Protocols

General Lab Buffers: Buffers, Acid-base concentrations, Acid-base concentrations, excel sheet

Clarity semi-prep Oligo purification: Example using the O²-POB-dT oligo that was made in low yield Method

Agarose gel: For separation of large DNA molecules, 100 to 10,000 nucleotides Protocol
Protein SDS PAGE: Separtion of proteins with denaturing PAGE. Silver Staining Protocol
PAGE separation of oligodeoxynucleotides: Use of old sequencing gels to separate oligos. Protocol
PAGE purification of oligodeoxynucleotides: PAGE can seperate oligos with base pair resolution. Protocol

There are several silica-based systems plus the Marmur method to use:

Zymo kits comparisons: Summary of the Quick-DNA MicroPrep, MiniPrep, and MidiPrep Plus DNA Isolation Protocols
Zymo Quick DNA Midiprep Plus: Isolate genomic DNA from 30 million cells. The ‘Plus’ version of these kits use a proteinase K hydrolysis step Protocol and Manual
Zymo Quick DNA Miniprep Plus: Isolate genomic DNA from 5 million cells. Protocol and Manual
Qiagen Genomic-tip: Protocol from cultured cells and Manual. Protocol to make the Genomic-tipe buffers
Modified marmur method: Protocol uses proteinas K and CHCl₃ and iso-amyl alcohol to extract protein

There are several silica-based systems to use:

Zymo Genomic DNA Clean and Concentrator: DNA from impure preparations of genomic DNA (e.g., Proteinase K digestions), plasmid DNA, viral DNA, and whole genome amplified DNA. Capable of purifying small DNA fragments >50 bp and large sized DNAs up to 200 kb. Protocol and Manuals for gDCC-10 and gDCC-25
Zymo DNA Clean and Concentrator: Clean DNA smaller DNA 50 bp to 10 kb, the recovery is 70-90%. DNA 11 kb to 23 kb, the recovery is 50-70% Protocols and Manuals for DCC-5 and DCC-25
Zymo ChIP DNA Clean and Concentrator: Protocol
Thermo Fisher GeneJet PCR purification: Manual

DNA polymerase kappa: His-POLK and His-FLAG-POLK Protocol
Bacolu virus expression in SF9 cells: Passaging of sf9 cells, mutagenesis of clone, Bacmid preperation, formation of P₀, P₁, and P₂ stocks, Protein expression and BIICs formation Protocol

Nucleoside concentrations: UV-vis spectroscopy to determine concentrations with Molar extinction coefficients for dNTPs
Oligo Purification: PAGE Purification
HPLC Purification of oligodeoxynucleotides: Phemonex Clarity RP column. First capture DMT-on oligo, HOAc hydrolysis of DMT group, followed by second HPLC Protocol,
Example of O²-alkyl-dT containing oligos Protocol
HPLC Purification of DMT-off oligodeoxynucleotides: RP-HPLC Protocol