Biophysical, chemical, and functional probes of RNA structure, interactions and folding: B
Saved in:
| Other Authors: | |
|---|---|
| Format: | Book |
| Language: | English |
| Published: |
Amsterdam [u.a.]
Elsevier, AP
2009
|
| Edition: | 1. ed. |
| Series: | Methods in enzymology
469 |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | XLVI, 503 S., [8] Bl. Ill., graph. Darst. |
| ISBN: | 9780123809223 |
Staff View
MARC
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| 245 | 1 | 0 | |a Biophysical, chemical, and functional probes of RNA structure, interactions and folding |n B |c ed. by Daniel Herschlag |
| 250 | |a 1. ed. | ||
| 264 | 1 | |a Amsterdam [u.a.] |b Elsevier, AP |c 2009 | |
| 300 | |a XLVI, 503 S., [8] Bl. |b Ill., graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
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Record in the Search Index
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|---|---|
| adam_text | Contents
Contributors
xiii
Preface
xvii
Volumes in Series
xix
Section I. Preparative Methods for
Biophysical Studies of
RNA
ι
1.
Large-Scale Native Preparation of In Vitro Transcribed
RNA
3
Amanda Y. Keel, Laura E. Easton, Peter J. Lukavsky, and Jeffrey S. Kieft
1.
Introduction
4
2.
Native Purification of
RNA:
Affinity Chromatography Method
5
3.
Native Purification of
RNA: Anion-Exchange
Chromatography
14
Acknowledgments
24
References
24
2.
Assembly of Complex RNAs by Splinted Ligation
27
Benjamin M. Akiyama and Michael D. Stone
1.
Introduction
28
2.
General Considerations for Splinted
RNA
Ligation
29
3.
Preparation of Unmodified
RNA
Ligation Precursor Molecules
31
4.
Preparation of Modified (Dye Labeled)
RNA
Ligation
Precursor Molecules
37
5.
RNA
Ligation Methods
40
6.
Application: Single-Molecule FRET Measurements
44
Acknowledgments
45
References
45
3.
Methods of Site-Specific Labeling of
RNA
with Fluorescent Dyes
47
Sergey Solomatin and Daniel
Herschlag
1.
Introduction
48
2.
Design of Labeled
RNA
Constructs
49
3.
Dye Labeling of
RNA
Fragments
53
4.
Notes on In Vitro Transcription with T7
RNA Polymerase
55
vi
Contents
5.
Assembly
of Labeled
RNA
Constructs
56
6.
Examples of Protocols
58
Acknowledgments
66
References
66
4.
Fluorophore Labeling to Monitor tRNA Dynamics
69
Cuiping Liu, Thu Betteridge, and Ya-Ming
Hou
1.
Introduction
70
2.
Methodology
75
3.
Fluorescent Labeling of
D
Residues in Native and
Transcripts of tRNAs
75
4.
Fluorescent Labeling of the CCA Sequence
82
5.
Conclusions
89
Acknowledgments
90
References
90
5.
Use of Deoxyribozymes in
RNA
Research
95
Scott
K. Silverman
and Dana A. Baum
1.
Introduction
96
2.
Deoxyribozymes for
RNA
Cleavage
97
3.
Deoxyribozymes for
RNA Ligation:
Synthesis of Linear
RNA
Products
101
4.
Deoxyribozymes for
RNA
Ligation: Synthesis of Branched
RNA
Products
107
5.
Deoxyribozyme-Catalyzed Labeling (DECAL) of
RNA
110
Acknowledgments
114
References
114
6.
Strategies in
RNA
Crystallography
119
Francis E. Reyes, Andrew D.
Garst,
and Robert T.
Batey
1.
Introduction
120
2.
RNA
Selection and Initial Characterization
122
3.
Construction of Library of RNAs for Crystallization Trials
124
4.
Improving Crystal Quality Through Postcrystal Analysis
127
5.
Phasing Methods
130
6.
A Case Study in the Crystallization of
Lysine
Riboswitch
Regulatory Element
132
7.
Concluding Remarks
134
Acknowledgments
135
References
135
Contents
vii
Section II.
Biophysical Methods for
RNA
Conformational and Dynamics Studies
141
7.
Comparative Gel Electrophoresis Analysis of Helical
junctions in
RNA
143
David
M. J.
Lilley
1.
Principle and Theory of Electrophoresis of Bent or
Kinked Nucleic Acids
144
2.
Discrete Bending or Kinking of the Axis of a Duplex
145
3.
The Analysis of Helical Junctions Using the Long-Short Arm Method
146
4.
Experimental Strategies and Methods
147
5.
Kink Turns in
RNA
149
6.
Four-Way
RNA
Junctions
149
7.
Three-Way
RNA
Junctions
152
8.
Complexes of Branched
RNA
with Proteins
155
Acknowledgments
155
References
155
8.
The Structure and Folding of Branched
RNA
Analyzed
by Fluorescence Resonance Energy Transfer
159
David
M. J.
Lilley
1.
Theory of FRET
162
2.
The Possible Effects of Fluorophore Orientation
163
3.
Choice of Fluorophores
167
4.
Construction of Fluorophore-Labeled
RNA
Species
170
5.
Steady-State Measurements of FRET
171
6.
Time-Resolved Measurements of FRET
176
7.
Single-Molecule FRET
179
Acknowledgments
182
References
182
9.
Analysis of
RNA
Folding by Native Polyacrylamide Gel
Electrophoresis
189
Sarah A. Woodson and
Eda Koculi
1.
Introduction
190
2.
Theory of Gel Electrophoresis
191
3.
Electrophoresis Equipment
194
4.
Stability of Folded
RNA
Measured by Native PAGE
196
5.
RNA
Folding Kinetics
199
6.
RNA
Compactness and Native PAGE Mobility
200
7.
Probing the Function of Conformers Resolved by Native PAGE
201
v¡¡¡
Contents
8.
Controls
and Further Considerations
204
9.
Summary
205
Acknowledgments
205
References
205
10.
Using Analytical Ultracentrifugation (AUC) to Measure Global
Conformational Changes Accompanying Equilibrium Tertiary
Folding of
RNA
Molecules
209
Somdeb
Mitra
1.
Introduction
210
2.
Theoretical Background
211
3.
Materials and Instrumentation
216
4.
Performing an
RNA
Folding Experiment
218
5.
Data Analysis
224
6.
Case Studies
230
7.
Conclusions
232
Acknowledgments
233
References
233
11.
Use of Small Angle X-ray Scattering (SAXS) to Characterize
Conformational States of Functional RNAs
237
Sebastian Doniach and Jan Lipfert
1.
Small Angle X-ray Scattering (SAXS) as a Tool for Global
Structure Determination at Low Resolution
238
2.
SAXS and Conformational Changes in Small Functional RNAs
238
3.
SAXS Data Acquisition and Effects of Radiation Damage
239
4.
SAXS Data Analysis
239
5.
Low-Resolution Atomic Scale Models of
RNA:
Fitting Secondary
Structure
RNA
Models to Three-Dimensional Shape Models
243
6.
Determining the Thermodynamics of
RNA
Folding Using Bead Models
245
7.
Concluding Remarks
248
Acknowledgments
249
References
249
12.
Time-Resolved X-ray Scattering and
RNA
Folding
253
Lois Pollack and Sebastian Doniach
1.
Introduction
254
2.
SAXS Studies of
RNA
254
3.
Data Acquisition
255
4.
Time-Resolved SAXS Methods
256
5.
Mixer Fabrication
259
Contents ix
6. Data
Analysis of SAXS Measurements
262
7.
Concluding Remarks
266
Acknowledgments
266
References
267
13.
2-Aminopurine as a Probe of
RNA
Conformational Transitions
269
Kathleen B. Hall
1.
Introduction
269
2.
2AP Structure and Photophysics
270
3.
RNA
Oligonucleotides with 2AP
273
4.
Steady-State Fluorescence and
RNA
Folding
273
5.
Time-Resolved Fluorescence Intensity Decay
278
Acknowledgments
284
References
284
14.
Fluorescence Polarization Anisotropy to Measure
RNA
Dynamics
287
Xuesong Shi and Daniel
Herschlag
1.
Introduction
288
2.
General Information of FPA Measurement
289
3.
Choice of FPA Probes
291
4.
Measuring FPA in a Simple Duplex, using an llmer Control
RNA
Duplex as an Example
292
5.
Use of FPA to Study Helical Dynamics of
RNA,
with a Junction
Model Construct as an Example
294
6.
Use of FPA to Study Helical Dynamics in a Complex
RNA,
with the Tetrahymena Group I
Intron
Ribozyme as an Example
299
7.
Salt Dependence and Normalization of FPA with a
Short Control Duplex
301
Acknowledgments
301
References
301
15.
Studying
RNA
Using Site-Directed Spin-Labeling and
Continuous-Wave Electron Paramagnetic Resonance
Spectroscopy
303
Xiaojun Zhang,
Pavol
Cekan, Snorri Th.
Sigurdsson,
and Peter Z. Qin
1.
Site-Directed Spin-Labeling
304
2.
Acquisition and Processing of cw-EPR Spectrum
308
3.
Spectral Analysis
318
4.
Examples of Application
320
Acknowledgments
326
References
326
Contents
16.
Mapping
Global
Folds of Oligonucleotides by Pulsed
Electron-Electron Double Resonance
329
Olav Schiemann
1.
Introduction
330
2.
Overview
332
3.
The Experiment
335
4.
Structure Generation
339
5.
Beyond Distances
340
6.
Comparison with Other Methods
346
Acknowledgments
347
References
347
17.
Laser-Induced Temperature Jump Infrared Measurements
of
RNA
Folding
353
R. Brian Dyer and Eric B.
Brauns
1.
Introduction
354
2.
Infrared Spectral Properties of
RNA
356
3.
Experimental Methods
361
4.
Examples
366
5.
Conclusions
371
References
371
Section III. Electrostatics, and the Ion Atmosphere
373
18.
Probing Nucleic Acid-Ion Interactions with Buffer
Exchange-Atomic Emission Spectroscopy
375
Max Greenfeld and Daniel
Herschlag
1.
Introduction
375
2.
Description of BE-AES
377
3.
Buffer Equilibration
379
4.
ICP-AES
382
5.
Measuring Anions
383
6.
Example Protocol
384
Acknowledgments
388
References
388
19.
Using Anomalous Small Angle
Х
-Ray Scattering to Probe the Ion
Atmosphere Around Nucleic Acids
391
Suzette A. Pabit, Kenneth D. Finkelstein, and Lois Pollack
1.
Introduction
392
2.
Background: SAXS and ASAXS
393
Contents
3.
Experimental
Setup:
Samples
398
4.
Experimental Setup: Beamline
398
5.
Data Acquisition
400
6.
Results and Data Analysis
403
7.
Conclusion
407
Acknowledgments
409
References
409
20.
Simulations of
RNA
Interactions with
Monovalent Ions
411
Alan A. Chen,
Marcelo Marucho,
Nathan A. Baker, and Rohit V. Pappu
1.
Introduction
412
2.
Finite Size Artifacts in All-Atom Simulations of Ion-Nucleic
Acid Interactions
414
3.
On the Use of Neutralizing Counterions Only in
All-Atom Simulations
421
4.
Results from Simulations of Canonical
A-Form RNA
and
B-Form DNA
Helices
421
5.
Comparison with Predictions of the Nonlinear
Poisson-Boltzmann Equation
426
Acknowledgment
430
References
430
21.
lon-RNA Interactions: Thermodynamic Analysis of the
Effects of Mono- and Divalent Ions on
RNA
Conformational Equilibria
433
Desirae Leipply, Dominic Lambert, and David E. Draper
1.
Introduction
434
2.
Thermodynamic Descriptions of lon-RNA Interactions
435
3.
Analysis of Experimental Salt Dependence Data
444
Acknowledgment
461
References
461
22.
Predicting Electrostatic Forces in
RNA
Folding
465
Zhi-Jie Tan and Shi-Jie Chen
1.
Introduction
466
2.
Overview of Experimental Results for the Ion-Dependence of
RNA
Thermal Stability
467
3.
Overview of Theoretical Methods for Predicting Ion
Electrostatics for
RNA
Folding
471
4.
Tightly Bound Ion Model
474
xii Contents
5.
Enhancing the Computational Efficiency for the Numerical
Calculations of the TBI Model
477
6.
Applications of the TBI Model
478
7.
Summary
482
Acknowledgments
484
References
484
Author Index
489
Subject Index
497
|
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| genre_facet | Aufsatzsammlung |
| id | DE-604.BV035969602 |
| illustrated | Illustrated |
| indexdate | 2024-07-09T22:08:46Z |
| institution | BVB |
| isbn | 9780123809223 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-018863638 |
| oclc_num | 643851523 |
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| physical | XLVI, 503 S., [8] Bl. Ill., graph. Darst. |
| publishDate | 2009 |
| publishDateSearch | 2009 |
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| publisher | Elsevier, AP |
| record_format | marc |
| series | Methods in enzymology |
| series2 | Methods in enzymology |
| spelling | Biophysical, chemical, and functional probes of RNA structure, interactions and folding B ed. by Daniel Herschlag 1. ed. Amsterdam [u.a.] Elsevier, AP 2009 XLVI, 503 S., [8] Bl. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Methods in enzymology 469 Methods in enzymology ... Methode (DE-588)4038971-6 gnd rswk-swf RNS (DE-588)4076759-0 gnd rswk-swf Strukturanalyse (DE-588)4183787-3 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content RNS (DE-588)4076759-0 s Strukturanalyse (DE-588)4183787-3 s Methode (DE-588)4038971-6 s DE-604 Herschlag, Daniel edt (DE-604)BV035912186 2 Methods in enzymology 469 (DE-604)BV000000938 469 Digitalisierung UB Regensburg application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=018863638&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Biophysical, chemical, and functional probes of RNA structure, interactions and folding Methods in enzymology Methode (DE-588)4038971-6 gnd RNS (DE-588)4076759-0 gnd Strukturanalyse (DE-588)4183787-3 gnd |
| subject_GND | (DE-588)4038971-6 (DE-588)4076759-0 (DE-588)4183787-3 (DE-588)4143413-4 |
| title | Biophysical, chemical, and functional probes of RNA structure, interactions and folding |
| title_auth | Biophysical, chemical, and functional probes of RNA structure, interactions and folding |
| title_exact_search | Biophysical, chemical, and functional probes of RNA structure, interactions and folding |
| title_full | Biophysical, chemical, and functional probes of RNA structure, interactions and folding B ed. by Daniel Herschlag |
| title_fullStr | Biophysical, chemical, and functional probes of RNA structure, interactions and folding B ed. by Daniel Herschlag |
| title_full_unstemmed | Biophysical, chemical, and functional probes of RNA structure, interactions and folding B ed. by Daniel Herschlag |
| title_short | Biophysical, chemical, and functional probes of RNA structure, interactions and folding |
| title_sort | biophysical chemical and functional probes of rna structure interactions and folding |
| topic | Methode (DE-588)4038971-6 gnd RNS (DE-588)4076759-0 gnd Strukturanalyse (DE-588)4183787-3 gnd |
| topic_facet | Methode RNS Strukturanalyse Aufsatzsammlung |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=018863638&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| volume_link | (DE-604)BV035912186 (DE-604)BV000000938 |
| work_keys_str_mv | AT herschlagdaniel biophysicalchemicalandfunctionalprobesofrnastructureinteractionsandfoldingb |