agarose Protocols

Category: BACs Bacterial Artificial Chromosome Protocols

Sequencing conditions tested for the ABI Big-Dye terminators (PE-ABI #4303150 for the 1000 reaction kit - Description: TF,KIT BTD RR-1000) with various templates. Important to quantitate all templates by agarose gel electrophoresis vs size and concentration standards and do a few tests with different template concentrations to determine the optimal conditions for your reactions. Several conditions are given. - [Read Dye Protocols and Notes for Cosmid, BAC, BAC, Fosmid Templates]

Category: Nucleic Acid Electrophoresis Protocols: DNA Electrophoresis Protocols: DNA Electrophoresis in Agarose Gels Protocols

Protocol for electrophoresis of single stranded DNA using agarose gel. - [Read Electrophoresis - Agarose Gels for Single Stranded DNA Protocol]

Category: Molecular Biology Protocols: Agarose Gel Preparation

Electrophoresis of DNA in Agarose Gels. Frank Lab. - [Read Electrophoresis of DNA in Agarose Gels.]

Category: Xenopus Protocols: Xenopus Embryo Manipulation Protocols

Protocol for embryo lysates and immunoprecipitation: protein A agarose & protein A magnetic beads. Includes: Embryo lysates; Immunoprecipitation with protein A agarose; Immunoprecipitation with protein A magnetic beads for silver stain/sequencing analysis. - [Read Embryo Lysates & Immunoprecipitation Protocol]

Category: DNA Protocols: DNA Extraction Protocols: Agarose Gel DNA Extraction Protocols

Isolation of DNA fragments using glass milk (GENE-CLEAN). Glass Milk Agarose Gel DNA Extracton Protocol. Minion Lab, College of Veterinary Medicine at Iowa State University. - [Read Glass Milk Agarose Gel DNA Extracton Protocol]

Category: Yeast Protocols: Yeast Genetics Protocols: YACs Protocols

Protocol describes methods for isolation of DNA from a strain of S. cerevisiae carrying a recombinant YAC. Because the linear YAC DNAs are sensitive to shearing forces, pipettes with wide-bore tips should be used to transfer DNAs. The method is suitable for preparing DNA that will be used for agarose gel electrophoresis, Southern blotting, subcloning, genomic library construction, PCR, or other methods that do not require intact high-molecular-weight DNA. - [Read Growth of S. cerevisiae and Preparation of DNA Protocol]

Category: Chromatography Protocols

His Tag Nickel Affinity Chromatography Protocol PDF. The Wallert and Provost Lab. Theory and Introduction: Ni-Affinity Chromatography uses the ability of His to bind nickel. Six histadine amino acids at the end of a protein (either N or C terminus) is known as a 6X His tag. Nickel is bound to an agarose bead by chelation using nitroloacetic acid (NTA) beads. Several companies produce these beads as His Tagged proteins are some of the most used affinity tags in today’s market. - [Read His Tag Nickel Affinity Chromatography Protocol PDF]

Category: Immunology: Immunoprecipitation Protocols

Protocol for immunoprecipitation with antibody:agarose conjugates. Includes: Denaturing Conditions; Native Conditions; Pre-clearing. - [Read Immunoprecipitation with Antibody:Agarose Conjugates Protocol]

Category: Viral Manipulation Protocols: Phage Lamda Manipulation Protocols

Protocol describes a plate method that gives very good yield for cloning. Includes: T-TYN Media + Mg+2; T-TYN Plates; T-TYN Top Agarose. - [Read Lambda DNA Preparation Protocol]

Category: Viral Manipulation Protocols: Phage Lamda Manipulation Protocols

Protocol for lambda gt22a screening. Includes: T-TYN Media + Mg+2; T-TYN Plates; T-TYN Top Agarose; Phage Dilution Buffer (PDB); 10X Kinase Buffer (-DTT); Calf Thymus DNA. - [Read Lambda gt22a Screening Protocol]

Category: Yeast Protocols: Yeast Genetics Protocols: YACs Protocols

Protocol describes the use of agarose plugs for isolation of yeast artificial chromosome (YAC) DNA. The DNA can then be run on a pulsed-field gel and used for microinjection to produce transgenic mice. - [Read Large-Scale Preparation of Agarose Plugs of Yeast DNA Protocol]

Category: Chromatography Protocols: Affinity Chromatography Protocols

Two methods are provided for purifying glycoproteins using wheat-germ agglutinin or concanavalin A-Sepharose.  Because lectin-affinity matrices can bind a few milligrams of protein per milliliter of affinity matrix, only a small amount of affinity gel matrix is required.  The batchwise method is recommended when protein volume is large. - [Read Lectin-Agarose Affinity Chromatography Protocol]

Category: Cloning Protocols

Protocol for ligating plasmid and target DNAs in low-melting-temperature agarose. Ligation in low-melting-temperature agarose is much less efficient than ligation with purified DNA in free solution and requires a large amount of DNA ligase. The method is used chiefly for rapid subcloning of segments of DNA in dephosphorylated vectors and assembling recombinant constructs. - [Read Ligating Plasmid and Target DNAs in Low-melting-temperature Agarose Protocol]

Category: DNA Protocols: DNA Extraction Protocols: Agarose Gel DNA Extraction Protocols

Phenol-based Protocol Isolation of DNA Fragments from Low-Melting Temperature Agarose. Reference: Favre, D. 1992. Biotechniques vol. 13. - [Read Phenol-based Protocol Isolation of DNA Fragments from Low-Melting Temperature Agarose]

Category: Molecular Biology Protocols: Agarose Gel Preparation

Photos depicting agarose gel preparation method. Karen Braun New Mexico State Univ. - [Read Picture Method of Agarose Gel Preparation]

Category: Nucleic Acid Electrophoresis Protocols: RNA Electrophoresis Protocols

Protocol for preparation of a denaturing agarose gel for the analysis of RNA samples. The integrity of RNA samples can be analyzed by electrophoresis on a denaturing agarose gel containing formaldehyde. - [Read Preparation of a Denaturing Agarose Gel for the Analysis of RNA Samples Protocol]

Category: Immunology: B Cell Protocols

Procedure permits the isolation of at least 5 µg of total RNA from a sample of purified mouse splenic B lymphocytes. The quality of the RNA is assessed by separation of an aliquot through 1% agarose and staining with ethidium bromide as described in AfCS protocol Visualization of RNA Preparations on 1% Agarose Gels. The isolated RNA is used for analysis of gene expression by microarray technology. analysis of gene expression by microarray technology. - [Read Preparation of B-Lymphocyte RNA for Microarray Analysis Protocol]

Category: Nucleic Acid Electrophoresis Protocols: Pulsed Field Gel Electrophoresis Protocols

Protocol for preparation of DNA for pulsed-field gel electrophoresis: isolation of DNA from mammalian cells and tissues. Genomic DNAs from mammalian cells are prepared for pulsed-field gel electrophoresis by lysing cells in situ in an agarose plug.  Following digestion with an appropriate restriction enzyme, the plug is loaded directly into the well of a pulsed-field gel or it can be melted before loading. - [Read Preparation of DNA for Pulsed-field Gel Electrophoresis: Isolation of DNA from Mammalian Cells]

Category: Nucleic Acid Electrophoresis Protocols: Pulsed Field Gel Electrophoresis Protocols

Protocol for preparation of DNA for pulsed-field gel electrophoresis: isolation of intact DNA from yeast. Yeast cells are first treated enzymatically to break down the cell walls and then resuspended in low-melting-temperature agarose plugs.  The DNA is liberated by infusing the plugs with lysis buffer and proteases.  This method is used to prepare both conventional and artificial yeast chromosomes. - [Read Preparation of DNA for Pulsed-field Gel Electrophoresis: Isolation of Intact DNA from Yeast]

Category: Yeast Protocols: Yeast Nucleic Acid Protocols: Yeast DNA Isolation Protocols

Protocol for preparation of Yeast DNA embedded in agarose plugs. - [Read Preparation of Yeast DNA Embedded in Agarose Plugs Protocol]

Category: Chromatography Protocols: Affinity Chromatography Protocols

Protocol describes the coupling of peptides or proteins to Affi-Gel 10 (Bio-Rad).  Affi-Gel 10 is a cross-linked agarose derivatized with N-hydroxysuccinimide (NHS) ester on a 10-atom-long spacer arm.  The NHS ester allows spontaneous coupling of proteins via free amino groups. - [Read Protein Ligand Affinity Chromatography Protocol]

Category: Molecular Biology Protocols: Agarose Gel Preparation

Protocol for Preparation of 3-5% Agarose Gels. Fermentas - [Read Protocol for Preparation of 3-5% Agarose Gels]

Category: Immunology: Immunoprecipitation Protocols

Immunoprecopitation method, the protein from the cell or tissue homogenate is precipitated in an appropriate lysis buffer by means of an immune complex which includes the antigen (protein), primary antibody and Protein A-, G-, or L-agarose conjugate or a secondary antibody-agarose conjugate - [Read Protocol Immunoprecipitation]

Category: Chromatography Protocols: Ion Exchange Chromatography Protocols

Protocol for the purification of DNA recovered from agarose and polyacrylamide gels by anion-exchange chromatography. Fragments of DNA recovered from agarose gels are sometimes poor templates or substrates in subsequent enzymatic reactions.  This problem can be solved by binding the DNA to a positively charged matrix, such as DEAE-Sephadex or DEAE-Sephacel, in buffers of low ionic strength.  After washing the matrix, the DNA is eluted by raising the strength of the buffer. - [Read Purification of DNA Recovered Anion-exchange Chromatography Protocol]

Category: Chromatography Protocols: Affinity Chromatography Protocols

Recombinant proteins, constructed in pGEX vectors, are fused to glutathione S-transferase (GST) and can be purified to near homogeneity by affinity chromatography on glutathione-agarose.  Bound GST-fusion proteins are readily displaced from the column by elution with buffers containing free glutathione. - [Read Purification of Fusion Proteins by Affinity Chromatography on Glutathione Agarose Protocol]