METHODS IN ENZYMOLOGY
TABLE OF CONTENTS SECTION I TRANSCRIPTION ELONGATION 1 ON MODELS AND METHODS FOR STUDYING POLYMERASE TRANSLOCATION 2 EVALUATION OF FLUORESCENCE SPECTROSCOPY METHODS FOR MAPPING MELTED REGIONS OF DNA ALONG THE TRANSCRIPTION PATHWAY 3 SINGLE DNA MOLECULE ANALYSIS OF TRANSCRIPTION COMPLEXES 4 ASSAY FOR MOVEMENTS OF RNA POLYMERASE ALONG DNA 5 KINETICS OF MULTISUBUNIT RNA POLYMERASES: EXPERIMENTAL METHODS AND DATA ANALYSIS 6 PRINCIPLES AND METHODS OF AFFINITY CLEAVAGE IN STUDYING TRANSCRIPTION 7 IODINE-125 RADIOPROBING OF E COLI RNA POLYMERASE TRANSCRIPTION ELONGATION COMPLEXES 8 FORMATION OF LONG DNA TEMPLATES CONTAINING SITE-SPECIFIC ALKANE–DISULFIDE DNA INTERSTRAND CROSS-LINKS FOR USE IN TRANSCRIPTION REACTIONS 9 PROBING THE ORGANIZATION OF TRANSCRIPTION COMPLEXES USING PHOTOREACTIVE 4-THIO- SUBSTITUTED ANALOGS OF URACIL AND THYMIDINE 10 FLUORESCENCE RESONANCE ENERGY TRANSFER (FRET) IN ANALYSIS OF TRANSCRIPTION- COMPLEX STRUCTURE AND FUNCTION 11 METHODS OF WALKING WITH THE RNA POLYMERASE 12 STEPWISE WALKING AND CROSS-LINKING OF RNA WITH ELONGATING T7 RNA POLYMERASE 13 CHARACTERIZATION OF PROTEIN–NUCLEIC ACID INTERACTIONS THAT ARE REQUIRED FOR TRANSCRIPTION PROCESSIVITY 14 STRATEGIES AND METHODS OF CROSS-LINKING OF RNA POLYMERASE ACTIVE CENTER 15 USING A LAC REPRESSOR ROADBLOCK TO ANALYZE THE E COLI TRANSCRIPTION ELONGATION COMPLEX 16 BIOCHEMICAL ASSAYS OF GRE FACTORS OF THERMUS THERMOPHILUS 17 ENGINEERING OF ELONGATION COMPLEXES OF BACTERIAL AND YEAST RNA POLYMERASES 18 ASSAY OF TRANSIENT STATE KINETICS OF RNA POLYMERASE II ELONGATION 19 ANALYSIS OF RNA POLYMERASE II ELONGATION IN VITRO 20 PREPARATION AND ASSAY OF RNA POLYMERASE II ELONGATION FACTORS ELONGIN AND ELL 21 USE OF RNA YEAST POLYMERASE II MUTANTS IN STUDYING TRANSCRIPTION ELONGATION 22 ACETYLATION OF HUMAN AP-ENDONUCLEASE 1, A CRITICAL ENZYME IN DNA REPAIR AND TRANSCRIPTION REGULATION 23 CHARACTERIZATION OF TRANSCRIPTION-REPAIR COUPLING FACTORS IN E COLI AND HUMANS (P-TEFB) TRANSCRIPTION ELONGATION FACTOR SECTION II TRANSCRIPTION TERMINATION 25 ASSAY OF INTRINSIC TRANSCRIPTION TERMINATION BY E COLI RNA POLYMERASE ON SINGLE-STRANDED AND DOUBLE-STRANDED DNA TEMPLATES 26 BACTERIOPHAGE HK022 NUN PROTEIN: A SPECIFIC TRANSCRIPTION TERMINATION FACTOR THAT EXCLUDES BACTERIOPHAGE 28 ANALYSIS OF THE INTRINSIC TRANSCRIPTION TERMINATION MECHANISM AND ITS CONTROL 29 RHO’S ROLE IN TRANSCRIPTION ATTENUATION IN THE TNA OPERON OF E COLI 30 ROLE OF RNA STRUCTURE IN TRANSCRIPTION ATTENUATION IN BACILLUS SUBTILIS: THE TRPEDCFBA OPERON AS A MODEL SYSTEM 31 TRAP–RNA INTERACTIONS INVOLVED IN REGULATING TRANSCRIPTION ATTENUATION OF THE BACILLUS SUBTILIS TRP OPERON 32 ANALYZING TRANSCRIPTION ANTITERMINATION IN LAMBDOID PHAGES ENCODING TOXIN GENES 33 GENETIC AND BIOCHEMICAL STRATEGIES TO ELUCIDATE THE ARCHITECTURE AND TARGETS OF A PROCESSIVE TRANSCRIPTION ANTITERMINATOR FROM BACTERIOPHAGE LAMBDA 34 ASSAY OF TRANSCRIPTION ANTITERMINATION BY PROTEINS OF THE CSPA FAMILY 35 ASSAY OF ANTITERMINATION OF RIBOSOMAL RNA TRANSCRIPTION , SECTION III CHROMATIN 36 PURIFICATION OF ELONGATING RNA POLYMERASE II AND OTHER FACTORS FROM YEAST CHROMATIN 38 TYING C’ ENDS OF H2A AND H2B USING A MOLECULAR GLUE, TISSUE-TYPE TRANSGLUTAMINASE 39 CHROMATIN DECOMPACTION METHOD BY HMGN PROTEINS 40 ASSAY OF ACTIVATOR RECRUITMENT OF CHROMATIN- MODIFYING COMPLEXES 41 INSIGHTS INTO STRUCTURE AND FUNCTION OF GCN5/ PCAF AND YESA 1 HISTONE ACETYLTRANSFERASE DOMAINS: 42 ASSAY OF THE FATE OF THE NUCLEOSOME DURING TRANSCRIPTION BY RNA POLYMERASE II 43 PROBING CHROMATIN IMMUNOPRECIPITATES WITH CPG-ISLAND MICROARRAYS TO IDENTIFY GENOMIC SITES OCCUPIED BY DNA-BINDING PROTEINS 44 ISOLATION OF RNA POLYMERASE SUPPRESSORS OF A (P)PPGPP DEFICIENCY 45 ANALYSIS OF TRANSCRIPTIONAL REPRESSION BY MIG1 IN SACCHAROMYCES CEREVISIAE USING A REPORTER ASSAY 46 MUTATIONAL ANALYSIS OF DROSPHILA RNA POLYMERASE II