Handbook of RNA biochemistry 2
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| 245 | 1 | 0 | |a Handbook of RNA biochemistry |n 2 |c ed. by Roland K. Hartmann ... |
| 264 | 1 | |a Weinheim |b WILEY-VCH |c (2005) | |
| 300 | |a XXXI S., S. 491 - 931 |b Ill., graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 700 | 1 | |a Hartmann, Roland K. |d 1956- |0 (DE-588)12993643X |4 edt | |
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| adam_text | VII
Contents
Preface
List of Contributors
Volume
Part I RNA Synthesis
1.1
1
Heike
1.1
1.2
1.2.1
1.2.2
1.2.2.1
5
1.2.2.2
1.3
1.3.1
1.3.2
1.3.3
1.4
1.4.1
1.4.2
1.5
1.5.1
1.5.2
1.5.2.1
1.5.2.2
1.5.3
Handbook of RNA Biochemistry. Edited by R.
Copyright
ISBN:
VIH
Acknowledgement
References
2
Mario Mori, Esther
2.1
2.2
2.2.1
2.2.1.1
2.2.1.2
2.2.1.3
Groups
2.2.2
Ends
2.2.3
2.3
Troubleshooting
2.3.1
2.3.2
2.3.3
2.3.4
References
3
MikkoJ.
3.1
3.2
3.3
3.4
3.5
3.6
3.7
3.8
3.9
Acknowledgments
References
4
Tina Persson, Dagmar
4.1
4.2
4.2.1
4.2.2
4.2.3
4.3
Contents IX
4.3.1
End-labeling
4.3.2
Circularization
4.3.3
Intermolecular Ligation of Polynucleotides
4.4
T4
4.5
Application Examples and Protocols
4.5.1
Production of Full-length tRNAs
4.5.2
Specific Protocols
4.5.3
General Methods (GM)
4.5.4
Chemicals and Enzymes
4.5.4.1
Chemical Synthesis and Purification of Oligoribonucleotides
70
4.5.4.2
Chemicals
4.5.4.3
Enzymes
4.6
Troubleshooting
Acknowledgments
References
5
Including Photoreactive Croups into
Nathan H.
5.1
5.1.1
5.1.2
5.2
5.2.1
5.2.2
5
5.2.3
Phosphorothioate
5.2.4 3
5.3
References
6
Dagmar
6.1
6.2
6.3
6.3.1 3
6.3.1.1
6.3.1.2
6.3.2
3
6.3.3
6.3.3.1
6.3.3.2
XI Contents
6.3.4
6.4
6.4.1
6.4.2
6.4.3
References
1.2
7
Brian S. Sproat
7.1
7.2
7.2.1
7.2.1.1
7.2.1.2
7.2.2
7.2.2.1
7.2.2.2
7.2.2.3
723
7.2.3.1
7.2.3.2
7.2.3.3
7.2.3.4
7.2.4
7.3
References
8
Thomas E. Edwards and Snorri Th. Sigurdsson
8.1
8.1.1
8.1.2
8.2
8.2.1
8.2.1.1
8.2.1.2
8.2.1.3
8.3
8.3.1
8.3.2
8.3.3
8.3.4
8.3.5
References
Contents
Part II Structure
11.1
9
Methods
OlafCimple and
9.1
9.2
9.2.1
9.2.1.1
9.2.1.2
Assay
9.2.1.3
9.2.2
9.2.2.1 5
9.2.2.2 3
9.2.3
9.2.3.1
RNA
9.2.3.2
Cleavage
9.2.4
9.2.4.1
9.2.4.2
9.3
Acknowledgments
References
10
In Vivo
Eric Huntzinger, Maria Possedko,
Ehresmann and
10.1
10.2
10.2.1
10.2.2
10.2.3
10.3
10.3.1
10.3.2
10.3.3
RNA
10.3.4
10.3.5
10.3.6
XII Contents
10.3.6.1 In Vivo DMS
10.3.6.2 In Vivo Lead(II)-induced
10.4
10.4.1
10.4.2
10.5
10.5.1
10.5.2
Acknowledgments
References
11
Particles
Virginie
11.1
11.2
11.2.1
11.2.2
11.2.2.1
11.2.2.2
11.2.3
11.2.3.1
11.2.3.2
11.2.3.3
Coupled to a Second Gel Electrophoresis and Western Blot
Analysis
11.2.4
11.2.4.1
11.2.4.2
11.2.4.3
11.2.5
11.2.5.1
11.2.5.2
11.3
11.3.1
11.3.1.1
11.3.1.2
11.3.2
11.3.2.1
11.3.2.2
11.3.3
11.3.3.1
11.3.3.2
11.3.4
11.3.4.1
Contents XIII
11.4
11.4.1 RNP
11.4.2
11.4.3 UV Crosslinking 202
11.4.4 Immunoprecipitations 202
Acknowledgments
References
12 Terbium(lll) Footprinting
Sites
Dinari
12.1
12.2
12.2.1
12.3
12.4
References
13
LeifA. Kirsebom and
13.1
13.2
Structure and RNA-iigand Interactions
13.2.1
13.2.2
13.2.3
13.3
13.4
13.4.1
13.4.2
Acknowledgments
References
14
Christina
14.1
14.2
14.2.1
14.2.2
14.2.3
14.3
In Vivo
14.4
References
XIV Contents
15
Cesine
15.1
15.2
15.2.1
15.2.2
Reactions
15.3
References
16
A.J. Andrews and Carol Fierke
16.1
16.2
16.3
Magnesium Ions
16.4
Ions
16.5
Flow-through
16.6
RNA
16.7
16.8
References
17
Applications in Studies of
Mechanism and RNA-Protein Interactions
Olga
17.1
17.1.1
17.1.2
Analysis
17.1.2.1
17.1.2.2
17.1.3
Interaction Interfaces
17.1.3.1
17.1.3.2
Ribozymes
17.2
17.2.1
17..2.2
17.2.3
Contents
17.2.4
Function
17.2.4.1
Transesterification
17.2.4.2
17.2.4.3
Transcription Termination
17.2.5
17.2.6
17.2.6.1
17.3
17.3.1
17.3.2
17.3.3
173
Acknowledgments
References
18
System
Simona
18.1
18.1.1
Approach
18.1.2
18.1.2.1
18.1.2.2
18.1.2.3
18.1.3
18.1.4
18.2
18.2.1
Conjugate
18.2.2
18.2.3
18.2.4
18.2.5
18.3
References
19
Ion Rescue
Eric L Christian
19.1
19.2
19.2.1
XVI Contents
19.2.2
19.2.3
19.2.4
19.2.5
19.2.6
19.2.7
19.2.8
19.3
19.3.1
19.3.2
19.3.3
19.4
Acknowledgments
References
20
Enzymes by Fe(ll)-mediated Hydroxyl Radical Cleavage
Yan-Guo
20.1
20.2
20.2.1
20.2.2
20.2.3
Probes
20.3
20.4
References
21
Henning Urlaub,
21.1
21.2
21.3
21.4
Primer Extension Analysis
21.5
21.6
21.7
Acknowledgments
References
22
6-Thioguanosine
Michael E. Harris and Eric L Christian
22.1
22.2
Contents XVII
22.2.1
Interacting Species
22.2.2
22.2.3
22.3
References
11.2
23
X-ray Scattering
Tao Pan and
23.1
23.2
23.2.1
23.2.2
23.3
23.4
Holoenzyme
23.5
23.6
23.7
23.7.1
23.7.2
23.7.3
23.8
Acknowledgments
References
24
Detlev Riesner
24.1
24.2
24.2.1
24.2.2
24.2.3
24.3
24.3.1
TGGE
24.3.2
24.3.3
24.3.4
24.4
24.4.1
24.4.2
Specific Structures by Oligonucleotide Labeling
XVIII Contents
24.4.3
24
Detection of Protein-RNA Complexes
24.4.5
References
25
Andreas Werner
25.1
25.2
25.3
25.4
25.5
25.6
25.7
References
26
Jan Medenbach,
26.1
26.2
26.2.1
26.2.2
26.2.3
26.2.3.1
26.2.3.2
26.2.3.3
26.2.3.4
26.2.3.5
26.2.3.6
26.3
Centrifugation
26.3.1
26.3.2
26.3.3
26.3.3.1
26.3.3.2
26.3.3.3
26.3.3.4
Acknowledgments
References
27
Boris Francois,
27.1
Contents XIX
27.2 Design
27.3
27.3.1
27.3.2
27.3.3
27.3.3.1
27.3.3.2
27.4
27.4.1
27.4.2
27.43
Aminoglycosides
27.4.4
27.4.5
27.5
References
11.3
28
Filipp Oesterhelt, Enno Schwemberger and
28.1
28.2
28.2.1
28.3
Fluorescence
28.3.1
28.3.2
28.3.2.1
28.3.2.2
28.3.3
28.3.3.1
28.3.3.2
28.4
28.4.1.1
28.4.1.2
28.4.1.3
28.5
28.5.1
28.5.2
28.5.2.1
28.5.2.2
28.5.2.3
28.5.2.4
28.5.3
28.5.3.1
XX I Contents
28.5.3.2
28.5.3.3
28.5.4
28.5.4.1
28.5.4.2
28.5.5
28.6
28.6.1.1
28.6.1.2
28.6.1.3
28.6.1.4
28.6.1.5
References
29
Wolfgang
29.1
29.2
29.3
29.4
29.5
29.6
29.7
29.8
Acknowledgments
References
Volume
Part III
30
James W. Brown and], Christopher Ellis
30.1
30.1.1
30.1.2
30.1.3
30.1.4
30.2
30.2.1
30.2.2
30.2.3
30.2.4
30.2.5
30.2.6
Contents XXI
30.2.7 Subapical
30.2.8 Potential
30.2.9
30.2.10
30.3
Acknowledgments
References
31
Gerhard
31.1
31.2
31.3
31.4
31.4.1
31.4.1.1
31.4.1.2
31.4.1.3
31.4.1.4
31.4.1.5
31.4.2
31.4.2.1
31.4.2.2
31.4.2.3
31.4.2.4
31.4.2.5
31.4.2.6
31.4.2.7
31.5
31.5.1
31.5.1.1
31.5.1.2
31.5.1.3
31.5.2
31.5.2.1
31.5.2.2
31.5.2.3
31.5.2.4
31.6
References
32
Hierarchical Framework
Benoît
32.1
XXII Contents
32.2
32.2.1
32.2.1.1
32.2.1.2
32.2.1.3
32.2.1.4
32.3
References
33
Jason A Mean, Scott M. Stagg and Stephen
33.1
33.2
33.2.1
33.2.2
33.2.3
33.2.4
33.2.5
33.3
33.3.1
33.3.2
Representation
33.4
33.5
References
34
Pascal
34.1
34.2
34.3
34.3.1
34.3.1.1
34.3.1.2
34.3.1.3
34.3.2
34.3.2.1
34.3.2.2
34.3.2.3
34.3.3
34.3.4
34.3.5
34.3.5.1
34.3.5.2
34.3.5.3
Contents XXIII
34.3.6
34.3.6.1
34.3.6.2
34.3.6.3
34.3.6.4
34.3.7
34.3.8
34.3.8.1
34.3.8.2
34.3.8.3
34.3.8.4
34.3.9
34.3.10
34.3.10.1
34.3.10.2
34.3.10.3
34.4
34.4.1
34.4.1.1
34.4.1.2
34.4.1.3
34.4.2
34.4.3
34.4.4
34.5
Acknowledgments
References
35
Matthieu Legendre
35.1
35.2
35.3
35.4
35.5
35.6
35.7
35.8
35.8.1
35.8.1.1
35.8.1.2
35.8.2
35.8.2.1
35.8.2.2
Acknowledgments
References
XXIV
I
36
36.1
36.2
36.2.1
36.2.2
36.2.3
36.2.4
36.2.5
36.2.6
36.2.7
36.2.8
36.3
37
37.1
37.2
37.2.1
37.2.2
37.2.3
37.2.4
37.2.5
37.2.6
37.2.7
37.2.8
37.2.9
37.2.10
37.2.11
37.3
37.3.1
37.3.2
37.3.3
37.3.4
37.3.5
37.4
37.5
Approaches to Identify Novel Non-messenger RNAs in Bacteria and to
Investigate their Biological Functions:
Jörg Vogel
Introduction
Searching for Small, Untranslated RNAs
Introduction
Direct Labeling and Direct Cloning
Functional Screens
Biocomputational Screens
Microarray Detection
Shotgun Cloning (RNomks)
Co-purification with Proteins or Target RNAs
Screens for Cis-encoded Antisense RNAs
Conclusions
Acknowledgments
References
Approaches to Identify Novel Non-messenger RNAs in Bacteria and to
Investigate their Biological Functions: Functional Analysis of Identified
Non-mRNAs
E. Cerhart H. Wagner and
Introduction
Approaches for Elucidation of Bacterial sRNA Function
Large-scale Screening for Function
Preparing for Subsequent Experiments: Strains and Plasmids
Experimental Approaches
Physiological Phenotypes (Lethality, Growth Defects, etc.)
Analyzing sRNA Effects on Specific mRNA Levels by Microarrays
Analyzing sRNA Effects by Proteomics
Analyzing sRNA Effects by Metabolomics
Finding Targets by Reporter Gene Approaches
Bioinformatics-aided Approaches
Prediction of Regulatory Sequences in the Vicinity of sRNA Gene
Promoters
Finding Interacting Sites (Complementarity/Antisense)
Additional Methods Towards Functional and Mechanistic
Characterizations
Finding sRNA-associated Proteins
Regulation of the Target
Northern Analyses
Analysis of sRNAs
Structures of sRNAs and Target RNAs
Conclusions
Protocols
Acknowledgments
References
Contents XXV
38
in Model Organisms
Alexander
38.1
38.2
38.2.1
38.2.2
38.2.3
38.2.4
38.3
38.4
38.5
Acknowledgments
References
39
Young-Soo Ku/on, Hai-Ri Li and Xiang-Dong
39.1
39.2
39.3
39.3.1
39.3.2
39.3.3
39.3.4
39.3.5
39.3.6
39.3.7
39.3.8
39.4
39.4.1
39.4.2
References
IV Analysis of
IV.l RNA-Protein Interactions in vitro
40
Proteins
Steffen Schiffer,
Anita
40.1
40.2 Materials 668
40.2.1 CNBr-activated Sepharose 4B
40.2.2 NHS-activated HiTrap
40.3
XXVI Contents
40.3.1
40.3.2
40.4
40.4.1
40.5
References
41
Zsofia Palfi, Jingyi
41.1
41.2
41.2.1
41.2.2
41.2.3
41.2.4
41.2.5
41.3
41.3.1
41.3.1.1
(Pre-dearing)
41.3.1.2
41.3.1.3
41.3.1.4
Strategy
41.3.2
RNAs
41.4
41.4.1
41.4.2
41.4.3
Low
41.4.4
Background is Too High
References
42
Ribonucleoprotein Complexes
Cindy L Will, Evgeny M. Makarov,
42.1
42.2
42.3
42.4
42.5
Complexes
42.6
Anti-peptide Antibodies against the SKIP Protein
Contents XXVII
Acknowledgments
References
43
from cDNA Expression Libraries and the Analysis of RNA-Protein
Interactions
Angel
43.1
43.2
43.2.1
43.2.1.1
43.2.1.2
43.2.1.3
43.2.2
Proteins from cDNA Expression Libraries
43.2.2.1
43.2.2.2
43.2.2.3
43.2.2.4
43.2.2.5
43.2.2.6
43.2.3
Protein Interactions
43.2.3.1
43.2.3.2
43.2.3.3
43.2.3.4
43.3
43.3.1
43.3.2
43.3.3
43.3.4
43.3.5
43.3.6
43.3.7
43.3.8
43.3.9
References
IV.2 RNA-Protein Interactions in vivo
44
in Cell Nuclei
Jennifer
44.1
44.2
XXVIII Contents
44.2.1
44.2.2
44.2.2.1
44.2.2.2
44.2.3
44.2.4
Acknowledgments
References
45
Three-hybrid Analysis
Felicia Scott and David R. Engelke
45.1
45.2
45.3
45.3.1
45.3.2
45.3.3
45.3.3.1
45.3.4
45.3.4.1
45.3.5
45.4
45.4.1
45.4.2
45.4.3
45.5
45.6
45.7
Acknowledgments
References
46
Yesheng Tang, Tatyana Novoyatleva, Nota/ya Benderska, Shivendra Kishore,
Alphonse Thanaraj
46.1
46.2
46.3
46.3.1
46.3.2
46.3.3
46.3.3.1
4(>.Ъ.Ъ2
46.3.4
46.3.5
46.3.6
Contents XXIX
46.4
46.5
46.6
References
IV.3 SELEX
47
Ico
Mali Illangasekare, Vasant Jadhav,
Jeremy
47.1
47.2
AT.
47.2.2
47.2.3
47.2.4
47.3
Al
47.3.2
47.3.3
Al
47.4.1
47.4.2
47A3
47.4.4
47.4.5
47.4.6
47.4.7
47.5
47.5.1
47.5.2
47.5.3
47.5.4
47.5.5
Acknowledgments
References
48
Carbohydrates
C. Stefan Vb rtier and Maria
48.1
48.2
48.2.1
48.2.1.1
48.2.1.2
XXX Contents
48.2.2
48.2.3
48.2.4
48.3
48.4
48.5
48.6
Acknowledgments
References
49
Thomas A Cooper
49.1
49.2
49.2.1
49.2.2
49.2.3
49.2.4
Splicing Enhancers
49.2.5
49.3
Acknowledgments
References
50
Dirk Eulberg, Christian Maasch, Werner C. Purschke and
50.1
50.2
50.2.1
50.2.1.1
50.2.1.2
50.2.1.3
50.2.2
50.3
50.3.1
50.3.2
50.4
50.4.1
50.4.2
50.4.3
50.5
50.6
50.6.1
50.6.2
50.6.3
References
Contents XXXI
51 SELEX
Heterogeneous Nuclear Ribonucleoprotein Complexes
Martin Lützelberger,
51.1
51.1.1
51.1.2
51.2
51.2.1
DNA 883
51.2.2
51.3
51.4
Ligands
51.5
51.6
51.6.1
51.6.2
51.6.3
51.6.4
51.6.5
51.6.6
51.7
References
V RNAi
52
Short Interfering RNAs
Matthias John,
Olaf Heidenreich
52.1
52.2
52.3
52.3.1
52.3.1.1
52.3.1.2
52.3.1.3
52.3.2
52.3.3
52.3.4
52.4
References
Appendix: UV Spectroscopy for the
Index
|
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