segment Protocols

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

The goal of this method is to identify transcriptionally active genes in cloned segments of genomic DNA. The protocol uses hybridization and affinity purification to recover biotin-labeled cDNAs that bind to a 500-kb segment of human DNA cloned in a BAC vector. However, the method can be easily adapted to other clones of genomic DNAs cloned in high-capacity vectors. - [Read Direct Selection of cDNAs with Large Genomic DNA Clones Protocol]

Category: Antibody Protocols: Epitope Mapping Antibody Protocols

A set of overlapping synthetic peptides is synthesized, each corresponding to a small segment of the linear sequence of a protein antigen and arrayed on a solid phase. The panel of solid-phase peptides is then probed with a test antibody, and bound antibody is detected using an enzyme-labeled secondary antibody. This method is very rapid and can be extraordinarily successful. - [Read Epitope Mapping Using Synthetic Biotin-Labeled Peptides Protocol]

Category: DNA Protocols: cDNA Library Protocols: cDNA Library Construction Protocols

Shotgun sequencing of a large segment of DNA involves random fragmentation of the target region into smaller segments that are subsequently cloned into a bacteriophage M13 vector. The goal is to create a library of overlapping clones that provide at least fivefold coverage over the entire length of the target fragment. - [Read Generation of a Library of Randomly Overlapping DNA Inserts Protocol]

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

In this method, the nuclease BAL 31 is used to make uni- or bidirectional deletions in a segment of cloned DNA. BAL 31 is a complex enzyme and tends to digest a population of double-stranded DNA targets in an asynchronous fashion, Deletions created by BAL 31 are therefore far more heterogeneous in size than those created by processive enzymes such as exonuclease III. - [Read Generation of Bidirectional Sets of Deletion Mutants by Digestion with BAL 31 Nuclease Protocol]

Category: Fungi Protocols: Neurospora Protocols

Information and tips on how to obtain and recognize partial-diploid strains that are duplicated for known chromosome segments. - [Read How to Obtain and Recognize Partial-Diploid Strains that are Duplicated for Known Chromosome Segment]

Category: DNA Protein Interactions Protocols: Dnase Footprinting Assay Protocols

Dnase I is used to fragment a radiolabeled target DNA in the presence and absence of a nuclear extract.  A "footprint" is generated when a protein binds to the target and protects a specific segment of DNA from the nucleolytic activity of Dnase I. By comparing the electrophoretic mobility of the Dnase I cleavage products to those of a sequence ladder derived from the same DNA fragment, the position(s) of the DNA sequences recognized by DNA-binding proteins can be determined. - [Read Mapping Protein-binding Sites on DNA by Dnase I Footprinting Protocol]

Category: PCR Protocols: cDNA Synthesis Protocols

In MOPAC, the amino-terminal and carboxy-terminal sequences of a peptide are used to design two redundant families of oligonucleotides encoding the aminoand carboxy-terminal sequences of the peptide.  The primers are used either to amplify a segment of cDNA prepared by RT-PCR from a tissue known to express the protein or to amplify a segment of DNA from an established genomic or cDNA library. - [Read Mixed Oligonucleotide-primed Amplification of cDNA MOPAC Protocol]

Category: Cytoskeleton Protocols: Microtubules Protocols

Segmented and polarity-marked microtubules are very useful for many different types of in vitro assays. Segmented microtubules are microtubules with a bright seed and dim elongated segments on both ends. Polarity marked microtubules are microtubules with a bright seed and a dim elongated segment only on one end -- the plus end. - [Read Preparation of Segmented and Polarity Marked Microtubules Protocol]

Category: RNAi Technology Protocols: RNAi Mammalian Cells Protocols

To target a specific mRNA for degradation, a portion of the mRNA target sequence must be known, and a segment of the target mRNA must be chosen that will be used for targeting by the cognate siRNA duplex. Protocol describes the selection of siRNA sequences for mammalian RNAi. - [Read Selection of siRNA Sequences for Mammalian RNAi Protocol]

Category: PCR Protocols: Standard PCR Protocol

Protocol describes how to amplify a segment of double-stranded DNA in a chain reaction catalyzed by a thermostable DNA polymerase.  It is the foundation for all subsequent variations of the polymerase chain reaction. - [Read The Basic Polymerase Chain Reaction Protocol]