||Replication (Replication Enzymes)
||dNTP Incorporation Assay
||DNA Synthesis (Fast; Quantitative for Amount of Synth.).
|Filter Binding Assay
||Method to separate incorporated from unincorporated dNTPs.
||Method to separate DNA on the basis of length.
|Primer Extension Assay
||DNA Synthesis (Slow; Quantitative for Length of Synth.).
|Template Challenge Assay
||Assay for Processivity.
||Replication (Replication Fork)
||DNA Helicase Assay
||In vitro DNA Helicase Activity.
|Helicase Polarity Assay
||Assay for directionality of helicase movement; used to study function of replication termination sequences.
||Assay for changes in DNA topology; distinguish supercoiled, relaxed, nicked, linear, forms of DNA and measure catenation/decatenation.
||Replication (Prok. System)
||2-D Agarose Gels
||Assay for Origin of Replication (Must have an idea of where the origin is to test).
||Identifies specific DNA molecules transferred to membrane.
|DNA Microarray Assay
||Assays the relative amount of replicated DNA sequences during a synchronized round of DNA replication to identify sites of replication initiation.
|Plasmid Replicator Assay
||Identifies region of DNA sufficient for Replicator activity.
|Mutational Mapping Assay
||Identifies regions of DNA necessary for Replicator activity.
||Mechanism to purify biochemical activity that can be assayed in vitro.
||Combines mutant extracts with biochemical fractionation to identify proteins required for assay (in this case DNA replication).
||Replication (Euk. Systems)
||Genetic Screen for DNA Replication Mutants
|DNase I Protection Assay
||Assay for Sequence Specific DNA Binding (Slower and not quantitative; Gives Information about bound DNA sequence).
|Gel Mobility Shift Assay
||Assay for Sequence Specific DNA Binding (Fast and Quantitative but less information about bound sequence).
|DNA Unwinding Assay
||Assays for formation of ssDNA through the use of a ssDNA specific nuclease.
||Template Association Assay
||Uses gel filtration to separate molecules bound to a plasmid from molecules that are not bound to a plasmid.
||DNA Mismatch Repair
||Heteroduplex DNA analysis
||Assay for DNA repair in vivo.
||Assay for methylation state of DNA.
|Restriction site repair
||Assay of DNA repair in vitro; also used incorporation assay.
||DNA Repair II
||Assay for chemicals and other factors that increase the frequency of mutations.
|Nicking of Circular DNA
||Assay for excision-type mechanism of DNA repair.
|Lesion bypass DNA synthesis
||Assay for ability of replication/repair proteins to synthesize DNA off of a damaged template.
||DS Break Repair, Homologous Recombination
||Strand Exchange Assay
||Assay for homologous DNA pairing and branch migration.
||Homologous Recombination Enzymes
||Used in determining whether ATP binding or ATP-hydrolysis is required for a reaction.
||Assay for protection of the bases in DNA, rather than the phosphodiester backbone.
|Cooperative DNA Binding
||Gel-shift assay to measure cooperative vs. non-cooperative DNA binding.
||Identification of important elements by conservation.
|Native-Denaturing 2D Gel
||Detection of nicks vs DSBs in DNA.
||DNA Bending Assay
||Assay for whether a protein bends DNA upon binding and position of bend.
||Identifies specific DNA molecules transferred to membrane (here used for transposition).
||Assay for transposition in vivo by determining movement of drug resistance to a new plasmid.
||Transcription: Prok. Machinery and Promoters
||Assay for Transcription in vitro.
|S1 Protection Assay
||Assay for Transcription. Maps start site of transcription.
||Assay for Transcription. Maps steady state RNA in vivo.
|Microarray Analysis of RNA
||Assay for relative levels of gene expression. Can assay many genes at once.
|Pulse Labeling of in vivo RNA
||Assay for actively transcribing genes.
|Promoter Fusion Assay
||Assay to indirectly measure promoter activity.
||Transcription: Euk. Machinery and Promoters
||DNA Unwinding Assay
||Assay for open complex formation.
||Method to extend a labeled DNA primer to measure breaks or modification of DNA.
||Transcription: Regulation I
||Antibody Supershift Assay
||Assay to determine the components of protein-DNA complex in a gel shift assay.
||Transcription: Regulation II
||Transcription Factor DNA Binding Domain Mapping
|Transcriptional Factor Activation Domain Mapping
||Assay to determine the in vivo binding site of proteins.
||RNA Processing I
||Assay for regions of mRNA that anneal to different DNA fragments.
|Gel Electrophoresis Assay
||For intermediates and products formed during splicing in vitro (done using labeled RNA).
||RNA processing II
||Calculation of "Consensus Fold" and Rnase Digestion
||Determination of RNA secondary structures.
||RNA Processing: Regulation
||Determine mRNA sequence and structure, protein expression.
||Generate segments of amplified DNA starting with specific RNA template.
||Find exons in DNA fragments of regions thought to contain genes.
||RNA Editing, RNAi and miRNAs
||Translation: Basic Machinery I
||Translation: Basic Machinery II
||Translation: Regulation I
||Incorporation Assay for Translation Polysome Assay
||Identifies mRNAs that are being translated in vivo.
|Gel Filtration Analysis of Protein Binding
||Measures binding of small molecules to larger molecules (e.g., binding to ribosome).
|Filter Binding Assay
||Measures binding of RNA to protein.