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