probes Protocols

Category: DNA Protein Interactions Protocols: Dnase Footprinting Assay Protocols

Protocol for in vitro footprinting methods. Includes: Preparation of labeled probes; Gel purification. - [Read In Vitro Footprinting Methods Protocol]

Category: Bacterial Cell Culture Protocols: Bacterial Stocks Protocols

Plasmid (pUC series) containing genomic DNA fragments are maintained in E. coli strain DH5aTM. The E. coli cultures are routinely cultured at 37 C on Luria-Bertani (LB) agar on or in LB broth containing Ampicillin (30 µg/ml) or Carbenicillin (50 µg/ml broth, 100 µg/ml agar). E. coli strains are usually preserved in stab agar or glycerol for mid-term storage and lyophilized for long-term storage. - [Read Maintenance of Probes in Bacteria Including Escherichia coli Protocol]

Category: Nucleic Acid Modification Protocols: Nucleic Acid Radiolabeling Protocols

Preparations of RNA containing an mRNA of interest are hybridized to a radiolabeled single-stranded RNA probe. The method can be used to quantitate RNAs, to map the positions of introns, and to identify the locations of 5' and 3' ends of mRNAs on cloned DNA templates. - [Read Mapping RNA with Ribonuclease and Radiolabeled RNA Probes Protocol]

Category: Plant Biology Protocols

The standard protocol for in situ hybridizations in plants still involves fixing fresh tissue, embedding the tissue in wax, sectioning with a microtome and detection of the transcripts of interest using labeled RNA-probes. This protocol concentrates only on nonradioactive methods, as they are easy to perform, very sensitive and even faster than techniques involving radioisotope labels. - [Read Molecular and Biochemical Analysis of Arabidopsis Protocol]

Category: Molecular Imaging

Molecular Probes at Invitrogen - [Read Molecular Probes at Invitrogen]

Category: Molecular Imaging

The Handbook — A Guide to Fluorescent Probes and Labeling Technologies is a comprehensive resource for fluorescence technology and its applications. Newly revised, The Handbook contains detailed information describing the use of more than 3000 Molecular - [Read Molecular Probes Handbook Invitrogen]

Category: Cytogenetics Protocols: RNA In Situ Hybridization Protocols

Protocol for mRNA in situ hybridization with nick-translated probes. - [Read mRNA In Situ Hybridization with Nick-Translated Probes Protocol]

Category: Cytogenetics Protocols: In Situ Hybridization Protocols

Protocol for multiple-target DNA in situ hybridization with enzyme-based cytochemical detection systems. Includes: Cell preparations; Cell processing; Probe preparation; Multiple-target in situ hybridization (ISH); ISH with separate probe and target denaturation [for probes with repetitive (e.g., Alu) elements]; Post-hybridization washes; Enzyme-based cytochemical detection; etc.. - [Read Multiple-Target DNA In Situ Hybridization with Enzyme-Based Cytochemical Detection Systems Protocol]

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]

Category: Microscopy Protocols: Optical Microscopy Protocols

Near-field scanning optical microscopy can achieve spatial resolution performance beyond the classical diffraction limit by employing a sub-wavelength light source or detector positioned in close proximity to a specimen. Such a sub-wavelength source usually consists of an aperture at the end of a tapered probe, which functions basically as a wave guide. Includes info.: Fiber Probe Fabrication; Pulling Method; Meniscus Etching; Selective Etching; Apertureless and Alternative Probe Designs etc. - [Read Near-Field Scanning Optical Microscopy: NSOM Probes]

Category: Nucleic Acid Modification Protocols: Nucleic Acid Labeling Protocols

Protocol for nick-translation labeling of ds DNA with nick translation mixes for in situ probes. Includes: Labeling reaction with DIG-dUTP or Biotin-dUTP; Labeling reaction with Fluorescein-dUTP, or Tetramethylrhodamine-dUTP; Purification of labeled probe. - [Read Nick-Translation Labeling of ds DNA with Nick Translation Mixes for In Situ Probes Protocol]

Category: Real Time PCR: Real Time PCR Information

Allelic discrimination by nick-translation PCR with fluorogenic probes. Lee et al., 1993. - [Read Original Real Time Paper. Allelic discrimination by nick-translation PCR with fluorogenic probes.]

Category: Cytogenetics Protocols: DIG Biotin Labeled Probe Protocols

Protocol for PCR labeling of ds DNA with the PCR DIG Probe Synthesis Kit or PCR Labeling Mixes. Includes: PCR DIG labeling reaction for moderately labeled probes; PCR fluorescein labeling reaction for direct in situ probes.
- [Read PCR Labeling of Ds DNA with the PCR DIG Probe Synthesis Kit or PCR Labeling Mixes]

Category: Nucleic Acid Modification Protocols: DIG Biotin Labeled Probes Protocols

Protocol for PCR labeling of ds DNA with the PCR DIG Probe Synthesis Kit or PCR Labeling Mixes. Includes: PCR DIG labeling reaction for highly labeled probes containing unique sequences; PCR DIG labeling reaction for moderately labeled probes; PCR fluorescein labeling reaction for direct in situ probes. - [Read PCR Labeling of ds DNA with the PCR DIG Probe Synthesis Kit or PCR Labeling Mixes Protocol]

Category: Cell Biology and Cell Culture

Protocol for motor polarity using fluorescent microtubules using the materials: Rhodamine-tubulin (Molecular Probes),NEM- tubulin, PC-tubulin, Mg·GTP, MgCl2 and Glycerol. - [Read Protocol for Motor Polarity Using Fluorescent Microtubules]

Category: Cell Biology and Cell Culture: In Vitro Reconstitution Protocols

In vitro transcription reactions employing T3, T7 or SP6 phage-encoded RNA polymerases are widely used to synthesize RNA from recombinant vectors containing appropriate promoters. Production of large amounts of specific RNA is valuable in the preparation of hybridization probes and in vitro translation studies; in the synthesis of ribozymes, rRNA, SRP, antisense RNA and substrates for RNA splicing; and in RNA-protein interaction studies. - [Read Protocol: Purification of In Vitro Synthesized mRNA with Microcon or Centricon Centrifugal Filters]

Category: Nucleic Acid Modification Protocols: Nucleic Acid Labeling Protocols

Protocol for purification of labeled probes using the High Pure PCR Product Purification Kit. - [Read Purification of Labeled Probes Using the High Pure PCR Product Purification Kit Protocol]

Category: Nucleic Acid Purification Protocols

Protocol for purification of labeled probes using the High Pure PCR Product Purification Kit. - [Read Purification of Labeled Probes using the High Pure PCR Product Purification Kit Protocol]

Category: Nucleic Acid Modification Protocols: Nucleic Acid Radiolabeling Protocols

In this protocol, double-stranded DNA probes, labeled in each strand, are produced in conventional PCRs containing equal concentrations of two primers, a double-stranded DNA template, three unlabeled dNTPs at concentrations exceeding the Km, and one [{alpha}-32P]dNTP at a concentration at or slightly above the Km (2-3 µm) for a thermostable DNA polymerase such as Taq. - [Read Radiolabeling of DNA Probes by the Polymerase Chain Reaction Protocol]

Category: PCR Protocols

Protocol describes how double-stranded DNA probes, labeled in each strand, are produced in conventional PCRs containing equal concentrations of two primers, a double-stranded DNA template, three unlabeled dNTPs at concentrations exceeding the Km, and one [{alpha}-32P]dNTP at a concentration at or slightly above the Km (2-3 µm) for a thermostable DNA polymerase such as Taq. - [Read Radiolabeling of DNA Probes by the Polymerase Chain Reaction Protocol]

Category: DNA Protocols: EMSA DNA-Protein Protocols

Creation of Probe for EMSA using Oligonucleotide annealing, p-32, and T4 Polynucleotide Kinase. - [Read Radiolabeling of Probes for Electrophoretic Mobility Shift Assay]

Category: DNA Protein Interactions Protocols: Electrophoretic Mobility Shift Assays EMSA Protocols

Protocol for radiolabeling of probes for electrophoretic mobility shift assays. - [Read Radiolabeling of Probes for Electrophoretic Mobility Shift Assays Protocol]

Category: Nucleic Acid Modification Protocols: Nucleic Acid Radiolabeling Protocols

In this procedure, synthesis of cDNA is carried out in the presence of saturating concentrations of all four dNTPs and trace amounts of a single radiolabeled dNTP.  After subtraction hybridization, the enriched single-stranded cDNA is radiolabeled to high specific activity in a second synthetic reaction by extension of random oligonucleotide primers using the Klenow fragment of E. coli DNA polymerase. - [Read Radiolabeling of Subtracted cDNA Probes by Random Oligonucleotide Extension Protocol]

Category: Cell Biology and Cell Culture: In Vitro Reconstitution Protocols

In vitro transcription systems includes instructions for use of products P1420, P1430, P1440, P1450 and P1460.Includes information and protocols on RNA Transcription in vitro. Information on DNA Template Preparation;Synthesis of High-Specific-Activity Radio labeled RNA Probes;Determining Percent Incorporation and Probe Specific Activity;Removal of the DNA Template Following Transcription;Removal of unincorporated nucleotides;Synthesis of large amounts of RNA;Capping RNA for in vitro translation. - [Read Riboprobe In Vitro Transcription Systems]

Category: C. elegans Protocols

Protocol for RNA in situ hybridization of dissected gonads with digoxygenin-labeled probes. Includes: Preparation of single-stranded probes from cloned cDNA; Dissections and Fixation; Proteinase K digestion; Hybridization; Making a Mount. - [Read RNA In Situ Hybridization of Dissected Gonads with Digoxygenin-Labeled Probes Protocol]