List of the digital codes of experiments

• 1. Footprinting reactions:
• 1.1.DNAase I:
• 1.1.1. with crude nuclear extract
• 1.1.2. with mutated oligonucleotides
• 1.1.3. comparison between fragments of different genes
• 1.1.4. in the presence of increasing amounts of a competitor oligonucleotide
• 1.1.5. in the presence of pure protein
• 1.1.6. in the presence of crude nuclear extract and antibodies for transcription factor
• 1.2. methidiumpropyl-EDTA.Fe(II)
• 1.3. DNAse II footprint
• 1.4. hydroxyl radicals
• 1.5. footprinting in vivo
• 1.6. ortophenantroline cooper footprint (OPCU)

• 2. Exonuclease digests
• 2.1. exonuclease III
• 2.2. alpha exonuclease

• 3. Electrophoretic mobility shift assays (EMSA):
• 3.1. with crude nuclear extract
• 3.2. using oligonucleotides for comparison or competition
• 3.2.1. corresponding to the binding sites of the same type from different genes
• 3.2.2. corresponding to binding sites of different types
• 3.2.3  corresponding to binding sites and flanking sequences
• 3.3. with oligonucleotides carrying point mutations
• 3.4. cross-competition experiments
• 3.5. with purified or recombinant protein or with the extracts from cells producing recombinant transcription factor
• 3.5.1. gel mobility shift assay with extracts enriched with transcription factor
• 3.5.2. gel mobility shift assay with extracts deprived with transcription factor
• 3.6. with crude nuclear extract and antibodies (supershift).
  3.7. identification of transcription factor from DNA-protein complex corresponding to EMSA band

• 4. DNA modification reactions
• 4.1. methylation protection
• 4.2. methylation interference
• 4.3. ethylation protection
• 4.4. ethylation interference
• 4.5. demethylation

• 5. Primer extension assay
• 5.2 RACE ( rapid  amplification cDNA 5'end)
• 5.5 RNase protection analysis
• 5.6 S1 nuclease protection

• 6. Transient expression analysis and experiments on transgenic organisms or cells.

• 6.1. Analysis of deletions mutants:
• 6.1.1. deletion size is more than 30 b.p.
• 6.1.2. deletion size is up to 30 b.p.
• 6.1.3. an effect of insertions
• 6.2. An effect of point mutations on the expression
• 6.3. Conferring of sequence to a geterologous or homologous promoters
• 6.3.1. Conferring of the regions more than 30 b.p.
• 6.3.2. Conferring of the separate site (up to 30 b.p.)
• 6.3.3 Conferring of the region in direct and indirect orientations
• 6.4. Tandem repeats of the binding site.
• 6.5. Analysis of inducer (repressor) influence on the gene expression
• 6.6. analysis of a reporter gene expression in the presence of purified transcription factors or vectors expressing transcription factors of given types.
• 6.6.1. influence of purified or recombinant transcription factor on the reporter gene expression in vitro
• 6.6.1.1. wild type (intact) transcription factor
• 6.6.1.2. modified transcription factor (fusion proteins, truncated proteins, with mutations, deletions, killer-factors etc.)
• 6.6.2. (in vivo) cotransfection assay
• 6.6.2.1. wild type (intact) transcription factor
• 6.6.2.2. modified transcription factor (fusion proteins, truncated proteins, with mutations, deletions, killer-factors etc.)
• 6.6.3 analysis of a reporter gene expression in vitro using extracts deprived with transcription factor
• 6.6.3.2 analysis of a reporter gene expression in vivo using cells without transcription factor
• 6.3.3.3 analysis of a reporter gene expression in vivo using cells deprived with transcription factor (in the presence of  antibodies, oligonucleotides carrying binding site, etc)
• 6.7. Transcription competition assay.
• 6.7.1. In the presence of oligonucleotides carrying intact (wild type) binding site
• 6.7.2. In the presence of oligonucleotides carrying mutated binding site.
• 6.8. expression of the reporter gene by plasmid constructions containing regulatory region or unit being investigated.
•  
• 7. Homology of the binding site:
• 7.1. with consensus of fixed type
• 7.2. with the binding site from regulatory region of the homologous gene
• 7.3. with the binding site of the same type from regulatory region of dissimilar gene

• 8. ABCD-assay (avidin-biotin complex DNA-binding assay) 

• 9. Filter binding assay
• 9.2. using for comparison oligonucleotides corresponding to binding sites of different types
• 9.3. with oligonucleotides carrying point mutations
• 9.5. In situ binding of cloned transcription factors to synthetic oligonucleotides

• 10. DNA-cellulose competition binding assay

• 11.1  Protein- DNA immunoprecipitation assay (immunoselection)
• 11.2  Chromatin immunoprecipitation

• 12. In situ mutagenesis

revised October , 2003