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Nucleic Acids in Chemistry and Biology
Edited by
G Michael Blackburn;
G Michael Blackburn
University of Sheffield, UK
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Michael J Gait;
Michael J Gait
MRC Laboratory of Molecular Biology (LMB), UK
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Jonathan K Watts
Jonathan K Watts
University of Massachusetts, USA
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Hardback ISBN:
978-1-78801-904-0
EPUB ISBN:
978-1-83916-324-1
PDF ISBN:
978-1-83767-132-8
Product Type:
Textbooks
Publication date:
24 Jun 2022
Chapter Contents
- 15.1 Spectroscopic Techniques
- 15.1.1 UV Absorption
- 15.1.2 Fluorescence
- 15.1.3 Circular and Linear Dichroism
- 15.1.4 Infrared and Raman Spectroscopy
- 15.2 Nuclear Magnetic Resonance
- 15.3 Mass Spectrometry
- 15.3.1 Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry
- 15.3.2 Electrospray Ionization Mass Spectrometry
- 15.4 Diffraction Techniques
- 15.4.1 X-Ray Fibre Diffraction
- 15.4.2 Single Crystal X-Ray Crystallography
- 15.4.3 Neutron Diffraction
- 15.4.4 Electron Diffraction
- 15.5 Cryogenic Electron Microscopy (Cryo-EM)
- 15.5.1 The Basics of Cryo-EM
- 15.5.2 Brief History and Recent Advances that Propelled Cryo-EM as a Method
- 15.5.3 The Power of Single-Particle Cryo-EM: High Resolution and Structural Ensembles Resolve Individual Nucleotides and Reconstruct Molecular Mechanisms
- 15.5.4 Negative-Stain EM and Electron Tomography
- 15.6 Optical Microscopy of Nucleic Acids
- 15.6.1 Fluorescence Microscopy of Nucleic Acids
- 15.6.2 Fluorescence In Situ Hybridization (FISH)
- 15.6.3 Super-Resolution Microscopy – DNA-Paint
- 15.6.4 Förster Resonance Energy Transfer (FRET) in Nucleic Acids
- 15.7 Atomic Force Microscopy
- 15.8 Electrophoresis
- 15.8.1 Principles of Electrophoresis
- 15.8.2 Electrophoresis and Topology
- 15.8.3 Electrophoretic Mobility Shift Assay (EMSA)
- 15.8.4 Pulsed Field Electrophoresis
- 15.8.5 Capillary Electrophoresis
- 15.9 Chromatographic Methods
- 15.9.1 Reverse-Phase HPLC
- 15.9.2 Ion-Exchange HPLC
- 15.9.3 Size-Exclusion Chromatography
- 15.10 Centrifugation
- 15.11 Light Scattering Techniques
- 15.11.1 Static Light Scattering
- 15.11.2 Dynamic Light Scattering
- 15.11.3 Small Angle X-ray Scattering
- 15.12 Thermodynamic Analysis of Nucleic Acids
- 15.12.1 UV Melting Assay
- 15.12.2 Calorimetry
- 15.13 Molecular Mechanics and Dynamics
- 15.13.1 Molecular Mechanics and Nucleic Acid Force Fields
- 15.13.2 Conformational Ensemble and Energy Minimization
- 15.13.3 Molecular Dynamics Can Elucidate the Full Conformational Ensemble
- 15.14 QM/MM Methods for Modelling Nucleic Acids Reactions
- 15.14.1 Overview of the QM/MM Method
- 15.14.2 QM/MM Studies of DNA Repair
- References
Book Chapter
CHAPTER 15: Online Content: Physical and Structural Techniques Applied to Nucleic Acids
By
Yitzhak Tor
;
Yitzhak Tor
Department of Chemistry and Biochemistry, University of California
San Diego
La Jolla
CA
92093
USA
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Kalle Gehring
;
Kalle Gehring
Department of Biochemistry, McGill University
Montreal
QC
H3G 0B
Canada
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Daniele Fabris
;
Daniele Fabris
Department of Chemistry, University of Connecticut
Storrs
CT
06269
USA
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Martin Egli
;
Martin Egli
Department of Biochemistry, Vanderbilt University, School of Medicine
Nashville
TN
37232
USA
[email protected]
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Andrei A. Korostelev
;
Andrei A. Korostelev
RNA Therapeutics Institute, University of Massachusetts Medical School
Worcester
MA
01605
USA
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Timothy D. Craggs
;
Timothy D. Craggs
Department of Chemistry, University of Sheffield
Sheffield
S3 7HF
UK
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Alice Pyne
;
Alice Pyne
Department of Chemistry, University of Sheffield
Sheffield
S3 7HF
UK
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Keith T. Gagnon
;
Keith T. Gagnon
Department of Biochemistry and Molecular Biology, School of Medicine, Southern Illinois University
Carbondale
IL
62901
USA
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Jonathan K. Watts
;
Jonathan K. Watts
RNA Therapeutics Institute, University of Massachusetts Medical School
Worcester
MA
01605
USA
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Thomas E. Cheatham III
;
Thomas E. Cheatham III
Department of Medicinal Chemistry, University of Utah, College of Pharmacy
Salt Lake City
UT
84112
USA
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Nigel G. J. Richards
Nigel G. J. Richards
School of Chemistry, Cardiff University
Park Place
Cardiff
CF10 3AT
UK
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-
Published:24 Jun 2022
-
Product Type: Textbooks
Page range:
E1 - E50
Citation
Y. Tor, K. Gehring, D. Fabris, M. Egli, A. A. Korostelev, T. D. Craggs, ... N. G. J. Richards, in Nucleic Acids in Chemistry and Biology, ed. G. M. Blackburn, M. Egli, M. J. Gait, and J. K. Watts, The Royal Society of Chemistry, 4th edn, 2022, pp. E1-E50.
Download citation file:
This chapter looks at the physical and structural techniques that can be applied to nucleic acids. The first few sections focus on spectroscopic techniques, nuclear magnetic resonance, mass spectrometry and diffraction techniques. The following sections explore cryogenic electron microscopy, optical microscopy, atomic force microscopy and electrophoresis. Chromatographic methods, centrifugation and light scattering techniques are also discussed. Finally, the chapter concludes with sections on thermodynamic analysis, molecular mechanics and dynamics, and QM/MM methods for modelling nucleic acids reactions.
The online content of Chapter 15 is available as a PDF here: https://books.rsc.org/books/edited-volume/chapter-pdf/1773325/bk9781788019040-000e1.pdf
