| 1 |
Replication (Replication Enzymes) |
dNTP Incorporation Assay |
DNA Synthesis (Fast; Quantitative for Amount of Synth.). |
| Filter Binding Assay |
Method to separate incorporated from unincorporated dNTPs. |
| Gel Electrophoresis |
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. |
| 2 |
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. |
| Topoisomerase Assay |
Assay for changes in DNA topology; distinguish supercoiled, relaxed, nicked, linear, forms of DNA and measure catenation/decatenation. |
| 3 |
Replication (Prok. System) |
2-D Agarose Gels |
Assay for Origin of Replication (Must have an idea of where the origin is to test). |
| Southern Blotting |
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. |
| Biochemical Fractionation |
Mechanism to purify biochemical activity that can be assayed in vitro. |
| Biochemical Complementation |
Combines mutant extracts with biochemical fractionation to identify proteins required for assay (in this case DNA replication). |
| 4 |
Replication (Euk. Systems) |
Genetic Screen for DNA Replication Mutants |
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| 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. |
| 5 |
Chromatin Assembly |
Template Association Assay |
Uses gel filtration to separate molecules bound to a plasmid from molecules that are not bound to a plasmid. |
| 6 |
DNA Mismatch Repair |
Heteroduplex DNA analysis |
Assay for DNA repair in vivo. |
| Restriction Analysis |
Assay for methylation state of DNA. |
| Restriction site repair |
Assay of DNA repair in vitro; also used incorporation assay. |
| 7 |
DNA Repair II |
Ames Test |
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. |
| 8 |
DS Break Repair, Homologous Recombination |
Strand Exchange Assay |
Assay for homologous DNA pairing and branch migration. |
| 9 |
Homologous Recombination Enzymes |
ATPγS |
Used in determining whether ATP binding or ATP-hydrolysis is required for a reaction. |
| DMS Footprinting |
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. |
| 10 |
Meiotic Recombination |
Consensus Sequences |
Identification of important elements by conservation. |
| Native-Denaturing 2D Gel |
Detection of nicks vs DSBs in DNA. |
| 11 |
Site-specific Recombination |
DNA Bending Assay |
Assay for whether a protein bends DNA upon binding and position of bend. |
| 12 |
Transposition |
Genomic Southern |
Identifies specific DNA molecules transferred to membrane (here used for transposition). |
| Plasmid Mating |
Assay for transposition in vivo by determining movement of drug resistance to a new plasmid. |
| 13 |
Transcription: Prok. Machinery and Promoters |
Incorporation Assay |
Assay for Transcription in vitro. |
| S1 Protection Assay |
Assay for Transcription. Maps start site of transcription. |
| Northern Blot |
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. |
| 14 |
Transcription: Euk. Machinery and Promoters |
DNA Unwinding Assay |
Assay for open complex formation. |
| Indirect end-labeling |
Method to extend a labeled DNA primer to measure breaks or modification of DNA. |
| 15 |
Transcription: Regulation I |
Antibody Supershift Assay |
Assay to determine the components of protein-DNA complex in a gel shift assay. |
| 16 |
Transcription: Regulation II |
Transcription Factor DNA Binding Domain Mapping |
| Transcriptional Factor Activation Domain Mapping |
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| Chromatin Immunoprecipitation |
Assay to determine the in vivo binding site of proteins. |
| 17 |
RNA Processing I |
R-Loop Formation |
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). |
| 18 |
RNA processing II |
Calculation of "Consensus Fold" and Rnase Digestion |
Determination of RNA secondary structures. |
| 19 |
RNA Processing: Regulation |
cDNA Cloning |
Determine mRNA sequence and structure, protein expression. |
| RT-PCR |
Generate segments of amplified DNA starting with specific RNA template. |
| Exon Trapping |
Find exons in DNA fragments of regions thought to contain genes. |
| 20 |
RNA Editing, RNAi and miRNAs |
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| 21 |
Translation: Basic Machinery I |
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| 22 |
Translation: Basic Machinery II |
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| 23 |
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. |