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Amino-allyl Labeling (GeneTAC) Protocol - http://www.bcm.edu/mcfweb/?PMID=3551

Category: Microarray Protocols: Amino-allyl Microarray Methods

Protocol for amino-allyl labeling (GeneTAC). Includes: RT Reaction; Nucleotide Mix for one reaction; Coupling; Prehybridization of probe. - [Read Amino-allyl Labeling (GeneTAC) Protocol]

Calculating Concentrations for PCR - http://www.mcb.uct.ac.za//pcrconcn.htm

Category: PCR Protocols: PCR Optimization

Calculating Concentrations for PCR. Ed Rybicki. Calculating Primer and Nucleotide Concentrations for PCR - [Read Calculating Concentrations for PCR]

Custom Fluorescent Nucleotide Synthesis/Nucleic Acid Labeling Protocol - http://info.med.yale.edu/genetics/ward/tavi/n_coupling.html

Category: Cytogenetics Protocols: Fluorescent In Situ Hybridization FISH Protocol

Protocol for custom fluorescent nucleotide synthesis/nucleic acid labeling. - [Read Custom Fluorescent Nucleotide Synthesis/Nucleic Acid Labeling Protocol]

Fluorescent In Situ Transcription in Cells and Tissues Protocol - https://catalog.invitrogen.com/index.cfm?fuseaction=iProtocol.unitSectionTree&treeNodeID=9E6639A7FEDD7A49BBC3758516F99557&objectid=6677C9E8B913BFB72E9F654025F3C39A

Category: Cytogenetics Protocols: Fluorescent In Situ Hybridization FISH Protocol

Method assesses cellular mRNA transcripts in tissue sections and cell cultures using unique short anti-sense primers directed against sequences in particular protein(s). The unlabeled synthetic cDNA oligonucleotide primers are extended complementary to a sense mRNA transcript using reverse transcriptase and labeled through incorporation of a fluorescent-labeled dUTP nucleotide base. This procedure provides rapid detection of low abundance mRNA messages that can be related to other cellular.... - [Read Fluorescent In Situ Transcription in Cells and Tissues Protocol]

Generation of Sets of Nested Deletion Mutants with Exonuclease III Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/2/pdb.prot4078

Category: Genetics and Genomics: Genotyping Protocols: Mutation Detection Protocols

The double-stranded DNA of recombinant plasmid, phagemid, or bacteriophage M13 replicative form DNA is digested with two restriction enzymes whose sites of cleavage both lie between one end of the target DNA and the binding site for universal primer. The enzyme that cleaves nearer the target sequence must generate either a blunt end or a recessed 3' terminus; the other enzyme must generate a four-nucleotide protruding 3' terminus. - [Read Generation of Sets of Nested Deletion Mutants with Exonuclease III Protocol]

Mutation Detection by Solid-Phase Chemical Cleavage of Mismatches Using Radioactive Probes Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/14/pdb.prot4120

Category: Genetics and Genomics: Genotyping Protocols: Mutation Detection Protocols

This protocol is the first of two describing solid-phase chemical cleavage of mismatch (SpCCM), a method for the detection of mutations in genomic DNA. DNA fragments up to 2 kb in length can be analyzed to determine the position (within 10-15 bp) and identity of the mismatched nucleotide. - [Read Mutation Detection by Solid-Phase Chemical Cleavage of Mismatches Using Radioactive Probes Protocol]

RNA Labeling by In Vitro Transcription of DNA with DIG, Biotin or Fluorescein RNA Labeling Mix - http://www.roche-applied-science.com/PROD_INF/MANUALS/InSitu/pdf/ISH_54-57.pdf

Category: Cytogenetics Protocols: RNA In Situ Hybridization Protocols

Protocol for RNA labeling by in vitro transcription of DNA with DIG, Biotin or Fluorescein RNA Labeling Mix. A PCR fragment that has the appropriate promoter ligated to its 5’-ends can also serve as a transcription template. The procedure described incorporates one modified nucleotide (DIG-, Biotin-, or Fluorescein-UTP) at approximately every 20 – 25th position in the transcripts. - [Read RNA Labeling by In Vitro Transcription of DNA with DIG, Biotin or Fluorescein RNA Labeling Mix]

Singel Nucleotide Primer Extension (SNuPE) - http://www.methods.info/Methods/DNA_methylation/SNuPE.html

Category: Epigenetics and Methylation Protocols: Bisulfite Treatment Methylation Assay Protocol

Single Nucleotide Primer Extension can be used for the analysis of methylation in a certain position. Treat DNA with bisulphite and then anneal a primer which ends immediately before the site of analysis. Dr. A. Gratchev Methods.info - [Read Singel Nucleotide Primer Extension (SNuPE)]

Single Nucleotide Polymorphisms as Tools in Human Genetics - http://www.nslij-genetics.org/ld/gray00.pdf

Category: Genetics and Genomics: Genotyping Protocols

Describe the current efforts to identify and characterize the large number of SNP's required and discuss the practicalities of association studies for the identification of genes involved in complex traits. - [Read Single Nucleotide Polymorphisms as Tools in Human Genetics]

Site-Specific Protein-DNA Photo-Cross-Linking: Analysis of Structural Organization of Protein-DNA - http://www.cshprotocols.org/cgi/content/abstract/2006/29/pdb.prot4588

Category: DNA Protein Interactions Protocols

The multiprotein-DNA complex of interest is formed using the site-specifically derivatized DNA fragment. The complex is then UV-irradiated, initiating covalent cross-linking with proteins in direct physical proximity to the cross-linking agent. Extensive nuclease digestion is performed to eliminate uncross-linked DNA and convert cross-linked DNA to a cross-linked, radiolabeled nucleotide "tag." - [Read Site-Specific Protein-DNA Photo-Cross-Linking: Analysis of Structural Organization of Protein-DNA]

SNP detection with mutagenic primers - http://insilico.ehu.es/restriction/mutation_seq/

Category: DNA Protocols: SNP Protocols

SNP detection with mutagenic primers. Input sequence will be searched to find changes in one nucleotide near the location of the SNP, so that mutagenic primers may be easily designed. Bikandi, J., San MillÃ¡n, R., Rementeria, A., and Garaizar, J. In silico analysis of complete bacterial genomes: PCR, AFLP-PCR, and endonuclease restriction. Bioinformatics 2004 Mar 22;20(5):798-9. - [Read SNP detection with mutagenic primers]

Articles (1-2 of 2)

DNA Ligation Protocol

The DNA Ligation protocol described here contains the steps required to join together using ligase enzyme both plasmid DNA and insert DNA fragments in order to create a new plasmid. This new ligated plasmid can be transformed after into competent bacteria to produce DNA for mini, midi or maxi-prep isolation.

3' Rapid Amplification of cDNA Ends RACE Using PCR Protocol

3' Rapid Amplification of cDNA Ends RACE Using PCR Protocol. This protocol contains the steps for 3' end rapid amplification of mRNA by PCR. The first-strand cDNA is synthesized from total or poly(A+) RNA by priming from the poly-A tail of the mRNA using a oligo (dT) adaptor primer. The cDNA is then amplified via PCR using a gene-specific primer and an adaptor primer.

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