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 of the human genome's
Agents that Damage DNA
 Certain wavelengths of radiation
 ionizing radiation such as gamma rays , X-rays and heavy ions
 ultraviolet radiation, especially the UV-C rays (~220-290 nm) that
are absorbed strongly by DNA but also the longer-wavelength UV-B
that penetrates the ozone shield.
 Highly-reactive oxygen radicals produced during normal
cellular respiration as well as by other biochemical
pathways.
 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
The effect of different type of
radiation
 UV light causes crosslinking between adjacent cytosine
and thymine bases creating pyrimidine dimers. This is
called direct DNA damage.
 Ionizing radiation such as that created by radioactive
decay or in cosmic rays and particle accelerators
causes DNA damages of various types. There two type
of effect of ionizing radiation: direct and indirect.
Types of DNA Damage
 Breaks in the DNA backbone
 can be limited to one of the two strands (a single-stranded break,
SSB)
 on both strands (a double-stranded break (DSB).
 Base damage
 Sugar damage
 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.
 Crosslinks Covalent linkages can be formed between
bases
 on the same DNA strand ("intrastrand") or
 on the opposite strand ("interstrand").
What’s the DNA Repair?
DNA repair refers to a collection of
processes by which a cell identifies
and corrects damage to the DNA
molecules that encode its genome
Types of single strand breaks
 5'OH –terminus
 5'PO4 –terminus
 3' Free end group
 3' OH –terminus in ds DNA excluded
 3' OH –terminus in single strand site
 3'PO4 –terminus
 3'OH and 5'PO4 not divided by gaps
DNA Single-Strand Breaks (SSBs) Repair
 Breaks in a single strand of the DNA molecule are
repaired by three types of mechanisms in Escherichia
coli bacterial cells
 Type I
 Type II
 Type III
Type I Repair Mechanism
 ultrafast repair, which mends single-strand breaks within
1 min at 0⁰C
 Nicks can be repaired by a DNA ligase if all that has
happened is that a phosphodiester bond has been broken,
without damage to the 5′-phosphate and 3′-hydroxyl
groups of the nucleotides either side of the nick. This is
often the case with nicks resulting from the effects of
ionizing radiation. (DNA ligase is the same enzyme used
to bond DNA strands together without DNA damage)
Type I Repair Mechanism
Type II Repair Mechanism
The DNA polymerase I (which have 3'-5' exonuclease
activity) binds to single strand break to produce
3'OH group then start to produce new nucleotides
2. DNA ligase enzyme joining of the newly synthesized
segment to the original strain
1.
 Repair of 5'OH , 3'PO4 and 3'OH in single stranded
sites
Type II Repair Mechanism
Type III Repair Mechanism
DNA exonuclease III attack single strand break
2. The enzyme produce 3'OH termini suitable as primers for
DNA polymerase I
3. The DNA polymerase I use 3'OH group as primer
4. DNA polymerase I starts to synthesize a new strand while
displacing the DNA segment
5. The final step of the repair process is joining of the newly
synthesized segment to the original strand by DNA ligase
1.
 Repair of 5'OH ,3'PO4, and 3‘ free group
Type III Repair Mechanism
STEPS TO MAKE
MATHEMATICAL
MODEL FOR REPAIR
SYSTEM
1. On the basis of experimental
facts, determine the key
processes making the main
contribution to the functioning
of the chosen DNA repair
system.
2. Convert this mechanism into
chemical equations
 DNA repair by type III
 [3'PO4]+[Exo III]
 [3'OH]+[Pol I]
 [ULDNA]+[DNA
k1
k2
[3'PO4][Exo III]
k-1
k3
k4
[3'OH][Pol I]
k-3
ligase] k5 k-5 [ULDNA][DNA ligase]
[3'OH DNA]+[Exo III]
[ULDNA]+[Pol I]
k6 [RDNA] +[DNA ligase]
3. Find the numerical values of the
parameters of the chosen DNA repair
system
Numerical values of the model parameters for type III
Parameters
value
k1
k-1
k2
k3
k4
k-4
k5
11.977 sec-1
0.0627 sec-1
16.7sec-1
16.7sec-1
0.0335sec-1
0.0026sec-1
0.03sec-1
4. Construct a mathematical model of the chosen DNA repair
system using the deterministic and stochastic approaches.
Entire Simulation
Input cv ( v=1,…,M)
initi . Of Xi (i=1,…,N)
Set
t=0 & n=0
Generate random numbers r1 and r2
Gillespie,1976
Calculate
a0 = av
a1= hvcv ( v=1,…,M)
Generate random numbers r1 and r2
Take
•
•
•
Update t = t + t
Update X = [X1, X2, …XC]
Update n= n + 1
5.
Obtain and analyze solutions
of the proposed model.
RESULTS
Type I Repair
Complex between un legated
DNA and Ligase
DNA Ligase
Repaired DNA
RESULTS
Type II Repair
Repaired DNA
DNA polymerase I
Complex between break
DNA and polymerase
Complex between un legated
DNA and Ligase
DNA Ligase
RESULTS
Type III Repair
DNA exonuclease III
DNA Ligase
DNA polymerase I
RESULTS
Type III Repair
Repaired DNA
Complex between break DNA
and polymerase
Complex between
break DNA and
exonuclease iii
Complex between un legated
DNA and Ligase
Comparison between DNA ligase kineticks
in different type of repair
Type I Repair
Type II Repair
Type III Repair
Comparison between DNA polymerase I
kineticks in different type of repair
Type II Repair
Type III Repair
SUMMARY
 the mathematical model of repair of single strand
DNA breaks was developed
 the concentrations of key enzymes and DNA states was
calculated at use of two different mathematical
approaches
FUTURE TASKS
 we plan to use
this simulation results for
development of mathematical model of mutagenesis
induced by ionizing radiation (accelerator heavy ions)
 We plan to apply this model to other organisms
(lactobacillus sp)
Acknowledgements
Firstly and forever, Thanks to ALLAH, who give me
everything in my life, and I supplicate Allah to make
my life in a perfect way.
I wish to express my appreciation to Dr. Oleg Belov for
constant encouragement and offering of facilities. I
express my deepest gratitude and appreciation for
sponsoring this work, tremendous effort, unfailing
support, maximum accuracy and for his generous
guidance advice