Two DNA molecules exchange genetic information,
resulting in the production of a new combination of
New allele/gene combinations are created by crossing
over that occur during meiosis.
Mitotic recombination also generate new genes .
Plays an important role in DNA damage repair
DNA recombination studies used to map genes on
Recombination can occur both during mitosis
Only meiotic recombination serves the
important role of re-assorting genes
Mitotic recombination may be important for
repair of mutations in one of a pair of sister
1. Generating new gene/allele combinations (crossing over
Gene shuffling allows favourable and non favourable alleles
to be separated and tested in new assortments causing
escape and spreading of favourable allele and elimination of
unfavourable alleles- role in genetic diversity- natural
selection and evolution
2. Mitotic recombination has roles in
a) post replicational repair (repair of lesions at replication
forks and for restarting replication that stalled at these
b) Generating new genes (e.g., Immuno- globulin
rearrangement) also known as somatic recombination
c) Yeast mating type switching (sequence at an active locus
replaced by a sequence from a silent locus)
1. Used to map genes on chromosomes
- recombination frequency proportional to
distance between genes
2. Making transgenic cells and organisms
It is a physical phenomenon where exchange of
sequence occur with no net gain or loss of nucleotides
It is based on sequence complementarity.
- Occurs between sequences that are nearly identical (e.g.,
Homologous recombination is extensively studied in E.coli.
At least 25 proteins are involved in recombination in E.coli.
A Complex Enzyme complex with endonuclease
and helicase activity.
1. Endonuclease subunits (RecBC) that cut one DNA
strand close to Chi sequence.
2. DNA helicase activity in presence of a SSB(RecD
and Rec B ) and a DNA-dependent ATPase
Essential for 99% of recombination events
occurring at double-stranded breaks in
Binds double stranded break
Unwinds and degrades DNA
Pauses at chi sequence
Loads RecA on 3’ ssDNA extensions
38 kDa protein
Catalyzes strand exchange, also an ATPase
Also binds DS DNA, but not as strongly as SS
Involved in SOS response
Catalyses in strand transfer
Eukaryotes have multiple homologs of RecA
Rad51 is best studied
RecA can generate Holliday junction
By its strand transfer &displacement reactions.
Chi site (Χ-site)
• Recombination hotspot
• Modifies RecBCD enzymatic activity
5’ GCTGGTGG 3’
• 1009 chi (Χ) sites in E. coli genome.
• Recombination start point 10 kb right to the
Most popular model to explain homologous
It was proposed by Robin Holliday.
R. Holliday (1964)
- Holliday Junctions form during recombination
- HJs can be resolved 2 ways, only one produces true
It begins with two paired DNA duplexes or
In each of which an endonuclease introduces a single
stranded nick at an identical position chromosomes.
Ends of the strands produced these cuts are
displaced and pair with their complements on opposite
A ligase seals the loose ends creating hybrid duplexes
called heteroduplex DNA molecules.
The exchange creates a cross bridged structure
The position of this cross bridge can move down the
chromosome by the branch migration.
Ruv B is a DNA helicase that catalyzes branch migration.
It occur as a result of a zipper like action as Hydroygen bonds
Then reformed b/w complementary bases of the displaced
strands of each duplex.
Migration yields an increased length of heteroduplex DNA on
The duplex will separate ,bottom portions rotate about180*.
Now the duplex form a planar structure called a X-form That
is Holliday junction (Chi form)
Two strands on opposite homologs previously uninvolved in
the exchange are now nicked by an endonuclease
Then ligation occurs
Recombinant duplexes are created.
Resolution of H.J is achieved by Ruv protein.
RuvA tetramer binds to HJ (each DNA helix between
subunits), forces it into rotate about 180 to form
square planar conformation
Resolution of H.J is catalysed by RuvC : resolvase
It is an endonuclease that binds to HJ as a dimer .
That cuts 2 strands of HJ.
It decide whether to cut horizontally or tranverse cut
at the Holliday junction.
The two DNA molecules share limited homology
14-55 bp homology enzymes involved
E.g Integration of Lamda phage DNA into bacterial
O ‘core region - 15 bp sequence that is common between
phage DNA and bacterial chromosome
Site-specific recombination alters gene order, which would
not happen during general recombination
Site-specific recombination is guided by
recombination enzymes that recognize short, specific
nucleotide sequences present on one or both of the
recombining DNA molecules.
The best example of the conservative site-specific
recombination is Bacteriophage lambda.
Lysogenic cycle involves integration of phage into the host chromosome by SITE-
Molecular Biology of the Gene, 5th Edition
A special type of homologous recombination
Non-reciprocal transfer of genetic material from a ‘donor’
sequence to a highly homologous ‘acceptor’ sequence
Initiated by double strand DNA (dsDNA) breaks
5’ > 3’ exonucleases
Outcome: portion of ‘donor’ sequence copied to
‘acceptor’and original ‘donor’ copy unchanged
Gene Conversion is not uncommon
Yeast mating type switch (MAT) genes
Human repetitive sequence elements (Alu and LINE-1 sequences)*
Human gene families (e.g. MHC alleles, Rh blood group antigens,
olfactory receptor genes)
Chicken B cells Ig gene diversification
Pathogen clonal antigenic variation (e.g. African Trypanosomes
and Babesia bovis)
Here DNA elements moves from one site to the another .
Little sequence similarity is involved.
Transposition of genes takes place
Ability of genes to change position on chromosome.
A transposable element is removed from site & inserted into a
second site in the DNA.
A transposable element (TE, transposon ) is a DNA sequence
that can change its position within the genome.
sometimes creating or reversing mutations and altering the
cell's genome size