nuclease Protocols

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

The ability to synthesize RNA in the lab is critical to many techniques.Radiolabeled and nonisotopically labeled RNA probes, generated in small scale transcription reactions can be used in blot hybridizations and nuclease protection assays. This article includes information on: Requirements For Transcription, RNA Phage Polymerases, Template Options: Plasmids, PCR Products, Oligonuclotides and cDNA, Sense or Antisense, Conventional Or Large Scale Synthesis, Products for In Vitro Transcription. - [Read Basic Information on In Vitro Transcription]

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: Nucleic Acid Purification Protocols

Preparations of RNA containing an mRNA of interest are hybridized to a complementary single-stranded DNA probe.  At the end of the reaction nuclease S1 is used to degrade unhybridized regions of the probe, and the surviving DNA-RNA hybrids are then separated by gel electrophoresis and visualized by autoradiography or Southern hybridization.  Method 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 Nuclease S1 Protocol]

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

Protocol for preparation of messenger-dependent rabbit reticulocyte lysate. Informamtion also added to test that the lysate is working before doing the Nuclease inactivation - [Read Preparation of Messenger-Dependent Rabbit Reticulocyte Lysate]

Category: RNAi Technology Protocols: RNAi Drosophila Protocols

siRNAs produced upon the addition of dsRNA to Drosophila embryo extract are enriched in a micrococcus-nuclease-resistant fraction.  After proteinase K treatment and dephosphorylation with calf intestinal phosphatase, these siRNAs mediate efficient RNAi in vitro. - [Read Preparation of siRNAs from Drosophila Embryo Extracts Protocol]

Category: Molecular Biology Protocols

Protocol for S1 nuclease analysis. - [Read S1 Nuclease Analysis Protocol]

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]

Category: Nucleic Acid Purification Protocols: RNA Isolation Protocols

Protocol for total RNA isolation. This method is fast and works well for preparation of total RNA.  We typically use total RNA for quantitative S1 nuclease analysis of endogenous (or in vitro) gene expression, and this method works well for this purpose. - [Read Total RNA isolation (Guanidinium Thiocyanate-Phenol-Chloroform Extraction) Protocol]