The Resource Structures of large RNA molecules and their complexes, edited by Sarah A. Woodson, Frédéric H. T. Allain

Structures of large RNA molecules and their complexes, edited by Sarah A. Woodson, Frédéric H. T. Allain

Label
Structures of large RNA molecules and their complexes
Title
Structures of large RNA molecules and their complexes
Statement of responsibility
edited by Sarah A. Woodson, Frédéric H. T. Allain
Contributor
Editor
Subject
Genre
Language
  • eng
  • eng
Summary
This new volume of <i>Methods in Enzymology</i> continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers research methods in RNA folding and dynamics, RNA-protein interactions and large RNPs.<br><br><ul><li>Continues the legacy of this premier serial with quality chapters on structures of large RNA molecules and their complexes</li></ul>
Member of
Cataloging source
MiAaPQ
Dewey number
572.88
Illustrations
  • illustrations
  • plates
Index
index present
Language note
English
LC call number
QP623
LC item number
.S778 2015
Literary form
non fiction
Nature of contents
  • dictionaries
  • bibliography
http://library.link/vocab/relatedWorkOrContributorName
  • Woodson, Sarah A.
  • Allain, Frédéric H. T.
Series statement
Methods in Enzymology
Series volume
Volume 558
http://library.link/vocab/subjectName
RNA
Label
Structures of large RNA molecules and their complexes, edited by Sarah A. Woodson, Frédéric H. T. Allain
Instantiates
Publication
Copyright
Note
Description based upon print version of record
Bibliography note
Includes bibliographical references at the end of each chapters and indexes
Carrier category
online resource
Carrier category code
cr
Content category
text
Content type code
txt
Contents
  • Front Cover; Structures of Large RNA Molecules and Their Complexes; Copyright; Contents; Contributors; Preface; Section I: RNA Structure and Dynamics; Chapter 1: Native Purification and Analysis of Long RNAs; 1. Introduction; 2. Native Purification of Long Noncoding RNAs; 2.1. Construct design; 2.2. DNA plasmid linearization; 2.3. In vitro transcription of RNA; 2.4. DNase digestion; 2.5. Proteinase K treatment; 2.6. EDTA chelation of divalent ions (optional); 2.7. Buffer exchange and purification; 2.8. Size-exclusion chromatography
  • 3. Study of the RNA Tertiary Folding by Sedimentation Velocity Analytical Ultracentrifugation3.1. Preparation of samples for a study of RNA folding; 3.2. Assembly of the optical cells, sample loading, and instrument setup; 3.3. Setting up a sedimentation velocity experiment; 3.4. Data analysis; 4. Analysis of the RNA Tertiary Folding by Analytical Size-Exclusion Chromatography; 5. Determination of the Secondary Structure of LncRNAs by Chemical Probing; 5.1. Designing and coupling of primers; 5.2. Generation of sequencing ladders; 5.3. SHAPE reaction; 5.4. DMS reaction
  • 5.5. Primer extension reaction5.6. Reactions for mobility shift correction; 5.7. Spectral calibration of the instrument; 5.8. Preparation of samples for capillary electrophoresis; 5.9. Data analysis; 5.9.1. Determination of chemical probing reactivity profiles; 5.9.2. Normalization of SHAPE and DMS reactivity profiles; 5.9.3. RNA secondary structure prediction and analysis; Acknowledgments; References; Chapter 2: Characterizing RNA Excited States Using NMR Relaxation Dispersion; 1. Introduction; 2. NMR Relaxation Dispersion; 2.1. Chemical Exchange; 2.2. RD Experiments
  • 2.3. R1ρ with Low-to-High SL Fields3. General Protocol for Characterizing RNA ESs Using Low-to-High SL Field 13C and 15N Off-Resonance NMR R1ρ and Uniformly...; 3.1. Construct Design; 3.2. Sample Preparation and Purification; 3.3. Protocol for Measuring R1ρ RD in Uniformly Labeled Nucleic Acids; 3.3.1. Calibrating SL Power; 3.3.2. Measurement of 15N R1ρ Data; 3.3.3. Measurement of 13C R1ρ Data; 3.3.4. Trouble Shooting R1ρ; 3.4. Data Analysis; 3.4.1. Fitting Monoexponentials to Obtain R1ρ Values; 3.4.2. Fitting Off-Resonance R1ρ Data Using Algebraic Equations
  • 3.4.3. Fitting Off-Resonance R1ρ Data Using Bloch-McConnell Equations3.4.4. Determining the Chemical Shifts of the ES; 3.4.5. Plotting RD Profiles; 3.4.6. Estimating Uncertainties in Exchange Parameters; 3.4.7. Kinetic-Thermodynamic Analysis; 3.5. Inferring Structures of RNA ESs Using NMR Chemical Shifts and Secondary Structure Prediction; 3.5.1. 13C and 15N Chemical Shift-Structure Relationships in RNA; 3.5.2. Secondary Structure Prediction; 3.6. Testing Model RNA ESs; 3.6.1. Stabilizing GS and ES Using Mutations; 3.6.2. Stabilizing GS and ES Using Single-Atom Substitutions
  • 3.6.3. Stabilizing GS and ES by Changing pH
Dimensions
unknown
Edition
First edition.
Extent
1 online resource (675 p.)
Form of item
online
Isbn
9780128019344
Media category
computer
Media type code
c
Specific material designation
remote
System control number
  • (CKB)3710000000421220
  • (EBL)2066259
  • (SSID)ssj0001540855
  • (PQKBManifestationID)11831138
  • (PQKBTitleCode)TC0001540855
  • (PQKBWorkID)11534236
  • (PQKB)11762177
  • (MiAaPQ)EBC2066259
  • (EXLCZ)993710000000421220
Label
Structures of large RNA molecules and their complexes, edited by Sarah A. Woodson, Frédéric H. T. Allain
Publication
Copyright
Note
Description based upon print version of record
Bibliography note
Includes bibliographical references at the end of each chapters and indexes
Carrier category
online resource
Carrier category code
cr
Content category
text
Content type code
txt
Contents
  • Front Cover; Structures of Large RNA Molecules and Their Complexes; Copyright; Contents; Contributors; Preface; Section I: RNA Structure and Dynamics; Chapter 1: Native Purification and Analysis of Long RNAs; 1. Introduction; 2. Native Purification of Long Noncoding RNAs; 2.1. Construct design; 2.2. DNA plasmid linearization; 2.3. In vitro transcription of RNA; 2.4. DNase digestion; 2.5. Proteinase K treatment; 2.6. EDTA chelation of divalent ions (optional); 2.7. Buffer exchange and purification; 2.8. Size-exclusion chromatography
  • 3. Study of the RNA Tertiary Folding by Sedimentation Velocity Analytical Ultracentrifugation3.1. Preparation of samples for a study of RNA folding; 3.2. Assembly of the optical cells, sample loading, and instrument setup; 3.3. Setting up a sedimentation velocity experiment; 3.4. Data analysis; 4. Analysis of the RNA Tertiary Folding by Analytical Size-Exclusion Chromatography; 5. Determination of the Secondary Structure of LncRNAs by Chemical Probing; 5.1. Designing and coupling of primers; 5.2. Generation of sequencing ladders; 5.3. SHAPE reaction; 5.4. DMS reaction
  • 5.5. Primer extension reaction5.6. Reactions for mobility shift correction; 5.7. Spectral calibration of the instrument; 5.8. Preparation of samples for capillary electrophoresis; 5.9. Data analysis; 5.9.1. Determination of chemical probing reactivity profiles; 5.9.2. Normalization of SHAPE and DMS reactivity profiles; 5.9.3. RNA secondary structure prediction and analysis; Acknowledgments; References; Chapter 2: Characterizing RNA Excited States Using NMR Relaxation Dispersion; 1. Introduction; 2. NMR Relaxation Dispersion; 2.1. Chemical Exchange; 2.2. RD Experiments
  • 2.3. R1ρ with Low-to-High SL Fields3. General Protocol for Characterizing RNA ESs Using Low-to-High SL Field 13C and 15N Off-Resonance NMR R1ρ and Uniformly...; 3.1. Construct Design; 3.2. Sample Preparation and Purification; 3.3. Protocol for Measuring R1ρ RD in Uniformly Labeled Nucleic Acids; 3.3.1. Calibrating SL Power; 3.3.2. Measurement of 15N R1ρ Data; 3.3.3. Measurement of 13C R1ρ Data; 3.3.4. Trouble Shooting R1ρ; 3.4. Data Analysis; 3.4.1. Fitting Monoexponentials to Obtain R1ρ Values; 3.4.2. Fitting Off-Resonance R1ρ Data Using Algebraic Equations
  • 3.4.3. Fitting Off-Resonance R1ρ Data Using Bloch-McConnell Equations3.4.4. Determining the Chemical Shifts of the ES; 3.4.5. Plotting RD Profiles; 3.4.6. Estimating Uncertainties in Exchange Parameters; 3.4.7. Kinetic-Thermodynamic Analysis; 3.5. Inferring Structures of RNA ESs Using NMR Chemical Shifts and Secondary Structure Prediction; 3.5.1. 13C and 15N Chemical Shift-Structure Relationships in RNA; 3.5.2. Secondary Structure Prediction; 3.6. Testing Model RNA ESs; 3.6.1. Stabilizing GS and ES Using Mutations; 3.6.2. Stabilizing GS and ES Using Single-Atom Substitutions
  • 3.6.3. Stabilizing GS and ES by Changing pH
Dimensions
unknown
Edition
First edition.
Extent
1 online resource (675 p.)
Form of item
online
Isbn
9780128019344
Media category
computer
Media type code
c
Specific material designation
remote
System control number
  • (CKB)3710000000421220
  • (EBL)2066259
  • (SSID)ssj0001540855
  • (PQKBManifestationID)11831138
  • (PQKBTitleCode)TC0001540855
  • (PQKBWorkID)11534236
  • (PQKB)11762177
  • (MiAaPQ)EBC2066259
  • (EXLCZ)993710000000421220

Library Locations

  • Albert D. Cohen Management LibraryBorrow it
    181 Freedman Crescent, Winnipeg, MB, R3T 5V4, CA
    49.807878 -97.129961
  • Architecture/Fine Arts LibraryBorrow it
    84 Curry Place, Winnipeg, MB, CA
    49.807716 -97.136226
  • Archives and Special CollectionsBorrow it
    25 Chancellors Circle (Elizabeth Dafoe Library), Room 330, Winnipeg, MB, R3T 2N2, CA
    49.809961 -97.131878
  • Bibliothèque Alfred-Monnin (Université de Saint-Boniface)Borrow it
    200, avenue de la Cathédrale, Local 2110, Winnipeg, MB, R2H 0H7, CA
    49.888861 -97.119735
  • Bill Larson Library (Grace Hospital)Borrow it
    300 Booth Drive, G-227, Winnipeg, MB, R3J 3M7, CA
    49.882400 -97.276436
  • Carolyn Sifton - Helene Fuld Library (St. Boniface General Hospital)Borrow it
    409 Tache Avenue, Winnipeg, MB, R2H 2A6, CA
    49.883388 -97.126050
  • Concordia Hospital LibraryBorrow it
    1095 Concordia Avenue, Winnipeg, MB, R2K 3S8, CA
    49.913252 -97.064683
  • Donald W. Craik Engineering LibraryBorrow it
    75B Chancellors Circle (Engineering Building E3), Room 361, Winnipeg, MB, R3T 2N2, CA
    49.809053 -97.133292
  • E.K. Williams Law LibraryBorrow it
    224 Dysart Road, Winnipeg, MB, R3T 5V4, CA
    49.811829 -97.131017
  • Eckhardt-Gramatté Music LibraryBorrow it
    136 Dafoe Road (Taché Arts Complex), Room 257, Winnipeg, MB, R3T 2N2, CA
    49.807964 -97.132222
  • Elizabeth Dafoe LibraryBorrow it
    25 Chancellors Circle, Winnipeg, MB, R3T 2N2, CA
    49.809961 -97.131878
  • Fr. H. Drake Library (St. Paul's College)Borrow it
    70 Dysart Road, Winnipeg, MB, R3T 2M6, CA
    49.810605 -97.138184
  • J.W. Crane Memorial Library (Deer Lodge Centre)Borrow it
    2109 Portage Avenue, Winnipeg, MB, R3J 0L3, CA
    49.878000 -97.235520
  • Libraries Annex (not open to the public; please see web page for details)Borrow it
    25 Chancellors Circle (in the Elizabeth Dafoe Library), Winnipeg, MB, R3T 2N2, CA
    49.809961 -97.131878
  • Neil John Maclean Health Sciences LibraryBorrow it
    727 McDermot Avenue (Brodie Centre), 200 Level, Winnipeg, MB, R3E 3P5, CA
    49.903563 -97.160554
  • Sciences and Technology LibraryBorrow it
    186 Dysart Road, Winnipeg, MB, R3T 2M8, CA
    49.811526 -97.133257
  • Seven Oaks General Hospital LibraryBorrow it
    2300 McPhillips Street, Winnipeg, MB, R2V 3M3, CA
    49.955177 -97.148865
  • Sister St. Odilon Library (Misericordia Health Centre)Borrow it
    99 Cornish Avenue, Winnipeg, MB, R3C 1A2, CA
    49.879592 -97.160425
  • St. John's College LibraryBorrow it
    92 Dysart Road, Winnipeg, MB, R3T 2M5, CA
    49.811242 -97.137156
  • Victoria General Hospital LibraryBorrow it
    2340 Pembina Highway, Winnipeg, MB, R3T 2E8, CA
    49.806755 -97.152739
  • William R Newman Library (Agriculture)Borrow it
    66 Dafoe Road, Winnipeg, MB, R3T 2R3, CA
    49.806936 -97.135525
Processing Feedback ...