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Restriction Endonucleases
Also called restriction enzymes 1962: molecular scissors discovered in in bacteria
E. coli bacteria have an enzymatic immune system that recognizes and destroys foreign DNA
3,000 enzymes have been identified, around 200 have unique properties, many are purified and available commercially
Restriction Enzymes
Restriction Endonucleases
Restriction endonuclease recognizes a short and specific DNA sequence and cuts it from inside.
The specific DNA sequence is called recognition sequence
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Nomenclature
the source organism First letter from genus Next two letters represent species Additional letter or number represent the strain or serotypes
For example. the enzyme HindII was isolated from Haemophilus influenzae serotype d.
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Restriction Endonucleases
Named for bacterial genus, species, strain, and type
5' -->3'
Bam HI Eco RI Bacillus amyloliquefaciens Escherichia coli RY 13 G* G A T C C G* A A T T C
Hind III
Mbo I Pst I Sma I Taq I Xma I
Haemophilus inflenzae Rd
Moraxella bovis Providencia stuartii Serratia marcescens Thermophilus aquaticus Xanthamonas malvacearum
A* A G C T T
*G A T C CTGCA*G CCC*GGG T*CGA C*CCGGG
R-M System
Restriction-modification (R-M) system Endonuclease activity: cuts foreign DNA at the recognition site Methyltransferase activity: protects host DNA from cleavage by the restriction enzyme. Methylate one of the bases in each strand Restriction enzyme and its cognate modification system constitute the R-M system
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DNA sequencing
DNA storage libraries Transformation
PO4-A-A-T-T-C-A-G-C-T-A-C-G-3 HO-G-T-C-G-A-T-G-C-5
5-A-C-G-G-T-A-C-T-A-G-A-A-T-T-C-A-G-C-T-A-C-G-3 3-T-G-C-C-A-T-G-A-T-C-T-T-A-A-G-T-C-G-A-T-G-C-5
Bacteria protect their self DNA from restriction digestion by methylation of its recognition site. Methylation is adding a methyl group (CH3) to DNA. Restriction enzymes are classified based on recognition sequence and methylation pattern.
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Methylation
Classification
Evolved independently rather than diverging form a common ancestor Broadly classified into four Types
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Type I
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Type III
Large enzymes Combination restriction-and-modification Cleave outside of their recognition sequences Require two recognition sequences in opposite orientations within the same DNA molecule No commercial use or availability
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Type IV
Recognition sequences have not been well defined Cleavage takes place ~30 bp away from one of the sites.
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Type II
Most useful for gene analysis and cloning
More than 3500 REs Recognize 4-8 bp sequences Need Mg 2+ as cofactor Cut in close proximity of the recognition site Homodimers ATP hydrolysis is not required
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Recognition Sequences
Each restriction enzyme always cuts at the same recognition sequence. Produce the same gel banding pattern (fingerprint) Many restriction sequences are palindromic. For example,
5 GAATTC 3 3 CTTAAG 5
(Read the same in the opposite direction (eg. madam, race car)
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blunt end
sticky end
Most restriction enzymes make staggered cuts Staggered cuts produce single stranded sticky-ends DNA from different sources can be spliced easily because of sticky-end overhangs.
HindIII
EcoRI
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AluI
HaeIII
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Discovery of enzymes that cut and paste DNA make genetic engineering possible. Restriction enzyme cuts DNA and generates fragments Ligase joins different DNA fragments
DNA fragments from different species can be ligated (joined) to create Recombinant DNA
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Restriction Maps
Useful but now most commonly generated by computer from actual DNA sequence
Suspect
Evidence
Victim
b nucleases
ii Polynucleotide kinase
3 DNA ligase
DNA ligase used for both blunt and cohesive end ligation