rna-ligand interactions - gbv · 22. time-resolved synchrotron x-ray footprinting corie y. ralston,...
TRANSCRIPT
Methods in Enzymology
Volume 31 7
RNA-Ligand InteractionsPart A
Structural Biology Methods
Daniel W. Celander
John N. Abelson
CONTRIBUTORS TO VOLUME 317 '
ix
PREFACE xii i
VOLUMES IN SERIES XV
Section I . Semisynthetic Methodologie s
A. RNA Synthetic Methods
1 . Advanced 5'-Silyl-2'-Orthoester Approach to RNA STEPHEN A . SCARINGE
3Oligonucleotide Synthesis
2. Preparation of Specifically 2H- and 13C-Labeled LINCOLN G . ScoTT ,
Ribonucleotides
THOMAS J . TOLBERT, AND
JAMES R . WILLIAMSON
1 8
3. Base-Modified Phosphoramidite Analogs of Pyrimi- LEONID BEIGELMAN ,
dine Ribonucleosides for RNA Structure- JASENKA MATULIC-ADAMIC ,
Activity Studies
ALEXANDER KARPEISKY ,
PETER HAEBERLI, AND
DAVID SWEEDLER
39
B. Derivatization of RNA
4. Use of T7 RNA Polymerase and Its Mutants for Rut SOUSA
65Incorporation of Nucleoside Analogs into RN A
5 . Phosphorothioate Modification of RNA for Stereo- L. CLAUS S . VÖRTLER AN D
chemical and Interference Analyses
FRITZ ECKSTEIN
74
6. Chemical Probing of RNA by Nucleotide Analog SEAN P . RYDER,
Interference Mapping
LORI ORTOLEVA-DONNELLY,
ANNE B . KOSEK, AN D
SCOTT A . STROBEL
92
7. Joining of RNAs by Splinted Ligation
MELISSA J . MOORE AND
CHARLES C. QUERY
109
8. Heavy Atom Derivatives of RNA
BARBARA L. GOLDEN
124
9. Site-Specific Cleavage of Transcript RNA
JON LAPHAM AND
DONALD M. CROTHERS
132
10. Using DNAzymes to Cut, Process, and Map RNA ANNA MARIE PYLE ,
Molecules for Structural Studies or Modification VI T. CHU ,
ECKHARD JANKOWSKY, AND
MARC BOUDVILLAIN
140
Section II . RNA Structure Determination
A. X-Ray Crystallography
11 . Purification, Crystallization, and X-Ray Diffraction JOSEPH E . WEDEKIND AND
Analysis of Small Ribozymes
DAVID B . McKAY
14 9
12 . Solving Large RNA Structures by X-Ray Crystal- JAMIE H . CATE AN Dlography
JENNIFER A . DOUDNA
16 9
13 . Conventional and Time-Resolved Ribozyme WILLIAM G. Scorn AN D
X-Ray Crystallography
JAMES B . MURRAY
18 0
B. Nuclear Magnetic Resonance Spectroscopy
14. Nuclear Magnetic Resonance Methods to Study PETER BAYER ,
RNA-Protein Complexes
LUCA VARANI, AND
GABRIELE VARANI
198
15. Filamentous Bacteriophage for Aligning RNA, MARK R . HANSEN ,DNA, and Proteins for Measurement of Nuclear PAUL HANSON, AN DMagnetic Resonance Dipolar Coupling Interac- ARTHUR PARDI
220tion s
16. Biochemical and Nuclear Magnetic Resonance STEPHEN R. LYNCH ,
Studies of Aminoglycoside-RNA Complexes
MICHAEL I . RECHT, AN D
JOSEPH D . PUGLISJ
240
C . Electron Microscopy
17 . Experimental Prerequisites for Determination of FRANCISCO J. TRIANA-ALONSO ,
tRNA Binding to Ribosomes from Escherichia CHRISTIAN M . T . SPAHN ,
call
NILS BURKHARDT ,
BEATRIX RÖHRDANZ, AN D
KNUD H . NIERHAUS
26 1
18. Three-Dimensional Cryoelectron Microscopy of Ri- JOACHIM FRANK ,bosomes
PAWEL PENCZEK,
RAJENDRA K . AGRAWAL ,
ROBERT A . GRASSUCCI, AN DAMY B . HEAGLE
276
19. Preparation of Functional Ribosomal Complexes GREGOR BLAHA ,and Effect of Buffer Conditions on tRNA Posi- ULRICH STELZL ,
tions Observed by Cryoelectron Microscopy
CHRISTIAN M. T. SPAHN ,
RAJENDRA K. AGRAWAL,
JOACHIM FRANK, AND
KNUD H . NIERHAUS
292
Section III . Techniques for Monitoring RNA Conformatio nand Dynamics
A. Solution Method s
20. Probing RNA Structure and Function by Circular TAO PAN
31 3Permutatio n
21 . Kinetic Oligonucleotide Hybridization for Monitor- DANIEL K . TREIBER AN Ding Kinetic Folding of Large RNAs
JAMES R . WILLIAMSON
33 0
22. Time-Resolved Synchrotron X-Ray Footprinting CORIE Y . RALSTON,and Its Application to RNA Folding
BIANCA SCLAVI ,
MICHAEL SULLIVAN ,
MICHAEL L. DERAS ,
SARAH A . WOODSON,
MARK R. CHANCE, AND
MICHAEL BRENOWITZ
35 3
B. Electrophoretic and Spectroscopic Methods
23 . Analysis of Global Conformation of Branched DAVID M . J. LILLEY
368RNA Species Using Electrophoresis and Fluores-cenc e
24. Application of Circular Dichroism to Study RNA TOBIN R . SOSNICK ,Folding Transitions
XINGWANG FANG, AND
VALERIE M . SIIELTON
393
25 . Fluorescence Assays to Study Structure, Dynamics, NILS G. WALTER ANDand Function of RNA and RNA-Ligand Corn- JOHN M . BURKE
409plexes
26 . Transient Electric Birefringence for Determining PAUL J . HAGERMAN
440Global Conformations of Nonhelix Elements and
Protein-Induced Bends in RN A
Section IV. Modeling Tertiary Structure
27 . Structure-Function Relationships of RNA : A Mod- FABRICE LECLERC ,cling Approach
BELSIS LLORENTE, AND
ROBERT CEDERGREN
457
28. Computational Modeling of Structural Experimen- MICHAEL A . RADA AN Dtal Data
Russ B . ALTMAN
470
29. Modeling RNA Tertiary Structure from Patterns of FRANCOIS MICHEL ,Sequence Variation
MARIA COSTA,
CHRISTIAN MASSIRE, AND
ERIC WESTHOF
491
AUTHOR INDEX 51 1
SUBJECT INDEX 533