Methods of DNA and RNA sequencing:
Gespeichert in:
| Format: | Buch |
|---|---|
| Sprache: | English |
| Veröffentlicht: |
New York
Praeger
1983
|
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | XIX, 458 S. Ill. |
| ISBN: | 0030591740 |
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Datensatz im Suchindex
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|---|---|
| adam_text | Methods of
DNA and RNA
Sequencing
Edited by
Sherman M Weissman, M D
CONTENTS
List of Contributors v
Preface xvii
Acknowledgments xix
NEW METHODS FOR CHEMICALLY SYNTHESIZING
DEOXYOLIGONUCLEOTIDES 1
Marvin H Caruthers
General outline of DNA chemical synthesis
methodologies 2
A procedure for the rapid chemical synthesis of
deoxyoligonucleotides 5
The support 6
The synthesis cycle 7
Isolation of deoxyoligonucleotides 11
Experimental section 13
General methods 13
Synthesis of the support 13
Synthesis of deoxynucleosidephosphoramidites 15
Outline of the synthesis cycle 16
Isolation of synthetic deoxyoligonucleotides 17
Acknowledgments 17
References 18
SYNTHETIC OLIGODEOXYRIBONUCLEOTIDES AS
PROBES FOR NUCLEIC ACIDS AND AS PRIMERS IN
SEQUENCE DETERMINATION 23
Michael Smith
Introduction
Background
Oligonucleotide length and duplex stability
Effect of base composition on oligonucleotide
duplex stability
Stability of oligodeoxyribonucleotide-
oligoribonucleotide duplexes
Influence of base-pair mismatch on oligonucleotide
duplex stability
Ionic strength, polyvalent cations, and
oligodeoxyribonucleotide duplex stability
Oligonucleotide duplexes form very rapidly
Length of a genetically unique oligonucleotide
Synthetic oligodeoxyribonucleotide as probe for
genomic DNA fragment purification
Oligodeoxyribonucleotides as probes for monitoring
isolation of a genomic DNA clone
Oligodeoxyribonucleotides as probes for monitoring
isolation of a cDNA clone
Oligodeoxyribonucleotides as primers for reverse
transcriptase to produce specific cDNA probes
Use of synthetic oligodeoxyribonucleotides to prepare
double-strand cDNAs
Oligodeoxyribonucleotides as primers for DNA
sequence determination
Use of synthetic oligodeoxyribonucleotides as primers
for RNA sequence determination
Conclusion
References
f i n
SEQUENCING DNA BY THE SANGER CHAIN
TERMINATION METHOD 69
G Nigel Godson
Introduction 69
Principle of primed synthesis sequencing and the
chain termination method 70
Use of the filamentous phage cloning vectors for
chain termination sequencing 73
A model system for sequencing a 2-kB piece of DNA 74
Special strategies in cloning and sequencing 77
Cloning DNA fragments in a directed
orientation 78
Cloning internal DNA fragments only 79
Subcloning in situ 79
Turning cloned fragments around 79
Use of internal primers 80
Checking the sequence with restriction enzymes 81
Problems of random sequencing 82
Strategies for sequencing large pieces of DNA
(10-100 kB) 82
Appendixes v 83
Acknowledgments 108
References 108
NUCLEOTIDE SEQUENCE OF DNA 113
Allan Marshall Maxam
Introduction 113
Sequencing bases in nucleic acids 114
Distinguishing the bases 115
Ordering nucleotides 116
Phase one: Tract and block methods 123
Pyrimidine tracts 125
Copying DNA into RNA 126
Ribosubstitution 128
Phase two: Wandering-spot methods 129
Phase three: Base-specific nested-segment methods 132
f The chemical method 133
Comparison and assessment of the chemical and
enzymatic methods of DNA sequencing 144
Double-stranded DNA 144
Single-stranded DNA 147
Amount and specific activity of DNA 147
Sequencing labor 148
Sequence accuracy 148
Biologically significant DNA ends and
modifications 149
References 150
Addendum by Sherman M Weissman, M D 164
References 166
SELECTED POSTLABELING PROCEDURES FOR BASE
COMPOSITION AND SEQUENCE ANALYSIS OF
NUCLEIC ACIDS 169
Erika Randerath amp; Kurt Randerath
Radioactive derivative (postlabeling) methods for
structural analysis of nucleic acids 169
Fluorography and screen-intensified autoradiography
for enhanced detection of radioisotopes (3H, P , 12S I)
on chromatograms or gels 173
General aspects 173
Materials 174
Fluorography for the detection of 3H on
thin-layer chromatograms 175
Detection of H in polyacrylamide, mixed
polyacrylamide/agarose, or agarose gels by
fluorography
Detection of 3 2P and 1 2 5I on chromatograms
or gels by screen-intensified autoradiography
3H derivative method for base analysis of RNA
General aspects
Outline of method
Materials
Procedure
Comments
Radioiodination method for ribonucleoside analysis
General aspects
Outline of method
Materials
Procedure
Comments
P derivative method for base analysis of normal
and mutagen/carcinogen-modified DNA
General aspects
Outline of method
Materials
Procedures
Comments
3H derivative method for sequence analysis of RNA
General aspects
Outline of method
Combined 3H/32P derivative method for sequence
analysis of RNA
General aspects
Outline of method
32P gel readout method entailing partial enzymatic
degradation of end-labeled RNA
General aspects
Outline of method
Materials
Procedures
Comments •
32P thin-layer readout method based on single-hit
chemical cleavages of RNA
General aspects
Outline of method
Materials
Procedure
Comments
Sequence analysis of large RNAs
Conclusions
Acknowledgments
References
CHARACTERIZATION OF MODIFIED NUCLEOSIDES
IN tRNA 235
Susumu Nishimura amp; Yoshiyuki Kuchino
Identification of modified nucleosides by two-
dimensional thin-layer cellulose chromatography
and paper chromatography 239
Identification of modified nucleosides by high-
pressure liquid chromatography (HPLC) 243
Analysis of modified nucleosides by mass spectrometry 243
Analysis of modified nucleotides by postlabeling
procedures 245
Identification of modified nucleotides during
tRNA sequencing 245
Identification of modified nucleotides in total
tRNA by the postlabeling procedure 251
Structural elucidation of unknown modified
nucleosides 252
X I I
Materials 254
References 255
DIRECT CHEMICAL METHOD FOR SEQUENCING
END-LABELED RIBONUCLEIC ACIDS 261
Debra A Peattie
Principles of the chemical RNA sequencing
reactions
Chemical base modification
Aniline-induced strand scission
End-labeling the RNA
3 -end-labeling with (5 -32P)pCp and T4 RNA
ligase
5 -end-labeling with 32P
Practical considerations
Base-specific chemical cleavage reactions
Procedures
Practical considerations
Using the chemical reactions to probe RNA
conformation
Guanosine reaction
Cytidine reaction
Adenosine reaction
Practical Considerations
Acknowledgments
References
Appendix
Outline for four base-specific reactions for
chemical sequencing of end-labeled RNA
molecules
Diagnostic table for aid in correcting
aberrant RNA seauencine natterns
THE STUDY OF PROTEIN-DNA BINDING SPECIFICITY:
DNase FOOTPRINTING 305
Albert Schmitz amp; David J Galas
Introduction 305
Bovine pancreatic deoxyribonuclease I (DNase I) 306
/• Description of the method 307
The reactions 310
Typical footprinting reaction 311
Assignment of the DNase I-produced bands 312
Other enzymes suitable for footprinting reactions 313
Interactions analyzed by footprinting 315
Footprint of lac repressor on operator DNA 315
Footprints of RNA polymerase on the lac
promoter 320
Footprints of CRP on the lac control region DNA 327
Footprint of DNA gyrase 331
Nuclease specificities 333
Extensions of the method 334
Concluding remarks 335
Acknowledgments 336
References 336
Addendum 344
TRANSCRIPTION INITIATION AND
TERMINATION SIGNALS 349
Thomas Shenk
Prokaryotic promoters 349
Eukaryotic RNA polymerases 351
Cell-free transcription by eukaryotic polymerases 351
Polymerase III 352
Polymerase II 352
xiv
Polymerase I 353
5 -ends and initiation sites 353
Polymerase III 353
Polymerase II 353
Polymerase I 354
Transcriptional control regions 355
Polymerase III 355
Polymerase II 357
Polymerase I 368
Regulation of transcription by eukaryotic polymerases 368
Polymerase III 370
Polymerase II 372
Polymerase I 374
Termination of transcription in prokaryotes 374
Termination of transcription in eukaryotes 375
Acknowledgments 377
References 377
SIGNALS FOR THE SPLICING OF EUKARYOTIC
MESSENGER RNA TRANSCRIPTS 399
Stephen M Mount amp; Joan A Steitz
Splice junction signals 400
Are junction signals sufficient? 410
The versatility of splicing 412
What recognizes splicing signals? 417
The biochemistry of splicing 419
Why splicing? 421
Acknowledgments 423
References 424
Index 437
XV
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| spelling | Methods of DNA and RNA sequencing ed. by Sherman M. Weissman New York Praeger 1983 XIX, 458 S. Ill. txt rdacontent n rdamedia nc rdacarrier Base Sequence DNA Analysis DNA analysis Nucleotide sequence RNA Analysis RNA analysis Methode (DE-588)4038971-6 gnd rswk-swf DNS-Sequenz (DE-588)4150352-1 gnd rswk-swf RNS (DE-588)4076759-0 gnd rswk-swf Sequenzanalyse Chemie (DE-588)4132277-0 gnd rswk-swf DNS (DE-588)4070512-2 gnd rswk-swf DNS (DE-588)4070512-2 s Sequenzanalyse Chemie (DE-588)4132277-0 s Methode (DE-588)4038971-6 s DE-604 RNS (DE-588)4076759-0 s DNS-Sequenz (DE-588)4150352-1 s Weissman, Sherman M. Sonstige oth HEBIS Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=000081528&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Methods of DNA and RNA sequencing Base Sequence DNA Analysis DNA analysis Nucleotide sequence RNA Analysis RNA analysis Methode (DE-588)4038971-6 gnd DNS-Sequenz (DE-588)4150352-1 gnd RNS (DE-588)4076759-0 gnd Sequenzanalyse Chemie (DE-588)4132277-0 gnd DNS (DE-588)4070512-2 gnd |
| subject_GND | (DE-588)4038971-6 (DE-588)4150352-1 (DE-588)4076759-0 (DE-588)4132277-0 (DE-588)4070512-2 |
| title | Methods of DNA and RNA sequencing |
| title_auth | Methods of DNA and RNA sequencing |
| title_exact_search | Methods of DNA and RNA sequencing |
| title_full | Methods of DNA and RNA sequencing ed. by Sherman M. Weissman |
| title_fullStr | Methods of DNA and RNA sequencing ed. by Sherman M. Weissman |
| title_full_unstemmed | Methods of DNA and RNA sequencing ed. by Sherman M. Weissman |
| title_short | Methods of DNA and RNA sequencing |
| title_sort | methods of dna and rna sequencing |
| topic | Base Sequence DNA Analysis DNA analysis Nucleotide sequence RNA Analysis RNA analysis Methode (DE-588)4038971-6 gnd DNS-Sequenz (DE-588)4150352-1 gnd RNS (DE-588)4076759-0 gnd Sequenzanalyse Chemie (DE-588)4132277-0 gnd DNS (DE-588)4070512-2 gnd |
| topic_facet | Base Sequence DNA Analysis DNA analysis Nucleotide sequence RNA Analysis RNA analysis Methode DNS-Sequenz RNS Sequenzanalyse Chemie DNS |
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