Restriction Enzymes (also known as restriction ) What are restriction enzymes?

• An enzyme that cuts DNA at specific sequences known as restriction sites • Naturally found in and have evolved to provide a defense mechanism against invading viruses • In bacteria, restriction enzymes selectively cut up foreign DNA in a process called restriction Restriction Enzymes in Bacteria Restriction Enzymes

• Cut both strands of the DNA double helix • Over 3000 enzymes have been identified • More than 600 available commercially • Routinely used for DNA modification and manipulation in laboratories (“molecular scissors”) Restriction Sites

• Also known as recognition sites • Generally genetic palindromic sequences • A palindromic sequence in DNA one in which the 5’ to 3’ base pair sequence is identical on both strands • Usually a 4 or 6 base pair sequence

Restriction Sites

• The enzymes scan DNA sequences, find a very specific set of and make a cut

Hae III

• HaeIII is a that searches the DNA molecule until it finds this sequence of four nitrogen bases - GGCC

5’ TGACGGGTTCGAGGCCAG 3’ 3’ ACTGCCCAAGGTCCGGTC 5’ Hae III

• Once the recognition site was found HaeIII will go to work cutting (cleaving) the DNA Blunt Ends versus Sticky Ends • Hae III produces “blunt ends” when cleaving DNA • Other enzymes produce “sticky ends” blunt end

sticky end Restriction Enzyme Names

• Named after the type of bacteria in which the enzyme is found and the order in which the restriction enzyme was identified and isolated

EcoRI for example R strain of E.coli bacteria I as it is was the first E. coli restriction enzyme to be discovered. Restriction Enzymes and Cloning Separating Restriction Fragments

• Restriction enzymes are used to generate RFLPs (“rif-lips”) - Restriction fragment length polymorphisms • RFLPs are differences among individuals in the lengths of DNA fragments cut by enzymes • RFLPs can be separated using electrophoresis and then analyzed Generation of RFLPs Separating Restriction Fragments Gel Electrophoresis Applications Gel Electrophoresis Applications

• DNA sequencing (old school method) • Forensic purposes • Paternity testing • Examine evolutionary relationships among organisms (similarities and differences) • Diagnose genetic disorders or gene testing • Protein analysis • Determination of impurities in a sample DNA Sequencing

• Sanger Method - DNA sequencing using gel electrophoresis (method for ~25 years) • Uses radioactively labeled dideoxyribonucleotides

DNA Sequencing DNA Fingerprinting

• A test used to identify and evaluate genetic information DNA Fingerprinting Steps Forensics • Restriction enzymes and gel electrophoresis are used to create DNA fingerprints to analyze DNA samples from crime scenes Paternity Testing

• The pattern of DNA fragments (produced by the restriction enzyme digest) is compared and if the child's DNA looks like a combination of the two parents' DNA, then the child is theirs Evolutionary Relationships

• Which of the species, X or Y, is more closely related to species Z? Diagnose Genetic Disease

• Molecular diagnosis of a particular inherited disease