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What are the two ways by which discrete segments of DNA can move from one region of the genome to another?

1) Site-specific recombination 2) Transposition


Site Specific recombination structure.

a) CSSR conservative site-specific recombination (CATACA) recombination site. (b) Flanked by Cre binding sites that aid in recombination protein binding


Recombinase proteins

bind to the cre binding site. cleave phosphodiester backbone of DNA. Act like topoisomerases (no ATP involved)


What is the only way that SSR will occur?

the region of strand exchange between the two DNA molecules must be in the same direction.


Direction oreintation

sites are in the same direction - leads to excision


sites in inverted oreintation

sites are not in the same direction - leads to inversion


Mechanism of site specific recombination

1. regions of strand exchange line up 2. recombinase does nucleophilic attack on phosphodiester backbone (tyrosine leads to 5'OH formation, while serine leads to 3'OH formation) 3) tyro-phosphate groups and OH groups on opposite strands attract. 4) other set of topoisomerases produce OH and tryophosphates which combine and repair to form two different strands.


SSR on the same DNA molecule

If rec sites are in opposed direction, inversion; if rec sites are in the same direction you get an insertion and deletion.



jumping genes, short sequences (transposons) can excise and reinsert at a different place in the genome.


Inverted repeats

reads one way L-R and the same way R-L on a different site on DNA


Transpoase gene

encodes transpoases; transposases recognize IRs, cut piece of DNA out of site, and move it to different site.


mobile genetic element

can move from one region to another


Flanking DNA

regions on target DNA that recognize ends of transposons ( terminal repeats). gaps mad when transposon and target DNA are fixed by DNA repair mechanism. The flanking DNA act as templates.


Direct transposition

(DS breaks) 1) Cleavage of transposons 2) Free ends of transposons attack target DNA 3) Gaps filled (left) by DNA polymerase and ligase


Replicative transposition

1) Cleavage of transposons 2) Free ends of transposons attack target DNA 3) entire transposon replicated 4) Site specific recombination (with in the transposon) DNAP III mediated replication,


What type of recombination produces genetic diversity in adaptive immunity?

Site specific recombination during assembly of Ig genes.


VJ recombination

Occurs in light chain


VDJ recombination



VJ recombination process

1) RSS sequence associated with V segment and J segment 2) Recombinase binds to RSS sequence on V and J. 3) Rag1/2 form 3'OH and the 3'OH does a nucleophilic attack on its own strand watson-crick strand. 4) The genetic information in the middle gets removed.


VDJ Recombination

1) RAG 1/2 binds to V and D RSS 2) cleavage produces 3'OH 3) 3'OH attacks own watson crick strand 4) Ku70/80 involved in joining. Artemis opens hairpins and activates Ku70/80,

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