DNA INTRODUCTION CHEMICAL COMPOSITION NUCLEOSIDES & NUCLEOTIDES DNA REPAIR INTRODUCTION TYPES OF DNA REPAIR I)DIRECT REPAIR SYSTEM, II)BASE EXCISION REPAIR, III)NUCLEOTIDE EXCISION REPAIR, IV)MISMATCH REPAIR, V)RECOMBINATION REPAIR, DEFECTS IN DNA REPAIR UNDERLIE HUMAN DISEASE DNA RECOMBINATION INTRODUCTION MECHANISM OF DNA RECOMBINATION TYPES OF RECOMBINATION I) HOMOLOGOUS RECOMBINATION MODELS FOR HOMOLOGOUS RECOMBINATION:- I)HOLLIDAY MODEL, II)MESSELSON AND RADDING MODEL, III)DOUBLE STRAND BREAK MODEL, GENE CONVERSION II) NON-HOMOLOGOUS RECOMBINATION, i) SITE SPECIFIC RECOMBINATION, ii)TRANSPOSITIONAL RECOMBINATION.,

1. DNA REPAIR AND RECOMBINATION
By
KAUSHAL KUMAR SAHU
Assistant Professor (Ad Hoc)
Department of Biotechnology
Govt. Digvijay Autonomous P. G. College
Raj-Nandgaon ( C. G. )

2. SYNOPSIS:
 DNA
 INTRODUCTION
 CHEMICAL COMPOSITION
 NUCLEOSIDES & NUCLEOTIDES
 DNA REPAIR
 INTRODUCTION
 TYPES OF DNA REPAIR
I)DIRECT REPAIR SYSTEM
II)BASE EXCISION REPAIR
III)NUCLEOTIDE EXCISION REPAIR
IV)MISMATCH REPAIR
V)RECOMBINATION REPAIR
 DEFECTS IN DNA REPAIR UNDERLIE HUMAN DISEASE

3. DNA RECOMBINATION
INTRODUCTION
MECHANISM OF DNA RECOMBINATION
TYPES OF RECOMBINATION
I) HOMOLOGOUS RECOMBINATION
 MODELS FOR HOMOLOGOUS RECOMBINATION:-
I)HOLLIDAY MODEL
II)MESSELSON AND RADDING MODEL
III)DOUBLE STRAND BREAK MODEL
GENE CONVERSION
II) NON-HOMOLOGOUS RECOMBINATION
i) SITE SPECIFIC RECOMBINATION
ii)TRANSPOSITIONAL RECOMBINATION.

4. DEOXYRIBOSE NUCLEIC ACID(DNA):-
•DNA is present in cells of all plants, animals, prokaryotes and a no.
of viruses.
•In eukaryotes, it is present inside the nucleus, chloroplast and
mitochondria whereas in prokaryotes, it is dispersed in cytoplasm.
•The DNA of all plants, animals, & many viruses is double stranded
except some viruses. Eg. Psi x 174.
•In some viruses the genetic material is RNA.

5. CHEMICAL COMPOSITION OF DNA:-
•DNA is a polymer of deoxyribonucleotide monomer.
•DNA is formed of three important component i.e.
•Pentose Sugar:-In DNA deoxyribose is a pentose sugar.
•In DNA, all the sugars in one strand
are directed to one end i.e. strand has
polarity and sugars of two strands are
directed in opposite direction .

6. •Nitrogenous bases :-
Two types
•Purine :- They are double
ring compounds . In DNA
two purines are Adenine (A)
and Guanine (G).
•Pyrimidine:- They are single
ring compounds . In DNA
two Pyrimidines are Cytosine
(C) and Thymine(T).
•Phosphate Group :- It Contains alpha ,beta, gamma phosphate.
•In the DNA strand, the phosphate group alternate with
deoxyribose.

7. Nucleosides and Nucleotides:-
NUCLEOSIDE= Sugar (deoxyribose ) + Nitrogenous bases.
NUCLEOTIDE = Nucleoside +phosphate group.
• In other words, A nucleoside is a base - sugar combination and a
nucleotide is a nucleoside phosphate.
•In 1953, Watson and Crick, proposed the double helical model of
DNA and is the most widely accepted molecular model of DNA.

8. Fig:-DNA Double Helix.

9. DNA REPAIR:-
•DNA has a specific base sequence and the main objective of
biological system is to maintain these sequences of DNA from one
generation to other.
•In a multicellular organism,the death of a single somatic cell due to
DNA damage is less dangerous than to replicate its damaged DNA
,as it give rise to tumour or other cancerous growth.
•Thus, cell must possess an efficient repair system to avoid cell death
or mutation.
•This repair system removes many spontaneous errors that arises due
to chemical mutagens and radiations and also many damages arose
during replication.

10. Types of DNA repair:-
•Most cells possess four different categories of DNA
repair system. (Lindahl and Wood, 1999):

11. •DIRECT REPAIR SYSTEM:-
•Nicks are repaired by a DNA ligase . Nicks often results from the
effects of ionizing radiation.
Fig; Repair of a nick by DNA Ligase.
•Only a few types of damaged nucleotide can be repaired directly: i.e.

12. •Some forms of alkylation damage are directly reversible by
enzymes that transfer the alkyl group from the nucleotide to their
own polypeptide chains.
Eg. Ada enzyme of E. coli, it is involved in an adaptive process that
this bacterium is able to activate in response to DNA damage. Ada
removes alkyl group and can also repair phosphodiester bonds that
became methylated.
• Cyclobutyl dimers are repaired by a light-dependent direct system
called photoreactivation In E. coli, the process involves the enzyme
called DNA photolyase. When stimulated by light(wavelength
between 300 and 500 nm) the enzyme binds to cyclobutyl dimers
and converts it back to the original monomeric nucleotides.
A similar type of photoreactivation involves the
(6-4) photoproduct photolyase and results in repair of (6-4) lesions.

13. •EXCISION REPAIR:-
•These pathway is divided into two categories:
•Base Excision Repair
•Nucleotide Excision Repair
•Base Excision Repair:-
•It involves removal of a damaged nucleotide base, & excision of a
short piece of the polynucleotide around the AP site created, and
resynthesis with a DNA polymerase.

14. Fig:Base excision repair

15. NUCLEOTIDE EXCISION REPAIR:-
•Nucleotide excision repair has a much broader specificity than
base excision system.
•Used to correct more extensive type of damage.
• Eg. intrastrand crosslinks & modified bases by chemical
mutagens.
•similar to base excision except that it is not preceded by selective
base removal, and a longer stretch of polynucleotide is excised.
•Repair may be Short patch or Long patch.
•It also correct cyclobutyl dimers by a dark repair process (for
those organism that donot have photoreactivation system).

16. Fig; Short patch nucleotide-excision repair in E.coli.
•Short patch process of nucleotide excision repair is
generally studied by eg. of E.coli.

17. Fig:-Nucleotide excision repair in eukaryotes.
•E. coli also has a long patch nucleotide excision repair that involves
excision of DNA upto 2 kb in length and the eukaryotic nucleotide
excision repair process is also called ‘long patch'repair.

18. MISMATCH REPAIR SYSTEM:-
•It corrects the mismatches resulting from errors in
replication.
•Once a mismatch is found, the repair system excises part
of the daughter polynucleotide and fills in the gap, in a
manner similar to base and nucleotide excision repair.
•E. coli has three mismatch repair systems, called ‘long
patch', ‘short patch and ‘very short patch',

19. Fig. Long patch mismatch repair in E. coli.
•The long patch system requires the MutH, MutL and MutS proteins, as
well as the DNA helicase II during mismatch repair.
•Similar events occur during short and very short mismatch repair,
the difference is the specificities of the proteins that recognize the
mismatch.

20. RECOMBINATION REPAIR:-
•Recombination repair is used to mend double-strand breaks.
•Double strand break repair process
involves four sets of genes (Critchlow
and Jackson, 1998). These genes
specify a multi-component protein
complex that directs a DNA ligase to
the break.
•The complex includes a protein
called Ku,which binds the DNA ends
either side of the break.
Fig. Single- and double-strand-break repair.

21. • Recombination repair process is also called Non-
homologous End Joining (NHEJ), indicating that there is
no need of homology between two molecules whose end
are being joined.
•NHEJ is also a type of recombination, as it is used to join
together molecules that were not previously joined,
producing new combinations.
•A version of the NHEJ system is probably used during
construction of immunoglobulin and T-cell receptor
genes, but the details are likely to be different.

22. •DNA repair is very important as it can be analysed by the no. and
severity of inherited human diseases that are linked with defects in
one of the repair processes.
•For eg: Xeroderma pigmentosum,it is caused due to mutation in one
gene for protein that is involved in nucleotide excision repair(NER).
•TRichothiodistrophy is also caused by defects in NER ,but it is more
complex as it include problems with both the skin and the nervous
system.
•A few diseases are linked with defects in the transcription coupled
component of nucleotide excision repair.
RESULTS OF DEFECTS IN DNA REPAIR :-

23. DNA RECOMBINATION
•Genetic recombination is a process by which a segment of DNA is
broken and then joined to a different DNA molecule.
•Recombination is of great evolutionary significance , as it brings
about variation.
•Thus,recombination provides a means for spreading of favourable
alleles and a means to eliminate an unfavourable allele.
• Recombination was first recognized as the process responsible for
crossing-over and exchange of DNA segments between
homologous chromosomes during meiosis of eukaryotic cells, and
was subsequently implicated in the integration of transferred DNA
into bacterial genomes after conjugation, transduction or
transformation.
INTRODUCTION:-

24. •Mechanism oF Recombination:-Basically, there are three theories-
•Breakage and reunion:-Two homologous duplex of chromosome
lying in paired form breaks and rejoin crosswise and recombinants.
•Breakage and copying:-One helix of paired homologous
chromosome breaks in two segments and one of them is replaced by
a newly synthesized segment copied from other helix of paired
chromosome.
•Complete copy choice:-(Belling,1931)According to this theory,a
portion of one parental strand of homologous chromosome acts as
template for synthesis of copy of its DNA molecule. The process of
copying shifts to other parental strand.
Thus, recombinants contain some genetic
information of one parental strand and some of the other strand.

25. A.)Breakage and
reunion
B.)Breakage
and copying
C.)Complete copy
choice
Fig.Three possible Mechanism of recombination
a b a b+
a+ b+ a+ b

26. TYPES OF RECOMBINATION:-
Recombination is divided mainly into two categories:-
•Homologous recombination
•Non-Homologous recombination
HOMOLOGOUS RECOMBINATION:-
•Homologous recombination (also called Generalized
Recombination) involves exchange of precisely corresponding
sequences between homologous DNA duplexes.
•It is a reaction between two duplexes of DNA, and the enzyme
responsible for this can use any pair of homologous sequences as
substrates.

27. Models For Homologous Recombination:-
I.The Holliday model :-
•Proposed by Robin Holliday in
1964.
• Re-established by David Dressler
and Huntington Potter in 1976,
who demonstrated that the
proposed physical intermediates
existed
Fig; Holliday model for the homologous recombination.

28. II.Meselson and Radding Model:-
•Meselson and Radding in 1975,
proposes a model, and is a more
satisfactory scheme.
Here, a single stranded nick occurs
in just one of double helices
Fig: Meselson & Radding model.

29. III.Double strand break model:-
•According to this model, a double
strand break in one DNA molecule
initiates the process of recombination.
Fig: Double strand break model.

30. Fig:Resolution of two holliday junction in double strand break model.
Double strand break recombination results in two holliday
junction , which can be resolved in two ways:-

31. GENE CONVERSION:-
•Gene conversion is an event in DNA genetic recombination, it
occurs at high frequencies during meiotic division but also occurs in
somatic cells.
•When a pair of allele segregates, tetrads are expected to have 2:2
ratio of spores but sometime this expected pattern is replaced by
3:1ratio .This is called Gene conversion.
•It is a process by which DNA sequence information is transferred
from one DNA helix (which remains unchanged) to another DNA
helix, whose sequence is altered.
•Gene conversion has often been recorded in fungal crosses.

32. Fig: Gene conversion.

33. NON-HOMOLOGOUS RECOMBINATION:-
•Also called as specialized recombination.
TYPES OF NON-HOMOLOGOUS RECOMBINATION:-
•SITE-SPECIFIC RECOMBINATION
•TRANSPOSITION

34. •SITE-SPECIFIC RECOMBINATION:-
•Site-specific recombination involves a reaction between two
specific sites.
•Here, a region of extensive homology is not required , the
process can also be initiated between 2 DNA molecule that have
very short sequences in common.
The classic model for site-specific
recombination is illustrated by phage
lambda:

35. TRANSPOSITIONAL RECOMBINATION:
•Transposition is not a type of recombination but a process that
utilizes recombination, the end result being the transfer of a
segment of DNA from one position in the genome to another.
•Transposable element could be broadly divided into three
categories on the basis of their transposition mechanism:-
•DNA transposons that transpose replicatively, the original
transposon remaining in place and a new copy appearing elsewhere
in the genome.
•DNA transposons that transpose conservatively, the original
transposon moving to a new site by a cut-and-paste process.
•Retroelements, all of which transpose via an RNA intermediate.

36. Replicative And Conservative
Trasnsposition:-
•Many models have been
proposed over the years but
most are modifications of a
scheme originally outlined by
Shapiro (1979).
A model for the process resulting in replicative and conservative transposition.

37. •Transposition of Retroelements:-
•It takes place in two steps:-
•1st step:- An integrated
retroelement is copied into a
free double-stranded DNA
version. Firstly, there is
synthesis of an RNA copy,
which is then converted to
double-stranded DNA by a
series of events that involves
two template switches.

38. ii) 2nd step:- is the transposition of the retroelement.
Fig: Transposition of a retroelement :Part II.

39. One of the basic feature of the organisms, are to adapt in the
environment, and DNA repair & recombination helps the
organism to adapt to this feature .
DNA repair help to correct the error of replication and also the
damage caused due to chemical mutagens and radiations.
And, DNA recombination brings about variation and thus, leads to
evolution.
Recombination helps to distinguish between the favorable and
un-favorable changes occurred due to mutation and forms the
basis for natural selection.
Thus, repair and recombination, both play
an important role in the biological system.
CONCLUSION:-

40. REFERENCES:-
Genetics B.D.Singh
Textbook of Biochemistry David M. thomsan
Genome T.A.Brown
Gene VIII
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