Recombination

1
Recombination

• Breaking and rejoining of two parental DNA
  molecules to produce new DNA molecules

Benefits of recombination

• Greater variety in offspring Generates new
  combinations of alleles
• Negative selection can remove deleterious alleles
  from a population without removing the entire
  chromosome carrying that allele
• Repair damaged DNA
• Reconstitute damaged replication fork

2
Recombination occurs when two homologous
chromosomes are together

• Homologous or general recombination
• Recombination between two homologous chromosomes
• Nonhomologous or illegitimate recombination
• Two different chromosomes recombine. The segment
  at the sites of recombination may be related
• Site specific
• Integration of bacterial, viral or plasmid DNA
  into cellular chromosome
• Replicative Transposition

3
Types of recombination
A
B-
C-
A
B
C
Homologous or general
B
C
A-
A-
B-
C-
A
B
A
B
C
F
Nonhomologous or illigitimate
C
D
E
D
E
F
l
l
att
integrase
l
Site-specific
att
att
E. coli
att
Replicative recombination, transposition
transposase
A
B
C
A
B
C
Transposable element
4
Meiotic recombination generates new combinations
of alleles in offspring
Each line is duplex DNA, starting at pachytene of
meiosis I
Finish Meiosis I
Meiosis II
Fertilization
5
Homologous or General Recombination

• Holiday Model
• Double-strand DNA Break Repair Model (RecBCD
  model)

6
Holliday model for recombination

• Pairing align homologous duplexes
• Single strand invasion
• Endonuclease nicks at corresponding regions of
  the same strands of homologous chromosomes
• Ends generated by the nicks invade the other,
  homologous duplex
• Ligase seals nicks to form a joint molecule.
• (Holliday intermediate or Chi structure)
• Branch migration expands heteroduplex region.

7
Holiday model
a. Aligned homologous duplex
top duplex
b. Single-stranded breaks in each duplex
seal nick
bottom duplex
c. Strand invasion
Holiday junction
hetero duplex
hybrid duplexes
d. Branch migration
Molecular Biology of the Gene, Fig. 10-1
8
5. Resolution
site 2
site 1
DNA cleavage
splice or crossover products reassortment of
flanking genes
patch or non-crossover products no reassortment
Resolution can occur in one of two ways
Holiday junction cleavage
Molecular Biology of the Gene, Fig. 10-2
9
Gene conversion can occur by replication through
a heteroduplex
Patch or non-crossover product of resolution of
the Holliday intermediate
A
C
a
B
c
B
and
b
A
C
a
c
b
replicate
replicate
A
C
c
B
a
b
parental
A
a
c
b
C
B
In the lower duplex, the middle gene has been
converted from b to B with no recombination of
the flanking markers.
In the lower duplex, the middle gene has been
converted from B to b with no recombination of
the flanking markers.
10
Double Strand Break Repair Model

• This model provides a better explanation for
  recombination events in yeast
• A double strand break precedes recombination.
• One DNA molecule is used preferentially as the
  donor of genetic information.
• Gapped substrates can initiate recombination and
  in the process be repaired

11
double stranded break (DSB)
processing to generate gapped DNA with 3 ss tails
strand invasion of 3 3nd
Branch migration and formation of an intermediate
with two Holiday junctions
DSB repair model for homologues recombination
second strand invasion and DNA repair synthesis
of 3 ends
12
How to Resolve a Recombination Intermediate with
Two Holliday Junctions
13
Common Steps in Holiday and Double Strand Break
Repair Models

• Generate a single-stranded end
• Search for homology
• Strand invasion to form a joint molecule
• Branch migration
• Resolution
• Enzymes catalyzing each step have been isolated.

14
Difference in two models

• Holiday model
• Single-stranded nicks form in both DNA molecule.
  Single Holiday junction at strand invasion
• Double Strand Break Repair Model (RecBCD pathway)
• Double-stranded break forms in one DNA molecule.
  Two Holiday junctions at strand invasion. New DNA
  is synthesized by DNA polymerase