Handbook of RNA biochemistry: 1
Saved in:
| Other Authors: | |
|---|---|
| Format: | Book |
| Language: | English |
| Published: |
Weinheim
WILEY-VCH
2014
|
| Edition: | 2., completely rev. and enl. ed. |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Item Description: | Literaturangaben |
| Physical Description: | XLII, 546 S. Ill., graph. Darst. |
| ISBN: | 9783527327645 9783527647064 |
Staff View
MARC
| LEADER | 00000nam a2200000 cc4500 | ||
|---|---|---|---|
| 001 | BV039877258 | ||
| 003 | DE-604 | ||
| 005 | 20140718 | ||
| 007 | t | ||
| 008 | 120209s2014 gw ad|| |||| 00||| eng d | ||
| 020 | |a 9783527327645 |c print |9 978-3-527-32764-5 | ||
| 020 | |a 9783527647064 |c oBook |9 978-3-527-64706-4 | ||
| 035 | |a (OCoLC)876246137 | ||
| 035 | |a (DE-599)BVBBV039877258 | ||
| 040 | |a DE-604 |b ger |e rakwb | ||
| 041 | 0 | |a eng | |
| 044 | |a gw |c XA-DE-BW | ||
| 049 | |a DE-11 |a DE-188 |a DE-355 |a DE-19 |a DE-703 | ||
| 082 | 0 | |a 572.88 | |
| 245 | 1 | 0 | |a Handbook of RNA biochemistry |n 1 |c ed. by Roland K. Hartmann ... |
| 250 | |a 2., completely rev. and enl. ed. | ||
| 264 | 1 | |a Weinheim |b WILEY-VCH |c 2014 | |
| 300 | |a XLII, 546 S. |b Ill., graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 500 | |a Literaturangaben | ||
| 650 | 0 | 7 | |a RNS |0 (DE-588)4076759-0 |2 gnd |9 rswk-swf |
| 655 | 7 | |0 (DE-588)4143413-4 |a Aufsatzsammlung |2 gnd-content | |
| 689 | 0 | 0 | |a RNS |0 (DE-588)4076759-0 |D s |
| 689 | 0 | |5 DE-604 | |
| 700 | 1 | |a Hartmann, Roland K. |d 1956- |0 (DE-588)12993643X |4 edt | |
| 773 | 0 | 8 | |w (DE-604)BV019662557 |g 1 |
| 776 | 0 | 8 | |i Erscheint auch als |n Online-Ausgabe, EPUB |z 978-3-527-65054-5 |
| 776 | 0 | 8 | |i Erscheint auch als |n Online-Ausgabe, MOBI |z 978-3-527-65053-8 |
| 776 | 0 | 8 | |i Erscheint auch als |n Online-Ausgabe, PDF |z 978-3-527-65055-2 |
| 856 | 4 | 2 | |m Digitalisierung UB Regensburg - ADAM Catalogue Enrichment |q application/pdf |u http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=024736458&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |3 Inhaltsverzeichnis |
| 999 | |a oai:aleph.bib-bvb.de:BVB01-024736458 | ||
Record in the Search Index
| _version_ | 1804148821034270720 |
|---|---|
| adam_text | Contents
to
Volume 1
Preface XX
¡Π
Ust
of Contributors
XXV
Part I RNA Synthesis and Detection
?
Ί
Enzymatic RNA Synthesis Using Bacteriophage T7 RNA Polymerase
Markus
Göfiringer, Dominik
Helnwckť.
Karen Köhler. Astrid SY/ion,
Lei/A. Kirsebom, Alhreciü Bindereit , and
Roland
К.
Hartmann
1.1
Introduction
З
1.2
Description
oí
Method
-
Т7
Transcription in vitro
4
1.2.1
Templates
4
1.2.1.1
Strategy
(і):
insertion into
a Plasmici
4
1.2.1.2
Strategy (ii): Direct Use of Templates Generated by I CR
5
1.2.1.3
Strategy
(iii):
Annealing of a T7 Promoter
DNA
Oligonuclcotidc
to a Single-Stranded Template
5
1.2.2
Special Demands on the RNA Product
5
1.2.2.1
Homogeneous
5
and
3
Ends, Small RNAs, Functional Groups
at the
5
End
5
1.2.2.2
Modified Substrates
6
1.3
Transcription Protocols
H
1.3.1
Transcription with Unmodified
N
uclcotides
9
1.3.2
Transcription with
2 -
Fluoro-Modi
ficd Nucleotidrs
Í6
1.3.3
T7 Transcripts with 5-Cap Structures
17
1.3.4
Purification
IH
1.4
Trou
b
і
es h
оо
t i n g
20
1.4.1
Low or No Product Yield
20
1.5
Rapid Preparation
ОҐТ7
RNA Polymerase
2
і
J.S.I
Reť|!iired
Material
21
1.5.
M
Medium ¿J
1.5.1.2
Buffers and Solutions ¿I
1.5.1.3
Rlectrophoresis and Chromatography
22
1.5.2
Procedure
22
1.5.2.1
Cell Growth, Induction, and Test for Expression of T7 RNAP
¿¿
VI
I Contents
1.5.2.2
Purification of T7 RNAP
23
1.5.3
Notes and Troubleshooting
24
References
25
2
Production of RNAs with Homogeneous
5 -
and
З
-Ends
29
Mario Mori and Roland K.
Hartmann
2.1
Introduction
29
2.2
Description of Approach
30
2.2.1
Ct s-Cleaving Autocatalytic Ribozyme Cassettes
30
2.2.1.1
The S -Cassette
30
2.2.1.2
The
Ъ
-Cassette
30
2.2.1.3
Purification of Released
RNA
Product and Conversion of End
Groups
31
2.2.2
Trans-Cleaving Ribozymes for the Generation of Homogeneous
3
Ends
33
2.2.3
Further Strategies toward Homogeneous Ends
35
2.3
Critical Experimental Steps, Changeable Parameters,
Troubleshooting
36
2.3.1
Construction of Cis-Cleaving
5 -
and
З
-Cassettes
36
2.4
PCR Protocols
37
2.5
Potential Problems
42
References
42
3
RNA Ligation
45
Janne
J
.
Turunen, Liudmila V. Pavlova, Martin Hengesbach, Mark Helm,
Sabine
Müller,
Roland
К.
Hartmann,
and
Mikko
J.
Frilander
3.1
General
Introduction
45
3.1.1
Т4
Polynucleotide
Ligases
46
3.1.2
Reaction Mechanism
46
3.1.3
Advantages of T4
DNA
Ligase
for
RNA
Ligation
49
3.1.4
Chapter Structure
49
3.2
RNA
Ligation Using T4
DNA
Ligase
(Т4
Dni)
50
3.2.1
Overview of the
RNA
Ligation Method Using the T4
DNA
Ligase
(Т4
Dni)
51
3.2.2
Large-Scale
Transcription and Purification of RNAs
53
3.2.3
Generating Homogeneous Acceptor
З
-Ends
for Ligation
53
3.2.4
Site-Directed Cleavage with RNase
H
54
3.2.5
Dephosphorylation and Phosphorylation of RNAs
56
3.2.6
RNA
Ligation
57
3.2.7
Troubleshooting
58
3.3
Simultaneous Splint Ligation of Five
RNA
Fragments to Generate
RNAs for FRET Experiments
66
3.3.1
Introduction
66
3.3.2
Construct Design
68
3.3.3
Troubleshooting
70
Contents
VII
3.3.3.1
Low
Overall Ligation
Efficiency
70
3.3.3.2
Undesired Ligation By-products
70
3.3.3.3
RNA
Degradation
70
3.4
T4
RNA Ligase(s)
70
3.4.1
Introduction
70
3.4.2
Mechanism and Substrate Specificity
71
3.4.2.1
Early Studies
71
3.4.2.2
Substrate Specificity and Reaction Conditions
72
3.4.3
Applications of T4
RNA
Ligase
73
3.4.3.1
End-Labeling
73
3.4.3.2
Circuìarization
75
3.4.3.3
Intermolecular Ligation of Polymideotides
75
3.4.4
T4
RNA
Ligation of Large
RNA
Molecules
76
3.4.5
Application Examples and Protocols
79
3.4.5.1
Production of
F
ull-
Length tRN As
79
3.4.6
Troubleshooting
84
References S4
4
Northern Blot Detection of Small RNAs
#9
Benedikt
M.
Beckmann,
Arnold
Grünweiler,
and Roland
К.
Hartmann
4.1
Introduction
89
4.1.1
Isolation of
RNA
89
4.1.1.1
Kits
90
4.1.1.2
Do it Yourself
90
4.1
Л
3
Quality Control
90
4.1.2
Native versus Denaturing Gels
90
4.1.3
Transfer of
RNA
and Fixation to Membranes
91
4.1.4
Hybridization with a Complementary Probe
92
4.1.4.1
Design of DNA/LNA Mixmer Probes
92
4.1.5
Detection of DIG-Labeled Probes
95
4.1.6
Troubleshooting
95
4.1.7
Application Example
96
4.1.8
Limitations of the Method
96
4.2
Northern Hybridization Protocols
98
References
102
5
Rapid, Non-Denaturing, Large-Scale Purification of In Vitro Transcribed
RNA
Using Weak
Anion-Exchange Chromatograph/ 105
Laura E. Easton, Yoko Skibata. and Peter J. Lukavsky
5.1
Introduction
105
5.2
Materials
106
5.2.1
Cloning and
Pîasmîd
Purification
106
5.2.2
In Viim Transcription
106
5.2.3
Weak Anion-Exchange FPLC
107
VIII
Contents
5.3
Protocols for Plasmid Design and Preparation,
RNA
Transcription,
and Weak Anion-Exchange Purification
107
5.4
Troubleshooting
115
Acknowledgments
115
References
116
6
З
-Terminal
Attachment of Fluorescent Dyes and Biottn
117
Dagmar
К.
Willkomm
and Roland
К.
Hartmann
6.1
Introduction
117
6.2
Description of Method
118
6.3
History of the Method
118
6.4
Troubleshooting
124
6.4.1
Problems Caused Before the Labeling Reaction
224
6.4.1.1
Quality of the
RNA
3
Ends
224
6.4.1.2
Purity of the
RNA
to Be Labeled
124
6.4.2
Problems with the Labeling Reaction Itself
124
6.4.2.1 pH
of Reagents
124
6.4.2.2
Stability of Reagents
124
6 A3
Postlabeling Problems
125
6.4.3.1
Removal of Labeling Reagents
125
6.4.3.2
Loss of
RNA
Material during Downstream Purification
125
6.4.3.3
Stability of Labeled
RNA
125
Acknowledgment
125
References
125
7
Chemical
RNA
Synthesis, Purification, and Analysis
129
Brian S. Sproat
7.1
Introduction
129
7.2
Description
232
7.2.1
The Solid-Phase Synthesis of
RNA
132
7.2.2
Deprotection
136
7.2.3
Purification
138
7.2.3.1
Anion-Exchange HPLC Purification
139
7.23.2
Reversed-Phase HPLC Purification of Trityl-On
RNA
240
7.2.3.3
Detritylation of Trityl-On
RNA
142
7.2.3.4
Desalting by HPLC
242
7.2.4
Analysis of the Purified
RNA
143
73
Troubleshooting
144
References
147
8
Modified RNAs as Tools ¡n
RNA
Biochemistry
252
Thomas E. Edwards and
Snom
Th. Sigiirdsson
8.1
Introduction
151
8.1.1
Modification Strategy: the Phosphoramidite Method
252
8.1.2
Modification Strategy: Postsynthetic Labeling
154
Contents
IX
8.2
Description
of Methods
156
8.2.1
Postsynthetic Modification: the
2 -Amшo
Approach
256
8.2.2
Reaction of
Ž -Amino
Groups with Succinimidyl Esters
158
8.2.3
Reaction of
2 -Amino
Groups with Aromatic Isothiocyanates
158
8.2.4
Reaction of
г -Атіпо
Groups with Aliphatic Isocyanates
159
8.3
Experimental Protocols
259
8.3.1
Synthesis of Aromatic Isothiocyanates and Aliphatic
Isocyanates
260
8.3.2
Postsynthetic Labeling of
Ž -Ammo-Modffied
RNA
261
8.3.3
Postsynthetic Labeling of 4-Thiouridme-Modified
RNA
164
8.3.4
Verification of Label Incorporation
164
8.3.5
Potential Problems and Troubleshooting
165
References
266
Partii
Structure Determination
173
9
Direct Determination of
RNA
Sequence and Modification by
Radiolabeling Methods
175
OlafGimpL· and
Astrid Schön
9.1
Introduction
275
9.2
General Methods
275
9.3
Isolation of Pure
RNA
Species from Biological Material
276
9.3.1
Preparation of Size-Fractionated
RNA
276
9.3.2
Isolation of a Single Unknown
RNA
Species Following a Functional
Assay
176
9.3.2.1
Solutions for Electrophoresis, Staining, and Elution of RNAs from
Gels
276
9.3.2.2
Two-Dimensional Electrophoresis of
RNA
177
9.3.2.3
Comments on the Electrophoretic Purification and Elution of
RNA
Species
178
9.3.3
isolation of Single
RNA
Species with Partially Known
Sequence
178
9.3.3.1
Materials for Hybrid Selection of Single
RNA
Species
278
9.4
Radioactive Labeling of
RNA
Termini
280
9.4.1
Materials for S -End Labeling of RNAs
180
9.4.2 3
-Labeling of RNAs
287
9.4.2.1
Materials for
З
-End
Labeling of RNAs
282
9.5
Sequencing of End-Labeled
RNA
183
9.5.1
Sequencing by Base-Specific Enzymatic Hydrolysis of End-Labeled
RNA
184
9.5.1.1
Materials Required for Enzymatic Sequencing
785
9.5.1.2
Interpretation and Troubleshooting
186
9.5.2
Sequencing by Base-Specific Chemical Modification and
Cleavage
287
9.5.2.1
Materials Required for Chemical Sequencing
788
X Contents
9.5.2.2
Interpretation and Troubleshooting
189
9.6
Determination of Terminal
RNA
Sequences by Two-dimensional
Mobility Shift
290
9.6.1
Materials Required for Mobility Shift Analysis
190
9.7
Determination of Modified Nucleotides by Postlabeling
Methods
194
9.7.1
Analysis of Total Nucleotide Content
195
9.7.1.1
Materials Required for
RNA
Nucleotide Analysis
195
9.7.1.2
Interpretation and Troubleshooting
197
9.7.2
Determination of Position and Identity of Modified
Nucleotides
198
9.7.2.1
Interpretation and Troubleshooting
199
9.8
Conclusions and Outlook
201
Acknowledgments
202
References
202
10
Probing
RNA
Structure In Vitro with Enzymes and Chemicals
205
Anne-Catheiine Heifer,
Cédríc
Romilly, Clement Chevalier,
Efihimia Lioliou,
Stefano
Marzi,
and
Pascale
Romby
10.1
Introduction
205
10.2
Enzymatic and Chemical Probes
207
10.2.1
Enzymes
207
10.2.2
Base-Specific Chemical Probes
210
10.2.3
Backbone-Specific Chemical Probes
211
10.3
In Vivo DM
S
Modification
222
10.3.1
Generalities
222
10.3.2
In Vivo Probing
222
10.4
Commentary
223
10.4.1
Critical Parameters
223
10.4.1.1
RNA
Preparation
223
10.4.1.2
Homogeneous
RNA
Conformation
224
10.4.1.3
Chemical and Enzymatic Probing
224
10.4.1.4
In Vivo DMS Mapping
225
10.5
Troubleshooting
225
Acknowledgments
227
References
227
Π
Probing
RNA
Solution Structure by Photocrosslinking: Incorporation
of Photoreactive Croups at
RNA
Termini and Determination of
Crosslinked Sites by Primer Extension
231
Michael E. Harris
11.1
Introduction
231
11.1.1
Applications of
RNA
Modifications
231
11.1.2
Techniques for the Incorporation of Modified Nucleotides
232
11.2
Description
233
Contents
XI
11.2.4
11.3
11.4
11.4.
1
11.4.
2
11.4.
2.1
11.2.1 5 -End
Modification
by
Transcription
Priming
233
11.2.2
Chemical Phosphorylation
of Nucleosides to Generate
S -Monophosphate
or
S -Monophosphorothioate
Derivatives
234
11.2.3
Attachment of an Aryl Azide Photocrosslinking Agent to
а Б -Тегтіпаі
Phosphorothioate
236
3 -
Addition of an Aryl Azide Photocrosslinking Agent
238
Troubleshooting
240
Probing
RNA
Structure by Photoaffinity Crosslinking with
4-Thiouridine and 6-Thioguanosine
240
Introduction
240
Description
243
General Considerations: Reaction Conditions and Concentrations
of Interacting Species
243
11.4.2.2
Application Example
-
RNase
Ρ
RNA
and s^G-Modined Precursor
tRNA
244
11.4.2.3
Generation and Isolation of Crosslinked RNAs
246
11.4.2.4
Primer Extension Mapping of crosslinked Nucleotides
247
11.4.3
Troubleshooting
249
References
250
12
Terbium(III) Footprinting as a Probe of
RNA
Structure and Metal
Binding Sites
255
Dinari
A. Harris, Gabrielk C. Todd, and Nils G. Walter
12.1
Introduction
255
12.2
Application Example
263
12.3
Troubleshooting
265
12.4
Frontiers in Footprinting Data Analysis
265
References
266
13
Pb^-lnduced Cleavage of
RNA
269
Leif A.
Kirsebom and
Jerzy Ciesiołka
13.1
Introduction
269
13.2
Pb2~-Induced Cleavage to Probe Metal Ion Binding Sites,
RNA
Structure, and
RNA—
Ligand Interactions
272
13.2.1
Probing High-Affinity Metal Ion Binding Sites
271
13.2.2
Pb^-Induced Cleavage and
RNA
Structure
273
13.2.3
Pfr^-Induced Cleavage to Study RNA-Ligand
Interactions
274
13.2.4
Pb2+-Induced Cleavage of
RNA
in Vivo
275
13.3
Troubleshooting
279
13.3.1
No Pb2~ -Induced Cleavage Detected
279
13.3.2
Complete Degradation of the
RNA
280
13.3.3
In Vivo
280
Acknowledgments
280
References
281
XII Contents
14
Identification
and Characterization of Metal Ion Coordination
interactions with
RNA
by Quantitative Analysis of Thiophilic Metal
Ion Rescue of Site-Specific Phosphorothioate
Modifications
285
Michael E. Harris
14.1
Introduction
285
14.1.1
Thiophilic Metal Ion Rescue of
RNA
Phosphorothioate
Modifications
286
14.2
Purification of Phosphorothioate Stereoisomers by RP-HPLC
290
14.3
Techniques for Incorporation of Phosphorothioates into
RNA
291
14.4
Kinetic Analysis of Thiophilic Metal Ion Rescue
293
14.5
Data Analysis by Fitting to Simple Equilibrium Models
295
References
297
15
Probing
RNA
Structure and Ligand Binding Sites on
RNA
by Fenton
Cleavage
301
Corina
G.
Heidrich and Christian Berens
15.1
Introduction
302
15.2
Comments and Troubleshooting
312
References
314
16
Measuring the Stoichiometry of Magnesium Ions Bound to
RNA
319
Andrew
J.
Andrews and Carol A. Fierke
16.1
Introduction
319
16.2
Separation of Free Mg2+ from RNA-bound Mg2+
320
16.3
Forced Dialysis Is the Preferred Method for Separating Bound
and Free Mg2+
321
16.4
Alternative Methods for Separating Free and Bound Mg2+ Ions
323
16.5
Determining the Concentration of Free Mg24 in the
Flow-Through
324
16.6
How to Determine the Concentration of Mg2+ Bound to the
RNA
and the Number of Binding Sites on the
RNA
324
16.7
Conclusion
327
16.8
Troubleshooting
327
References
327
17
Nudeotide Analog interference Mapping and Suppression
(NAI
M/NAIS):
a Combinatorial Approach to Study
RNA
Structure,
Folding, and Interaction with Proteins
329
Olga
Fedorova, Marc Boudvillain, and
Christina
Waldsich
17
Λ
Introduction
329
17.1.1
NAIM: a Combinatorial Approach for
RNA
Structure-Function
Analysis
329
17.1.1.1
Description of the Method
330
17.1.2
NAIS:
a Chemogenetic Tool for Identifying
RNA
Tertiary Contacts
and Interaction Interfaces
332
Contents XIII
17.1.2.1 General
Concepts
332
17.1.2.2 Applications:
Elucidating Tertiary Contacts in Group I and Group II
Ribozymes
332
17.2
Experimental Protocols for NAIM
333
17.2.1
Nucleoside Analog Thiotriphosphates
333
17.2.2
Preparation of Transcripts Containing Phosphorothioate
Analogs
335
17.2.2.1
Tips and Troubleshooting
336
17.2.3
Radioactive Labeling of the
RNA
Pool
337
17.2.4
The Selection Step of NAIM: Three Applications to Studies of
RNA
Function
339
17.2.4.1
Group II
Intron Ribozyme
Activity: Selection through
Transesterification
339
17.2.4.2
Group II Ribozyme Folding: Selection through Mg2+-Induced
Compaction of
RNA
344
17.2.4.3
RNA-
Protein Interactions: a One-Pot Reaction for Studying
Rlio-Independent Transcription Termination
347
17.2.4.4
RNA-
Protein Interactions: Elucidation of the Rho
Helicase
Activation
Mechanism via Unwinding Activity
351
17.2.5
Iodine Cleavage of
RNA
Pools
354
17.2.5.1
Experimental Procedure
355
17.2.5.2
Tips and Troubleshooting
355
17.2.6
Analysis and Interpretation of NAIM Results
355
17.2.6.1
Quantification of Interference Effects
355
17.3
Experimental Protocols for
NAIS
358
17.3.1
Design and Construction of
RN
A Mutants
358
17.3.1.1
General Considerations
358
17.3.1.2
Preparation of
RNA
Molecules Containing Single-Atom
Substitutions
359
17.3.2
Functional Analysis of Mutants for
NAIS
Experiments
362
17.3.3
The Selection Step for
NAIS
362
17.3.4
Data Analysis and Presentation
363
Acknowledgments
364
References
364
18
Nudeotide Analog Interference Mapping (NAIM): Application to the
R
Nase P
System
369
Simona
CiiziC Feltms and Roland K.
Hartmann
18.1
Introduction
369
18.1.1
Nudeotide Analog Interference Mapping (NAIM}
-
the
Approach
369
18.1.2
Critical Aspects of the Method
371
18.1.2.1
Analog Incorporation
371
18.1.2.2
Functional Assays
372
18.1.2.3
Factors Influencing the Outcome of NAIM Studies
372
XIV
I Contents
18.1.3
Interpretation of Results
3 73
18.2
NAIM Analysis of as-Cleaving RNase
P RNA-tRNA
Conjugates
375
18.2.1
Biochemical and kinetic characterization of a cis-Cleaving
E. coli
RNase
Ρ
RNA-tRNA Conjugate
375
18.2.2
Application Example
378
18.2.3
Data Evaluation
386
18.3
Troubleshooting
387
18.3.1
RNA
Transcription Reaction Did Not Work
387
18.3.2
RNA
Degradation
389
18.3.3
Inefficient
RNA
Elution from Denaturing PAA Gels
389
18.3.4
RNA
Is Degraded after Elution
389
18.3.5
Inefficient
3 -
or
5
-End-Labeling
389
18.3.6
Iodine-Induced Hydrolysis Failed or Was Inefficient
391
18.3.7
Unsatisfactory Gel Performance after Iodine Cleavage (Band
Smearing, Curved Bands, Irregular Shape of Bands, Unequal Band
Migration in Different Lanes, and Insufficient Band Separation)
392
References
393
19
Identification of Divalent Metal Ion Binding Sites in
RNA/DNA-Metabolizing Enzymes by Fe(ll)-Mediated Hydroxyl Radical
Cleavage
397
Yan-Guo
Ren, Niklas
Henriksson,
and Anders Virtanen
19.1
Introduction
397
19.2
Probing Divalent Metal Ion Binding Sites
398
19.2.1
Fe(II)-Mediated Hydroxyl Radical Cleavage
398
19.2.2
How to Map Divalent Metal Ion Binding Sites
399
19.2.3
How to Use Aminoglycosides as Functional and Structural
Probes
401
19.3
Notes and Troubleshooting
403
References
404
20
RNA
Structure and Folding Analyzed Using Small-Angle X-Ray
Scattering
407
Nathan J. Baud, Jeremey West, and
Tobin R,
Sosnick
20.1
Introduction
407
20.2
Description of Method
410
20.2.1
General Requirements
410
20.2.2
SAXS Application Example
411
20.2.3
General Information
412
20.2.4
Question
1:
The Global Conformation of the S-Domain Folding
Intermediate
412
20.2.5
Question
2:
The Stable, Extended Conformation of the S-Domain
Folding Intermediate
414
20.2.6
Question
3:
The Utility of Low-Resolution Real-Space Reconstructions
in
RNA
Modeling
4І6
Contents
XV
20.3
Troubleshooting
421
20.3.1 Problem 1: Radiation
Damage and Aggregation
421
20.3.2
Problem
2:
High Scattering Background
422
20.3.3
Problem
3:
Scattering Results Cannot Be Fit to Simple Models
422
20.4
Conclusions
-
Outlook
422
Acknowledgments
423
Abbreviations
423
References
423
21
Temperature-Gradient Gel Electrophoresis of
RNA
427
Dethv Riesner and Gerhard
Steger
21.1
Introduction
427
21.2
Method
428
21.2.1
Principle
428
21.2.2
Instruments
429
21.2.3
Handling
429
21.3
Optimization of Experimental Conditions
430
21.3.1
Pore Size of the Gel Matrix
430
21.3.2
Electric Field
430
21.3.3
Ionic Strength and Urea
431
21.4
TGGE
—
General Interpretation Rules
431
21.5
Examples of TGGE Applications
433
21.5.1
Example
1:
Analysis of Different
RNA
Molecules in a Single
TGGE
434
21.5.2
Example
2:
Analysis of Structure Transitions in a Single
RNA
-
Detection of Specific Structures by Oligonucleotide
Hybridization
435
21.5.3
Example
3:
Analysis of Mutants
438
21.5
A Example
4:
Detection of Protein-RNA Complexes by TGGE
439
21.5.5
Outlook
442
References
443
22
UV Melting Studies with
RNA
445
Philippe Dumas, Eric Ennifar, Francois Disdier, and Philippe Walter
22.1
Introduction
445
22.2
A Simplified Account of the Physical Basis of UV Absorption
445
22.3
Definitions and Nomenclature
446
22.4
Well-Known and Less Weil-Known Characteristics of UV Absorption
by Nucleic Acids Bases
447
22.5
The Basis of UV Melting Experiments for Thermodynamic
Studies
449
22.5.1
The Only Valid Definition of a Melting Temperature
450
22.5.2
Reminders
450
22.53
UnimoiecuJar Transitions
453
22.5
A Bimolecular Transitions
452
XVI
I Contents
22.5
АЛ
Entropie
Considerations
452
22.5.4.2
Basic
and Less Basic Equations about Melting Curves Involving
Bimolecular Transitions
454
22.5.4.3
Higher Order Transitions
455
22.5.4.4
Influence of the Temperature Dependence of the Absorbance
Parameters
455
22.5.4.5
The Different Ways of Obtaining Tm, AH, and AS
455
22.6
The Two-State Approximation and Its Limitations
459
22.7
Equilibrium and Non-equilibrium
459
22.8
A Common Pitfall with
S
elf-Complementary Sequences
460
22.9
Extracting Thermodynamic Information from Melting Curves of
Large RNAs
461
22.10
Parameters Influencing the Melting Temperature
462
22.11
Practical Problems
463
22.11.1
Evaporation during Heating: an Important Improvement
463
22.11.2
Sloping Baseline
464
22.12
A Neat Experimental Solution to the Sloping Baseline
468
22.12.1 pH
Variation and Buffers
468
22.12.2
RNA
Degradation
470
22.12.3
Heating Rate and Data Sampling
471
22.12.4
Experimental Data Processing
472
22.12.5
Softwares
473
Acknowledgment
473
Appendix A: Difference between Tm and
Гмах
and DMC
Normalization
473
Appendix B: Experimental Setup against Evaporation
475
Appendix C: The Subtleties with Partial Derivatives for ACp
Determination
475
Appendix D: Buffer pKa Variation with the Temperature
476
References
476
23
RNA Crystafïization
481
Jiro
Rondo, Claude
Sauter, and Benoît Masquida
23.1
Introduction
482
23.2
RNA
Purification
482
23.2.1
HPLC Purification
482
23.2.2
Gel Electrophoresis
483
23.2.3
RNA
Recovery
484
23.2.3.1
Elution
of the RNA
from the
Gel
484
23.2.3.2
Concentrating and Desalting
484
23.3
RNA
Crystallization
485
23.3.1
Renaturing the
RNA
485
23.3.2
Search for Crystallization Conditions
485
23.3.3
Evaluation of Crystallization Assays
488
23.3.4
The Optimization Process
489
Contents XVII
23.3.5
Designing
RNA
Constructs with Improved Crystallization
Capabilities
491
23.3.6
Crystallizing Complexes with Organic Ligands: the Example of
Aminoglycosides
493
23.4
Conclusions
494
References
495
24
Studying
RNA
Using Single Molecule Fluorescence Resonance Energy
Transfer
499
Felix Spenkuch,
Oliven
Domingo, Gerald
Hinze,
Thomas
Basche,
and Mark Helm
24.1
Introduction
499
24.1.1
The Advantages of Single Molecule Fluorescence Resonance Energy
Transfer
499
24.1.2
Chapter Scope
500
24.1.3
Typical Topics of
RNA
Dynamics Addressed by Single Molecule
FRET
500
24.2
Theory of Fluorescence Resonance Energy Transfer
502
24.3
Experimental Design
503
24.3.1
Considerations for Construct Design
503
24.4
smFRET Experiments Using Immobilized Molecules
505
24.4.1
Instrumental Setup
505
24.4.2
Means of Signal Correction and Data Analysis
505
24.4.3
The Choice of Dye Pairs for FRET
507
24.4.4
Buffer Handling in Single Molecule Experiments
508
24.4.5
Strategies for Dye Labeling of
RNA
Constructs 50H
24.4.6
Postsynthetic Labeling of Alkyne-Containing
RNA
Oligonucleotídes
509
24
АЛ
Tuning Dye Endurance:
Antifading
Agents
520
24.5
Troubleshooting
520
24.5.1
RNase Contamination
520
24.5.2
Removal of Unbound Fluorophores
521
24.5.3
Drying of Samples
521
24.5.4
Donor-Only Populations
521
24.5.5
Too Dense or Too Sparse Surface Coverage
521
References
522
25
Atomic Force Microscopy Imaging and Force Spectroscopy of
RNA
527
Malie BussieL· Antonie
Schone,
and Wolfgang
Nellen
ISA Introduction
527
25.2
AFM Imaging of
RNA
Structures
528
25.2.1
General Preconditions: Mode of Operation, Data Analysis, and
Resolution
528
25.2.2
Surface Preparation Conditions
531
XVIII
Contents
25.2.3
Imaging in Liquid
535
25.2.4
Experimental Example of Salt-Dependent
RNA
Folding Using a
Designed
RNA
Construct
535
25.3
Example Protocol:
RNA
Preparation for AFM Imaging in Air Using
PL-Coated Mica
537
25.4
Troubleshooting
538
25.5
Force Spectroscopy AFM
540
25.6
Outlook
544
Acknowledgments
544
References
544
|
| any_adam_object | 1 |
| author2 | Hartmann, Roland K. 1956- |
| author2_role | edt |
| author2_variant | r k h rk rkh |
| author_GND | (DE-588)12993643X |
| author_facet | Hartmann, Roland K. 1956- |
| building | Verbundindex |
| bvnumber | BV039877258 |
| ctrlnum | (OCoLC)876246137 (DE-599)BVBBV039877258 |
| dewey-full | 572.88 |
| dewey-hundreds | 500 - Natural sciences and mathematics |
| dewey-ones | 572 - Biochemistry |
| dewey-raw | 572.88 |
| dewey-search | 572.88 |
| dewey-sort | 3572.88 |
| dewey-tens | 570 - Biology |
| discipline | Biologie |
| edition | 2., completely rev. and enl. ed. |
| format | Book |
| fullrecord | <?xml version="1.0" encoding="UTF-8"?><collection xmlns="http://www.loc.gov/MARC21/slim"><record><leader>01706nam a2200421 cc4500</leader><controlfield tag="001">BV039877258</controlfield><controlfield tag="003">DE-604</controlfield><controlfield tag="005">20140718 </controlfield><controlfield tag="007">t</controlfield><controlfield tag="008">120209s2014 gw ad|| |||| 00||| eng d</controlfield><datafield tag="020" ind1=" " ind2=" "><subfield code="a">9783527327645</subfield><subfield code="c">print</subfield><subfield code="9">978-3-527-32764-5</subfield></datafield><datafield tag="020" ind1=" " ind2=" "><subfield code="a">9783527647064</subfield><subfield code="c">oBook</subfield><subfield code="9">978-3-527-64706-4</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(OCoLC)876246137</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(DE-599)BVBBV039877258</subfield></datafield><datafield tag="040" ind1=" " ind2=" "><subfield code="a">DE-604</subfield><subfield code="b">ger</subfield><subfield code="e">rakwb</subfield></datafield><datafield tag="041" ind1="0" ind2=" "><subfield code="a">eng</subfield></datafield><datafield tag="044" ind1=" " ind2=" "><subfield code="a">gw</subfield><subfield code="c">XA-DE-BW</subfield></datafield><datafield tag="049" ind1=" " ind2=" "><subfield code="a">DE-11</subfield><subfield code="a">DE-188</subfield><subfield code="a">DE-355</subfield><subfield code="a">DE-19</subfield><subfield code="a">DE-703</subfield></datafield><datafield tag="082" ind1="0" ind2=" "><subfield code="a">572.88</subfield></datafield><datafield tag="245" ind1="1" ind2="0"><subfield code="a">Handbook of RNA biochemistry</subfield><subfield code="n">1</subfield><subfield code="c">ed. by Roland K. Hartmann ...</subfield></datafield><datafield tag="250" ind1=" " ind2=" "><subfield code="a">2., completely rev. and enl. ed.</subfield></datafield><datafield tag="264" ind1=" " ind2="1"><subfield code="a">Weinheim</subfield><subfield code="b">WILEY-VCH</subfield><subfield code="c">2014</subfield></datafield><datafield tag="300" ind1=" " ind2=" "><subfield code="a">XLII, 546 S.</subfield><subfield code="b">Ill., graph. Darst.</subfield></datafield><datafield tag="336" ind1=" " ind2=" "><subfield code="b">txt</subfield><subfield code="2">rdacontent</subfield></datafield><datafield tag="337" ind1=" " ind2=" "><subfield code="b">n</subfield><subfield code="2">rdamedia</subfield></datafield><datafield tag="338" ind1=" " ind2=" "><subfield code="b">nc</subfield><subfield code="2">rdacarrier</subfield></datafield><datafield tag="500" ind1=" " ind2=" "><subfield code="a">Literaturangaben</subfield></datafield><datafield tag="650" ind1="0" ind2="7"><subfield code="a">RNS</subfield><subfield code="0">(DE-588)4076759-0</subfield><subfield code="2">gnd</subfield><subfield code="9">rswk-swf</subfield></datafield><datafield tag="655" ind1=" " ind2="7"><subfield code="0">(DE-588)4143413-4</subfield><subfield code="a">Aufsatzsammlung</subfield><subfield code="2">gnd-content</subfield></datafield><datafield tag="689" ind1="0" ind2="0"><subfield code="a">RNS</subfield><subfield code="0">(DE-588)4076759-0</subfield><subfield code="D">s</subfield></datafield><datafield tag="689" ind1="0" ind2=" "><subfield code="5">DE-604</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Hartmann, Roland K.</subfield><subfield code="d">1956-</subfield><subfield code="0">(DE-588)12993643X</subfield><subfield code="4">edt</subfield></datafield><datafield tag="773" ind1="0" ind2="8"><subfield code="w">(DE-604)BV019662557</subfield><subfield code="g">1</subfield></datafield><datafield tag="776" ind1="0" ind2="8"><subfield code="i">Erscheint auch als</subfield><subfield code="n">Online-Ausgabe, EPUB</subfield><subfield code="z">978-3-527-65054-5</subfield></datafield><datafield tag="776" ind1="0" ind2="8"><subfield code="i">Erscheint auch als</subfield><subfield code="n">Online-Ausgabe, MOBI</subfield><subfield code="z">978-3-527-65053-8</subfield></datafield><datafield tag="776" ind1="0" ind2="8"><subfield code="i">Erscheint auch als</subfield><subfield code="n">Online-Ausgabe, PDF</subfield><subfield code="z">978-3-527-65055-2</subfield></datafield><datafield tag="856" ind1="4" ind2="2"><subfield code="m">Digitalisierung UB Regensburg - ADAM Catalogue Enrichment</subfield><subfield code="q">application/pdf</subfield><subfield code="u">http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=024736458&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA</subfield><subfield code="3">Inhaltsverzeichnis</subfield></datafield><datafield tag="999" ind1=" " ind2=" "><subfield code="a">oai:aleph.bib-bvb.de:BVB01-024736458</subfield></datafield></record></collection> |
| genre | (DE-588)4143413-4 Aufsatzsammlung gnd-content |
| genre_facet | Aufsatzsammlung |
| id | DE-604.BV039877258 |
| illustrated | Illustrated |
| indexdate | 2024-07-10T00:13:13Z |
| institution | BVB |
| isbn | 9783527327645 9783527647064 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-024736458 |
| oclc_num | 876246137 |
| open_access_boolean | |
| owner | DE-11 DE-188 DE-355 DE-BY-UBR DE-19 DE-BY-UBM DE-703 |
| owner_facet | DE-11 DE-188 DE-355 DE-BY-UBR DE-19 DE-BY-UBM DE-703 |
| physical | XLII, 546 S. Ill., graph. Darst. |
| publishDate | 2014 |
| publishDateSearch | 2014 |
| publishDateSort | 2014 |
| publisher | WILEY-VCH |
| record_format | marc |
| spelling | Handbook of RNA biochemistry 1 ed. by Roland K. Hartmann ... 2., completely rev. and enl. ed. Weinheim WILEY-VCH 2014 XLII, 546 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Literaturangaben RNS (DE-588)4076759-0 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content RNS (DE-588)4076759-0 s DE-604 Hartmann, Roland K. 1956- (DE-588)12993643X edt (DE-604)BV019662557 1 Erscheint auch als Online-Ausgabe, EPUB 978-3-527-65054-5 Erscheint auch als Online-Ausgabe, MOBI 978-3-527-65053-8 Erscheint auch als Online-Ausgabe, PDF 978-3-527-65055-2 Digitalisierung UB Regensburg - ADAM Catalogue Enrichment application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=024736458&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Handbook of RNA biochemistry RNS (DE-588)4076759-0 gnd |
| subject_GND | (DE-588)4076759-0 (DE-588)4143413-4 |
| title | Handbook of RNA biochemistry |
| title_auth | Handbook of RNA biochemistry |
| title_exact_search | Handbook of RNA biochemistry |
| title_full | Handbook of RNA biochemistry 1 ed. by Roland K. Hartmann ... |
| title_fullStr | Handbook of RNA biochemistry 1 ed. by Roland K. Hartmann ... |
| title_full_unstemmed | Handbook of RNA biochemistry 1 ed. by Roland K. Hartmann ... |
| title_short | Handbook of RNA biochemistry |
| title_sort | handbook of rna biochemistry |
| topic | RNS (DE-588)4076759-0 gnd |
| topic_facet | RNS Aufsatzsammlung |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=024736458&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| volume_link | (DE-604)BV019662557 |
| work_keys_str_mv | AT hartmannrolandk handbookofrnabiochemistry1 |