DNA Modifications

• Restriction Digestion
• Dephosphorylation
• Labelling
• Ligation
• Purification of labeled products
• Mutagenesis
• Methylation

Restriction Digestion

• DNA Modifying Enzymes  
• Restriction Disgestion : Know How? 
• Setting Up a Restriction Endonuclease Reaction 

• Restriction Digestion of DNA

• Restriction Enzyme Digests  
• Restriction Digestion of Plasmid, Cosmid, and Phage DNAs   
• Preparation of Bacteriophage Lambda  Concatamers for use as Size Standards in PFGE    
• Preparation of High Molecular Weight Human DNA Restriction Fragments in Agarose Plugs
• Restriction enzyme digestion of DNA  
• Partial Endonuclease Digestion  
• Restriction Digestion in the Presence of Agarose  
• Isolating DNA from the Restriction Digest Reaction Mixture  
• Restriction Enzyme Buffer Recipes

• Making blunt ended DNA fragments with T4 DNA polymerase  
• Alkaline phosphatase treatment of DNA (SAP)  
• CIP Dephosphorylation of Linearized DNA  
• Bisulfite Modification 
• Digestion of PCR Products 
• Cleavage Efficiency Close to the Termini of PCR Fragments  

• DNA Labeling using Klenow Fragment I
• End-labeling of DNA fragments
• Labeling of Oligonucleotides using polynucleotide kinase
• Random Primer Labeling
• Random Primed Labelling with P32
• Random Primer Labeling
• Random Hexamer Labeling of cDNA
• Alkaline phosphatase labeling of oligos
• PCR DNA Biotinylation (KPL)
• Determination of efficiency of digoxigenin labelling
• Non-isotopic Labeling
• PCR Products Labeling
• Kinase End-Labeling of DNA
• Endlabeling of DNA fragments with Klenow polymerase
• 5 -End Oligo Fluorescence Labeling
• 5 end labeling of oligonucleotides with gamma ³²P ATP

• 3-end Labeling
• Fill in Labeling of DNA
• Oligonucleotide labeling with ³²P

• DNA ligation  
• Standard Ligation
• Self-circularization of Linear DNA
• Linker Ligation 
    
• DNA Insert Ligation into Vector DNA 

Purification of Labeled Products

• 5 end labeling of oligonucleotides and purification
• Oligo Purification on Acrylamide Gels
• Spin Column chromatography
• Oligonucleotide Purification by PAGE and DEAE
• PAGE Purification of Oligonucleotides

• Site-directed Mutagenesis by PCR method 
• Site-directed mutagenesis 
• Oligonucleotide-directed mutagenesis 
• Site-directed Mutagenesis 
• Site Directed Mutagenesis Using the Ung-Dut System 
• In Vitro Mutagenesis by Altered Sites 
• In vitro Mutagenesis with dut ung single stranded DNA 
• Nested Deletions 
• Deletion Mutagenesis
• ExoIII/S1 Deletion 
• Exo/S1 Deletion Series 
• Nested Deletions by Exonuclease-III and Mung Bean Nuclease 
• In vitro Mutagenesis by Altered Sites 
• Unidirectional deletions (erase-a-base) 
• Design of Mutagenic Oligonucleotides 

• Methylation-Sensitive PCR (MSP) 
• Bisulfite-PCR (for restriction and/or sequencing) 
• Bisulfite Modification 
• Bisulfite Treatment of DNA 
• Methylated CpG Island Amplification (MCA) 
• DNA-Methyltransferase Assay