair
4. Denaturation (biochemistry)
The team has recently published two structural biology articles related to RecA family
recombinases. One paper is to be published in the journal PLoS One on September 12,
2007 and the other has been already published in the Nucleic Acids Research on Feb.
28, 2007.
Homologous recombination (HR) is a mechanism that repairs damaged DNA with
perfect accuracy, it utilizes the homologous sequence from a partner DNA as a
template. This process involves the bringing together of 2 DNA molecules, a search for
homologous sequences, and exchange of DNA strands.
RecA family proteins are the central recombinases for HR. The family includes
prokaryotic RecA, archaeal RadA, and eukaryotic Rad51 and Dmc1. They have
important roles in cell proliferation, genome maintenance, and genetic diversity,
particularly in higher eukaryotes. For example, Rad51-deficient vertebrate cells
accumulate chromosomal breaks before death. Rad51 and its meiosis-specific
homolog, Dmc1, are also indispensable for meiosis, a specialized cell cycle for
production of gametes. Mammalian Rad51 and Dmc1 proteins are known to interact
with tumor suppressor proteins such as BRCA2.
Since scientists discovered RecA family proteins, it has been assumed that RecA (and
other homologs) forms only 61 right-handed filaments (six protein monomers per helical
turn), and then hydrolyzes ATP to promote HR and recombinational DNA repair.
Whereas a controversial puzzle came out, how the energy of ATP facilitating DNA
rotation during the strand exchange reaction.
By X-ray crystallography and atomic force microscopy approaches, Dr. Wangs' team
provided the answer. They reported that archaeal Sulfolobus solfataricus RadA proteins
can also self-polymerize into a 31 right-handed filament with 3 monomers per helical
turn (reported in PLoS ONE) and a 43 right-handed helical filament with 4 monomers
per helical turn (reported in Nucleic Acids Research).
Additional biophysical and biochemical analyses revealed that RecA family proteins
may couple ATP binding and hydrolysis to the DNA strand exchange reaction in a
manner that promotes clockwise axial rotation of nucleoprotein filaments. Specially, the
61 RadA helical filament undergoes clockwise axial rotation in 2 discrete 120° steps to
the 31 extended right-handed filament and then to the 43 left-handed filament. As a
result, all the DNA-binding motifs (denoted L1, L2 and HhH) in the RadA proteins move
concurrently to mediate DNA binding, homology pairing, and strand exchange,
respectively. Therefore, the energy of ATP is used to rotate not only DNA substrates but
also the RecA family protein filaments.
This new model is in contrast to all current hypotheses, which overlooks the fact that
RecA family proteins are flexible enough to form both right-handed and left-handed
helical filaments. From this perspective, these researchers in Taiwan have opened a
new avenue for understanding the molecular mechanisms of RecA family proteins.
Article 1.Citation: Chen L-T, Ko T-P, Chang Y-W, Lin K-A, Wang AH-J, et al (2007)
Structural and Functional Analyses of Five Conserved Positively Charged Residues in
the L1 and N-Terminal DNA Binding Motifs of Archaeal RadA Protein. PLoS ONE 2(9):
e858. doi:10.1371/journal.pone.0000858
Article 2. "Crystal structure of the left-handed archaeal RadA helical filament:
identification of a functional motif for controlling quaternary structures and enzymatic
functions of RecA family proteins" (Nuclei Acid Research 2007. 35: 1787-1801).
New Information About DNA Repair Mechanism Could Lead To
Better Cancer Drugs
ScienceDaily (July 20, 2009) — Researchers at Washington University School
of Medicine in St. Louis have shed new light on a process that fixes breaks in
the genetic material of the body's cells. Their findings could lead to ways of
enhancing chemotherapy drugs that destroy cancer cells by damaging their
DNA.

See also:

Health & Medicine

 1. Genes
2. Human Biology
3. Cancer
Plants & Animals
1. Biotechnology
2. Biochemistry Research
3. Genetics
Reference
1. BRCA1
2. Chromosomal crossover
3. Genetic recombination
4. Tumor suppressor gene
Using yeast cells, the scientists studied protein molecules that have an important role in
homologous recombination, which is one way that cells repair breaks in the DNA double
helix. The process in yeast is similar to that in humans and other organisms.
Earlier research had established that a protein molecule named Srs2 regulates
homologous recombination by counteracting the work of another protein, Rad51.
Reporting in the July 10 issue of the journal Molecular Cell, the research team reveals
the mechanism of how Srs2 removes Rad51 from DNA and thereby prevents it from
making repairs to broken strands.
"Our findings may make it possible to uncover ways to augment the effect of DNA-
damaging agents that are used for cancer chemotherapy," says senior author Tom
Ellenberger, D.V.M, Ph.D., the Raymond H. Wittcoff Professor and head of the
Department of Biochemistry and Molecular Biophysics. "Many chemotherapeutic agents
work by causing DNA damage in cancer cells, leading to their death, and tumors can
become resistant to chemotherapy by using DNA repair mechanisms to keep the cells
alive. Drugs that inhibit the DNA repair process could help increase the efficiency of
chemotherapeutic agents."
Ellenberger is also co-director of the Pharmacology Core at Siteman Cancer Center at
Barnes-Jewish Hospital and Washington University. The facility aids in the development
of anti-cancer agents.
Srs2 is a helicase molecule — a motor protein that's able to walk or slide along a strand
of DNA and remove other proteins from DNA or separate the two strands of the twisted
double helix. For studies of Srs2, Ellenberger's laboratory collaborated with Timothy
Lohman, Ph.D., the Marvin A. Brennecke Professor of Biochemistry and Molecular
Biophysics, a prominent expert in the biochemistry of motor proteins like Srs2.
Rad51's job in the cell is to promote the exchange of sequences between two related
DNA molecules, which can be used to repair breaks in DNA where both strands of the
double helix are compromised. As a DNA matchmaker, Rad51 forms long filaments on
DNA. Srs2 can remove these to prevent unwanted exchanges of DNA sequences.
Without Srs2, cells lose their ability to maintain the normal structure of chromosomes,
and DNA sequences become shuffled.
The biochemists found that Srs2 possesses a small arm that interacts with Rad51 and
triggers a chemical reaction within the Rad51 protein causing it to fall off the DNA.
"Scientists had assumed that as Srs2 moved along the DNA strand, it just pushed off
everything in its path," says lead author Edwin Antony, Ph.D., a postdoctoral research
associate in biochemistry and molecular biophysics. "This isn't the case — we showed
that Srs2 has a specialized structure that allows it to interact specifically with Rad51."
This finding shows how a motor protein like Srs2 can perform the specialized task of
remodeling a protein-DNA complex without interference by other similar helicases, he
adds.
Because they now know more precisely the nature of this interaction between Srs2 and
Rad51, the researchers can narrow their search for drugs that will block DNA repair by
Rad51. This type of drug could make a lower dose of a DNA-damaging drug effective in
treating cancer.
The research team is now trying to identify the Srs2 homologue in human cells and will
study its structure in combination with Rad51. That will allow a more rational approach
to understanding how cells cope with DNA damage and how some tumors evade cancer
therapeutics, they say.
"In the long-term, my laboratory will look for drug-like molecules that influence this
interaction," Ellenberger says. "We are using the Chemical Genetics Screening Center
here at the University. It has vast libraries of molecules that may have the activity we
want. Edwin's work on Srs2 and Rad51 will allow us to develop an assay to screen for
agents that augment or supersede Srs2's interference with DNA repair."
Funding from the National Institutes of Health and the Young Scientist Program at
Washington University supported this research.

Journal reference:
1. Antony et al. Srs2 Disassembles Rad51 Filaments by a Protein-Protein Interaction Triggering
ATP Turnover and Dissociation of Rad51 from DNA. Molecular Cell, 2009; 35 (1): 105 DOI:
10.1016/j.molcel.2009.05.026
Adapted from materials provided by Washington University School of Medicine.
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Real-time Observation Of DNA-repair Mechanism

ScienceDaily (May 25, 2008) — For the first time, researchers at Delft
University of Technology have witnessed the spontaneous repair of damage to
DNA molecules in real time. They observed this at the level of a single DNA
molecule. Insight into this type of repair mechanism is essential as errors in
this process can lead to the development of cancerous cells.

See also:

Health & Medicine

1. Genes
2. Human Biology
3. Forensics
Plants & Animals
1. Developmental Biology
2. Biochemistry Research
3. Biotechnology
Reference
1. Chromosomal crossover
2. Vector (biology)
3. Genetic recombination
4. Introduction to genetics
Researchers from the Kavli Institute of Nanoscience Delft are to publish an article on
this in the journal Molecular Cell.
Cells have mechanisms for repairing the continuous accidental damage occurring in
DNA. These damages can vary from a change to a single part of the DNA to a total
break in the DNA structure. These breaks can, for instance, be caused by ultraviolet
light or X-rays, but also occur during cell division, when DNA molecules split and form
two new DNA molecules. If this type of break is not properly repaired it can be highly
dangerous to the functioning of the cell and lead to the creation of a cancerous cell.
One major DNA-repair mechanism involved in repairing these breaks is known as
homologous recombination. This mechanism has been observed for the first time by
Delft University of Technology researchers in real time and at the level of a single DNA
molecule.
To observe this, a DNA molecule is stretched between a magnetic bead and a glass
surface. A force is exerted on the magnetic bead using a magnetic field, enabling
researchers to pull and rotate a single DNA molecule in a controlled fashion. As the
position of the bead changes when the DNA molecule is repaired, researchers are able
to observe the repair process in detail.

Adapted from materials provided by Delft University of Technology.

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Delft University of Technology (2008, May 25). Real-time Observation Of DNA-repair Mechanism.
ScienceDaily. Retrieved July 29, 2009, from http://www.sciencedaily.com
/releases/2008/05/080522120610.htm
Researchers have witnessed the spontaneous repair of damage to DNA molecules in real time. (Credit:
Image courtesy of Delft University of Technology)
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