rna polymerase and associated factors, part d

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rna polymerase and associated factors, part d

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METHODS IN ENZYMOLOGY EDITORS-IN-CHIEF John N. Abelson Melvin I. Simon DIVISION OF BIOLOGY CALIFORNIA INSTITUTE OF TECHNOLOGY PASADENA, CALIFORNIA FOUNDING EDITORS Sidney P. Colowick and Nathan O. Kaplan Contributors to Volume 371 Article numbers are in parentheses and following the names of contributors. Affiliations listed are current. Todd E. Adamson (19), Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242 Michael Anikin (9), Morse Institute of Molecular Genetics, Department of Microbiology and Immunology, SUNY Downstate Medical Center, 450 Clarkson Avenue, Brooklyn, New York 11203-2098 Ekaterina Avetissova (13), Skirball Institute, New York University Medical Center, New York, New York 10016 Paul Babitzke (30), Department of Bio- chemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802 Gil Bar-Nahum (11), Department of Bio- chemistry, New York University Medical Center, New York, New York 10016 Irina Bass (14), Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia Jodi Becker (17), NCI Center for Cancer Research, National Cancer Institute— Frederick Cancer Research and Develop- ment Center, Frederick, Maryland 21702 Oxana Bereshchenko (14), Public Health Research Institute, 455 First Avenue, New York, New York 10016 Philip C. Bevilacqua (30), Department of Chemistry,ThePennsylvaniaStateUniver- sity, University Park, Pennsylvania 16802 Kishor K. Bhakat (22), Sealy Center for Molecular Science and the Department of Human Biological Chemistry and Genet- ics, University of Texas Medical Branch, Galveston, Texas 77555 Yehudit Birger (39), Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Insti- tute, National Institutes of Health, Bethesda, Maryland 20892-4255 Sergei Borukov (16), Department of Microbiology and Immunology, SUNY Health Science Center at Brooklyn, 450 Clarkson Avenue Brooklyn, New York 11203-2098 Zachary FBurton (18), Department of Biochemistry, Michigan State University, East Lansing, Michigan 48824 Michael Bustin (39), Protein Section, Laboratory of Metabolism, Center Na- tional Cancer Institute, National Insti- tutes of Health, Bethesda, Maryland 20892-4255 Marian Carlson (45), Department of Gen- etics & Development and Institute of Cancer Research, Columbia University, New York, New York 10032 Michael J. Carrozza (40), Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802-4500 Michael Cashel (44), Laboratory of Mo- lecular Genetics, NICHD, NIH Building 6, Room 3B314 Bethesda, Maryland 20892-2785 Hyon Choy (38), Genome Center for En- teropathogenic Bacteria, Department of Microbiology, Chonnam National Univer- sity Medical College, Dong-Gu, Hak-1- Kwang-Ju 501-746, South Korea xi Adrienne Clements (41), The Wistar In- stitute, Philadelphia, Pennsylvania 19104 Ronald Conaway (20), Stowers Institute for Medical Research, Kansas City, Mis- souri 64110; Department of Biochemistry and Molecular Biology, Kansas Univer- sity Medical Center, Kansas City, Kansas 66160 Joan Weliky Conaway (20), Stowers In- stitute for Medical Research, Kansas City, Missouri 64110; Department of Bio- chemistry and Molecular Biology, Kansas University Medical Center, Kansas City, Kansas 66160 Ciara ´ n Condon (35), CNRS UPR9073, Institute de Biologie Physico-Chimigue, 75005 Paris, France Asis Das (33), University of Connecticut Health Center, Farmington, Connecticut 06030-3205 Saul A. Datwyler (6), Abbott Laborator- ies, 100 Abbott Park Rd, Abbott Park, Illinois 60064 Richard H. Ebright (10), Waksman Insti- tute, Howard Hughes Medical Institute, Rutgers University, 190 Frelinghuysen Road, Piscataway, New Jersey 08854 Yon W. Ebright (10), Waksman Institute, Howard Hughes Medical Institute, Rut- gers University, 190 Frelinghuysen Road, Piscataway, New Jersey 08854 Vitaly Epshtein (14), Institute of Molecu- lar Genetics, Russian Academy of Sci- ences, Moscow, 123182, Russia Dorothy A. Erie (5), Department of Chemistry, CB 3290, Venable and Kenan Laboratories, University of North Caroli- na at Chapel Hill, Chapel Hill, North Carolina 27599-3290 Peggy J. Farnham (43), McArdle Labora- tory for Cancer Research, University of Wisconsin Medical School 1400 Univer- sity Avenue, Madison, Wisconsin 53706- 1599 Jane Fellows (36), Cancer Research UK, London Research Institute, Clare Hall Laboratories, South Mimms, Hertford- shire, EN6 3LD United Kingdom J. Estelle Foster (5), Department of Chemistry, CB 3290, Venable and Kenan Laboratories, University of North Caroli- na at ChapelHill, ChapelHill, North Car- olina 27599-3290 David I. Friedman (32), Department of Cell and Structure Biology, University of Colorado School of Medicine, 4200 E. Ninth Avenue, UCHSC Campus, Box B-111 Denver, Colorado 80262 Dmitry V. Fyodorov (37), Section of Mo- lecular Biology, University of California, San Diego, La Jolla, California 92093- 0347 Michell E. Garber (24), Regulatory Biol- ogy Laboratory, Salk Institute for Bio- logical Studies, 10010 North Torrey Pines Road La Jolla, California 92037-1099 Alex Goldfarb (14), Public Health Re- search Institute, 455 First Avenue, New York, New York 10016 Paul Gollnick (31), Department of Bio- logical Sciences, Hochstetter Hall 613, State University of New York Buffalo, New York 14260 Nathan Gomes (24), Regulatory Biology Laboratory Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037-1099 Xue Q. Gong (18), Department of Bio- chemistry and Molecular Biology, Mich- igan State University, East Lansing, Michigan 48824 Feng Gong (29), Department of Biological Sciences, Stanford University, Stanford, California 94305-5020 Max E. Gottesman (26), Institute of Cancer Research, Department of Bio- chemistry and Molecular Biophysics, Col- umbia University, New York, New York 10032-2798 xii contributors to volume 371 Mikhail Grachev (14), Limnological Insti- tute, Russian Academy of Sciences, Ulan- batorskaya 3 664033, Russia Ivan Gusarov (11, 28), Department of Bio- chemistry, New York University Medical Center, New York, New York 10016 Martin Guthold (3), Department of Phys- ics, Wake Forest University Winston- Salem, North Carolina 27109-7507 Hiroshi Handa (18), Frontier Collabora- tive Research Center, Tokyo Institute of Technology, Yokohama 226-8503, Japan Ahmed H. Hassan (40), Howard Hughes Medical Institute, Department of Bio- chemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania Shannon F. Holmes (4), Department of Chemistry, CB 3290, Venable and Kenan Laboratories, University of North Caroli- na at Chapel Hill, Chapel Hill, North Carolina 27599-3290 Masayori Inouye (34), Department of Bio- chemistry, Robert Wood Johnson Medical School, Piscataway, New Jersey 08854- 5635 Akira Ishihama (6), Nippon Institute for Biological Science, Shin-machi, 9-221 Ome, Tokyo 198-09924, Japan Nandan Jana (33), University of Connecti- cut Health Center, Farmington, Connecti- cut 06030-3205 Manli Jiang (9), Morse Institute of Mo- lecular Genetics, Department of Micro- biology and Immunology, SUNY Downstate Medical Center 450 Clarkson Avenue, Brooklyn, New York 11203-2098 Katherine A. Jones (24), Regulatory Biol- ogy Laboratory, Salk Institute for Bio- logical Studies, 10010 North Torrey Pines Road, La Jolla, California 92037- 1099 James Kadonaga (37), Section of Molecu- lar Biology, University of California, San Diego, La Jolla, California 92093-0347 Changwon Kang (12), Department of Bio- logical Sciences, Korea Advanced Insti- tute of Science and Technology, 373-1 Guseong-dong, Yuseong-gu, Daejeon 701, Republic of Korea Achillefs N. Kapanidis (10), Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095 Valeri N. Karamychev (7), Department of Nuclear Medicine, Warren G. Magnuson Clinical Center, National Institutes of Health, Bethesda, Maryland 20892 Mikhail Kashlev (7, 14, 17, 42), NCI Center for Cancer Research, National Cancer Institute—Frederick Cancer Re- search and Development Center, Fred- erick, Maryland 21702 Hyeong C. Kim (26), Department of Bio- chemistry and Molecular Biophysics Col- umbia University New York, New York 10032-2798 Jae-Hong Kim (38), Aging and Apoptosis, Research Center, Dept. of Biochemistry and Molecular Biology, College of Medi- cine, Seoul National University, 28 Yon- gon-Dong, Chongno-GU, Seoul 110-799, South Korea Rodney A. King (15), Laboratory of Mo- lecular Genetics, NICHD, NIH, Building 6B, Room 3B-308, Bethesda, Maryland 20892 Maria L. Kireeva (17, 42), NCI Center for Cancer Research, National Cancer Insti- tute—Frederick Cancer Research Devel- opment Center, Frederick, Maryland 21702 Natalia Komissarova (7, 17), NCI Center for Cancer Research National Cancer In- stitute—Frederick Cancer Research and Development Center, Frederick, Mary- land 21702 contributors to volume 371 xiii Stephanie Kong (20), Stowers Institute Medical Research, 1000 E. 50th Street, Kansas City, Missouri 64110 Ekaterine Kortkhonjia (10), Waksman Institute, Howard Hughes Medical Insti- tute, Rutgers University, 190 Frelinghuy- sen Road, Piscataway, New Jersey 08854 Nataliya Korzheva (13, 14), Public Health Research Institute, 225 Warren Street, Newark, New Jersey 07103-3535 Maxim Kozlov (14), Public Health Re- search Institute, 455 First Avenue, New York, New York 10016 Sergei Kuchin (45) Institute of Cancer Re- search, Columbia University, New York, New York 10032 Oleg Laptenko (16), Morse Institute of Molecular Genetics, Department of Microbiology and Immunology, SUNY Health Science Center at Brooklyn, 450 Clarkson Avenue, Brooklyn, New York 11203-2098 David Lazinski (33), University of Con- necticut Health Center, Farmington, Con- necticut 06030-3205 Lasse Lindahl (27), Department of Bio- logical Sciences, University of Maryland, Baltimore Country, 1000 Hilltop Circle, Baltimore, Maryland 21250 Cuihua Liu (2), Wyeth Research, 87 Cam- bridgepark Drive, Cambridge, Massachu- setts 02140 Eugeny Lukhtanov (14), Epoch Pharma- ceuticals, Inc., Bothell, Washington 98021 Kaiyu Ma (9), Morse Institute of Molecular Genetics, Department of Microbiology and Immunology, SUNY Downstate Medical Center, Brooklyn, New York 11203-2098 Vadim Markovtsov (14), Public Health Research Institute, 455 First Avenue, New York, New York 10016 Ronen Marmorstein (41), The Wistar In- stitute, Philadelphia, Pennsylvania 19104 Craig T. Martin (2), Department of Chem- istry, University of Massachusetts, Am- herst, Massachusetts 01003-9336 Tatyana Maximova (14), Limnological In- stitute, Russian Academy of Sciences, Ulanbatorskaya 3 664033, Russia William T. McAllister (9), Morse Insti- tute of Molecular Genetics, Department of Microbiology and Immunology, SUNY Downstate Medical Center 450 Clarkson Avenue Brooklyn, New York 11203-2098 Claude F. Meares (6), Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, Cali- fornia 95616-5295 Vladimir Mekler (10), Waksman Insti- tute, Howard Hughes Medical Institute, Rutgers University, 190 Frelinghuysen Road, Piscataway, New Jersey 08854 Jaime Garcia Mena (33), University of Connecticut Health Center, Farmington, Connecticut 06030-3205 Gregory Michaud (33), University of Connecticut Health Center, Farmington, Connecticut 06030-3205 Sankar Mitra (22), Sealy Center for Mo- lecular Science, University of Texas, Medical Branch, 6.136 Medical Research Building, Galveston, Texas 77555 Mark Mortin (46), Laboratory of Molec- ular Genetics NICHD, NIH, Building 6B, Room 3B-331, Bethesda, Maryland 20892-4255 Jayanta Mukhopadhyay (10), Waksman Institute, Howard Hughes Medical Insti- tute, Rutgers University, 190 Frelinghuy- sen, Road, Piscataway, New Jersey 08854 Helen Murphy (44), Laboratory of Mo- lecular Genetics, NICHD, NIH Building 6, Room 3B-314, Bethesda, Maryland 20892-2785 Arkady Mustaev (13, 14), Public Health Research Institute, 455 First Avenue, New York, New York 10016 xiv contributors to volume 371 Yuri A. Nedialkov (18), Department of Biochemistry, Michigan State University, East Lansing, Michigan 48824 Melody N. Neeley (32), Department of Microbiology and Immunology, The Uni- versity of Michigan Medical School, Ann Arbor, Michigan 48109-0620 Ronald D. Neumann (7), Department of Nuclear Medicine, Warren G. Magnuson Clinical Center, National Institutes of Health, Bethesda, Maryland 20892 Vadim Nikiforov (14), Institute of Molecu- lar Genetics, Russian Academy of Sci- ences, Moscow, 123182, Russia Evgeny Nudler (11, 13, 28), Department of Biochemistry, New York University Med- ical Center, New York, New York 10016 Matthew J. Oberley (43), Department of Oncology, Room 417A McArdle Labora- tory of Cancer Research, University of Wisconsin-Madison, 1400 University Avenue, Madison, Wisconsin 53706-1599 Jeffrey Owens (6), IDEC Pharmaceut- icals, 3031 Science Park Road, San Diego, CA 92191 Igor G. Pantyutin (7), Department of Nu- clear Medicine, Warren G. Magnuson Clinical Center, National Institutes of Health, Bethesda, Maryland 20892 Sang Chul Park (38), Aging and Apop- tosis Research Center, Department of Biochemistry and Molecular Biology, College of Medicine, Seoul National Uni- versity, 28 Yongon-Dong Chongno-GU, Seoul 110-799, South Korea Thodoris G. Petrakis (36), Cancer Re- search UK, London Research Institute, Clare Hall Laboratories, South Mimms, Hertfordshire EN6 3LD, United Kingdom Sangita Phadtare (34), Department of Biochemistry, Robert Wood Johnson Medical School, 675 Hoes Lane Piscat- away, New Jersey 08854-5635 Yuri V. Postnikov (39), Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Insti- tute, National Institutes of Health, Bethesda, Maryland 20892-4255 David H. Price (19), Department of Bio- chemistry, University of Iowa, Iowa City, Iowa 52242 Daniel Reines (21), Department of Bio- chemistry, Emory University School of Medicine, 4023 Rollins Research Center, Atlanta, Georgia 30322 Claudio Rivetti (3), Dipartimento di Bio- chimica e Biologia, Molecolare Universita degli Studi, di Parma Parco Area, delle Scienze 23/A 43100, Parma, Italy Jeffrey W. Roberts (8), Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853 Aziz Sancar (23), Department of Biochem- istry and Biophysics, University of North Carolina, School of Medicine, Chapel Hill, North Carolina 27599-7260 Thomas J. Santangelo (8), Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853 Janell Schaak (30), Department of Bio- chemistry and Molecular Biology and De- partment of Chemistry, The Pennsylvania State University, University Park, Penn- sylvania 16802 Brian D. Schmidt (6), Onyx Pharmaceut- icals, 3031 Research Drive, Richmond, California 94806 C. P. Selby (23), Department of Biochemis- try and Biophysics, University of North Carolina, School of Medicine, Chapel Hill, North Carolina 27599-7260 Ranjan Sen (15), Laboratory of Molecular Genetics, NICHD, NIH, Bldg. 6B, Rm. 3B-308, Bethesda, Maryland 20892 contributors to volume 371 xv Sibani Sengupta (33), University of Con- necticut Health Center, 263 Farmington Avenue, Farmington, Connecticut 06030- 3205 Hyuk-Kyu Seoh (35), Department of Mo- lecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts 02111-1800 Konstantin Severinov (14, 34), Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, 190 Fre- linghuysen Road, Piscataway, New Jersey 08854 Haihong Shen (12), Department of Bio- logical Sciences, Korea Advanced Insti- tute of Science and Technology, 373-1 Guesong-dong, Yuseong-gu, Daejeon 305- 701 Korea Ali Shilatifard (20), Edward A. Doisey, Department of Biochemistry, St. Louis University School of Medicine, St. Louis, Missouri 63104 Nubuo Shimamoto (4), National Institute of Genetics, School of Life Science, The Graduate University for Advanced Studies, Mishima, 411-8540 Japan Sarah M. Shore (19), Department of Bio- chemistry, University of Iowa, Iowa City, Iowa 52242 Igor Sidorenkov (17), NCI Center for Cancer Research, National Cancer Insti- tute—Frederick, Cancer Research Devel- opment Center, Frederick, Maryland 21702 Younghee Sohn (12), Department of Bio- logical Sciences, Korea Advanced Insti- tute of Science and Technology, 373-1 Guseong-dong Yuseong-gu, Daejeon 305- 701, Republic of Korea Rui Sousa (1), Department of Biochemis- try, University of Texas Health Science Center, 7703 Floyd Court Drive, San An- tonio, Texas 78284-7760 Catherine L. Squires (35), Department of Molecular Biology and Microbiology, Tufts University, School of Medicine, Boston, Massachusetts 02111-1800 Vasily M. Studitsky (42), Department of Biochemistry and Molecular Biology, Wayne State University School of Medi- cine, Detroit, Michigan 48201 Jesper Q. Svejstrup (36), Cancer Research UK, London Research Institute, Clare Hall Laboratories, South Mimms, Hert- fordshire EN6 3LD, United Kingdom Alexi Tatusov (7), Department of Nuclear Medicine, Warren G. Magnuson Clinical Center, National Institutes of Health, Bethesda, Maryland 20892 Vladimir Tchernajenko (566), Depart- ment of Biochemistry and Molecular Biol- ogy, Wayne State University School of Medicine, Detroit, Michigan 48201 Dmitri Temiakov (9), Morse Institute of Molecular Genetics, Department of Microbiology and Immunology, SUNY Downstate 450 Clarkson Avenue, Brook- lyn, New York 11203-2098 Igor Tsarev (14), Limnological Institute, Russian Academy of Sciences, Ulanba- torskaya 3 664033, Russia Andrea U ´ jva ´ ri (2), Department of Mo- lecular Biology, Lerner Research Insti- tute, Cleveland Clinic Foundation, Cleveland, Ohio 44195 Susan Uptain (25), Department of Mo- lecular Genetics and Cell Biology, Univer- sity of Chicago, 5841 South Maryland Avenue, Chicago, Illinois 60637 Wendy Walter (7), Department of Bio- chemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan 48201 Robert A. Weisberg (15), Laboratory of Molecular Genetics, NICHD, NIH Build- ing 6B, Room 3B-308, Bethesda, Maryland 20892 xvi contributors to volume 371 Katherine L. West (39), Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Insti- tute, National Institutes of Health, Bethesda, Maryland 20892-4255 Jerry L. Workman (40), Howard Hughes Medical Institute, Department of Bio- chemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802-4500 Alexander V. Yakhnin (30), Department of Biochemistry and Molecular Biology, The Pennsylvania State University, Uni- versity Park, Pennsylvania 16802 Yuki Yamaguchi (18), Graduate School of Bioscience and Biotechnology, Tokyo In- stitute of Technology, Yokohama 226- 8503, Japan Suk Hoon Yang (22), Sealy Center for Molecular Science and the Department of Human Biological Chemistry and Gen- etics, University of Texas Medical Branch, Galveston, Texas 77555 Charles Yanofsky (29), Herzstein Profes- sor of Biology, Department of Biological Sciences, Stanford University, Stanford, California 94305-5020 Eugeny Zaychikov (14), Max-Planck-In- stitute for Biochemie 8033, Martinsreid bei, Munchen, Germany Janice M. Zengel (27), Department of Biological Sciences, University of Mary- land Baltimore Country, Baltimore, Maryland 21250 Zuo Zhang (33), University of Connecticut Health Center, Farmington, Connecticut, 06030-3205 Victor Zhurkin (7), Laboratory of Com- putational and Experimental Biology, Na- tional Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892 contributors to volume 371 xvii METHODS IN ENZYMOLOGY Volume I. Preparation and Assay of Enzymes Edited by Sidney P. Colowick and Nathan O. Kaplan Volume II. Preparation and Assay of Enzymes Edited by Sidney P. Colowick and Nathan O. Kaplan Volume III. Preparation and Assay of Substrates Edited by Sidney P. Colowick and Nathan O. Kaplan Volume IV. Special Techniques for the Enzymologist Edited by Sidney P. Colowick and Nathan O. Kaplan Volume V. Preparation and Assay of Enzymes Edited by Sidney P. Colowick and Nathan O. Kaplan Volume VI. Preparation and Assay of Enzymes (Continued) Preparation and Assay of Substrates Special Techniques Edited by Sidney P. Colowick and Nathan O. Kaplan Volume VII. Cumulative Subject Index Edited by Sidney P. Colowick and Nathan O. Kaplan Volume VIII. Complex Carbohydrates Edited by Elizabeth F. Neufeld and Victor Ginsburg Volume IX. Carbohydrate Metabolism Edited by Willis A. Wood Volume X. Oxidation and Phosphorylation Edited by Ronald W. Estabrook and Maynard E. Pullman Volume XI. Enzyme Structure Edited by C. H. W. Hirs Volume XII. Nucleic Acids (Parts A and B) Edited by Lawrence Grossman and Kivie Moldave Volume XIII. Citric Acid Cycle Edited by J. M. Lowenstein Volume XIV. Lipids Edited by J. M. Lowenstein Volume XV. Steroids and Terpenoids Edited by Raymond B. Clayton xix Volume XVI. Fast Reactions Edited by Kenneth Kustin Volume XVII. Metabolism of Amino Acids and Amines (Parts A and B) Edited by Herbert Tabor and Celia White Tabor Volume XVIII. Vitamins and Coenzymes (Parts A, B, and C) Edited by Donald B. McCormick and Lemuel D. Wright Volume XIX. Proteolytic Enzymes Edited by Gertrude E. Perlmann and Laszlo Lorand Volume XX. Nucleic Acids and Protein Synthesis (Part C) Edited by Kivie Moldave and Lawrence Grossman Volume XXI. Nucleic Acids (Part D) Edited by Lawrence Grossman and Kivie Moldave Volume XXII. Enzyme Purification and Related Techniques Edited by William B. Jakoby Volume XXIII. Photosynthesis (Part A) Edited by Anthony San Pietro Volume XXIV. Photosynthesis and Nitrogen Fixation (Part B) Edited by Anthony San Pietro Volume XXV. Enzyme Structure (Part B) Edited by C. H. W. Hirs and Serge N. Timasheff Volume XXVI. Enzyme Structure (Part C) Edited by C. H. W. Hirs and Serge N. Timasheff Volume XXVII. Enzyme Structure (Part D) Edited by C. H. W. Hirs and Serge N. Timasheff Volume XXVIII. Complex Carbohydrates (Part B) Edited by Victor Ginsburg Volume XXIX. Nucleic Acids and Protein Synthesis (Part E) Edited by Lawrence Grossman and Kivie Moldave Volume XXX. Nucleic Acids and Protein Synthesis (Part F) Edited by Kivie Moldave and Lawrence Grossman Volume XXXI. Biomembranes (Part A) Edited by Sidney Fleischer and Lester Packer Volume XXXII. Biomembranes (Part B) Edited by Sidney Fleischer and Lester Packer Volume XXXIII. Cumulative Subject Index Volumes I-XXX Edited by Martha G. Dennis and Edward A. Dennis Volume XXXIV. Affinity Techniques (Enzyme Purification: Part B) Edited by William B. Jakoby and Meir Wilchek xx methods in enzymology [...]... Barnes and David A Sirbasku Volume 147 Peptide Growth Factors (Part B) Edited by David Barnes and David A Sirbasku Volume 148 Plant Cell Membranes Edited by Lester Packer and Roland Douce Volume 149 Drug and Enzyme Targeting (Part B) Edited by Ralph Green and Kenneth J Widder Volume 150 Immunochemical Techniques (Part K: In Vitro Models of B and T Cell Functions and Lymphoid Cell Receptors) Edited by... Rate and Inhibitor Methods) Edited by Daniel L Purich Volume 64 Enzyme Kinetics and Mechanism (Part B: Isotopic Probes and Complex Enzyme Systems) Edited by Daniel L Purich Volume 65 Nucleic Acids (Part I) Edited by Lawrence Grossman and Kivie Moldave Volume 66 Vitamins and Coenzymes (Part E) Edited by Donald B McCormick and Lemuel D Wright Volume 67 Vitamins and Coenzymes (Part F) Edited by Donald B... Spectroscopy Edited by Ludwig Brand and Michael L Johnson Volume 279 Vitamins and Coenzymes (Part I) Edited by Donald B McCormick, John W Suttie, and Conrad Wagner methods in enzymology xxxv Volume 280 Vitamins and Coenzymes (Part J) Edited by Donald B McCormick, John W Suttie, and Conrad Wagner Volume 281 Vitamins and Coenzymes (Part K) Edited by Donald B McCormick, John W Suttie, and Conrad Wagner Volume... 351 Guide to Yeast Genetics and Molecular and Cell Biology (Part C) Edited by Christine Guthrie and Gerald R Fink methods in enzymology xxxix Volume 352 Redox Cell Biology and Genetics (Part A) Edited by Chandan K Sen and Lester Packer Volume 353 Redox Cell Biology and Genetics (Part B) Edited by Chandan K Sen and Lester Packer Volume 354 Enzyme Kinetics and Mechanisms (Part F: Detection and Characterization... Steroids and Isoprenoids (Part A) Edited by John H Law and Hans C Rilling Volume 111 Steroids and Isoprenoids (Part B) Edited by John H Law and Hans C Rilling Volume 112 Drug and Enzyme Targeting (Part A) Edited by Kenneth J Widder and Ralph Green Volume 113 Glutamate, Glutamine, Glutathione, and Related Compounds Edited by Alton Meister Volume 114 Diffraction Methods for Biological Macromolecules (Part. .. Nucleic Acids and Protein Synthesis (Part G) Edited by Kivie Moldave and Lawrence Grossman Volume LX Nucleic Acids and Protein Synthesis (Part H) Edited by Kivie Moldave and Lawrence Grossman Volume 61 Enzyme Structure (Part H) Edited by C H W Hirs and Serge N Timasheff Volume 62 Vitamins and Coenzymes (Part D) Edited by Donald B McCormick and Lemuel D Wright Volume 63 Enzyme Kinetics and Mechanism (Part. .. Carter, Jr., and Robert M Sweet Volume 369 Combinational Chemistry (Part B) Edited by Guillermo A Morales and Barry A Bunin Volume 370 RNA Polymerases and Associated Factors (Part C) Edited by Sankar L Adhya and Susan Garges xl methods in enzymology Volume 371 RNA Polymerases and Associated Factors (Part D) Edited by Sankar L Adhya and Susan Garges Volume 372 Liposomes (Part B) ¨ ¨ Edited by Negat Duzgunes,... Interactions Edited by Robert T Sauer Volume 209 Phospholipid Biosynthesis Edited by Edward A Dennis and Dennis E Vance methods in enzymology xxxi Volume 210 Numerical Computer Methods Edited by Ludwig Brand and Michael L Johnson Volume 211 DNA Structures (Part A: Synthesis and Physical Analysis of DNA) Edited by David M J Lilley and James E Dahlberg Volume 212 DNA Structures (Part B: Chemical and Electrophoretic... 184 Avidin-Biotin Technology Edited by Meir Wilchek and Edward A Bayer Volume 185 Gene Expression Technology Edited by David V Goeddel Volume 186 Oxygen Radicals in Biological Systems (Part B: Oxygen Radicals and Antioxidants) Edited by Lester Packer and Alexander N Glazer Volume 187 Arachidonate Related Lipid Mediators Edited by Robert C Murphy and Frank A Fitzpatrick Volume 188 Hydrocarbons and Methylotrophy... Protein Pathways (Part A: Receptors) Edited by Ravi Iyengar and John D Hildebrandt Volume 344 G Protein Pathways (Part B: G Proteins and Their Regulators) Edited by Ravi Iyengar and John D Hildebrandt Volume 345 G Protein Pathways (Part C: Effector Mechanisms) Edited by Ravi Iyengar and John D Hildebrandt Volume 346 Gene Therapy Methods Edited by M Ian Phillips Volume 347 Protein Sensors and Reactive Oxygen . David Barnes and David A. Sirbasku Volume 147. Peptide Growth Factors (Part B) Edited by David Barnes and David A. Sirbasku Volume 148. Plant Cell Membranes Edited by Lester Packer and Roland Douce Volume. XXXIV–LX Edited by Edward A. Dennis and Martha G. Dennis Volume 76. Hemoglobins Edited by Eraldo Antonini,Luigi Rossi-Bernardi, and Emilia Chiancone Volume 77. Detoxication and Drug Metabolism Edited. Vitamins and Coenzymes (Parts A, B, and C) Edited by Donald B. McCormick and Lemuel D. Wright Volume XIX. Proteolytic Enzymes Edited by Gertrude E. Perlmann and Laszlo Lorand Volume XX. Nucleic Acids

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  • 01.pdf

    • 01.pdf

      • On Models and Methods for Studying Polymerase Translocation

        • Model for Polymerase Translocation

        • Kinetic Consequences and Tests of the Model

        • Using Exonucleases to Study Translocation

        • Studying Translocation with RNAses

        • Future Studies

        • Acknowledgments

        • 02.pdf

          • Evaluation of Fluorescence Spectroscopy Methods for Mapping Melted Regions of DNA Along the Transcription Pathway

            • Fluorescent Base Analogs

              • Benefits of Fluorescence over Other Approaches

              • Preparation of Samples

              • Fluorescence Measurements

              • Considerations

                • Base Analogs Are Not Identical to the Bases They Replace

                • Fluorescent Probes Report Only Indirectly on Melting

                • Estimating Extent of Melting

                • Mapping Melted Bubbles in Transcription

                  • Mapping the Bubble in the Initial Promoter Complex

                  • Mapping the Bubble in a Stably Stalled Elongation Complex

                  • Monitoring Bubble Collapse on Promoter Clearance

                  • Monitoring Initial Dissociation of the 5' End of the RNA

                  • Concluding Remarks

                  • Acknowledgments

                  • 03.pdf

                    • Single DNA Molecule Analysis of Transcription Complexes

                      • Methods

                        • Surface Equilibration of DNA Molecules

                        • Sample Preparation

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