Single-molecule studies of nucleic acids and their proteins / David Bensimon ... [et al.]. -- Oxford, United Kingdom : Oxford University Press, 2019. – (58.17425/B474)

Contents

1  Introduction to DNA

     1.1 Introduction

     1.2 Single-molecule versus bulk studies

     1.3 DNA structures

2  Manipulating DNA

     2.1 Tailoring and labelling DNA

     2.2 Molecular combing

     2.3 Forces at the molecular scale

     2.4 Micromanipulation tools

     2.5 Choosing a single-molecule manipulation tool

     2.6 Problems

3  Fluorescence Spectroscopy and Microscopy Techniques

     3.1 Introduction

     3.2 Principles of fluorescence

     3.3 Illumination methods

     3.4 Detection techniques

     3.5 Single-molecule tracking

     3.6 Perspectives

     3.7 Problems

4  The Mechanical Properties of Nucleic Acids

     4.1 Models of stretched polymers

     4.2 Relaxation dynamics of DNA

     4.3 The elastic behaviour of twisted DNA

     4.4 Torque estimate from single-molecule thermodynamics

     4.5 Twist-stretch coupling in DNA

     4.6 The braiding of two DNA molecules

     4.7 Simulations of stretched, twisted, or braided molecules

     4.8 Single-stranded nucleic acids

     4.9 Pulling on RNA

     4.10 Problems

5  Structural Transitions in DNA

    5.1 Molecular transitions induced by twisting

    5.2 Molecular transitions induced by stretching

    5.3 Unzipping DNA

    5.4 Conclusions and perspectives

6  Single-Molecule Studies of DNA-Associated Motors

    6.1 Introduction to DNA-protein interactions

7  DNA and RNA Polymerases

    7.1 Introduction to polymerases

    7.2 An introduction to replication

    7.3 Single-molecule in vitro DNAP experiments

    7.4 In vivo studies of single replication complexes

    7.5 An introduction to transcription

    7.6 Single-molecule in vitro RNAP experiments

    7.7 In vivo studies of transcription

    7.8 Conclusions and perspectives

8  DNA Helicases

    8.1 Introduction to helicases

    8.2 Bulk versus single-molecule assays: the case of RecBCD

    8.3 Active and passive unwinding mechanisms: RecQ versus gp41

    8.4 The UvrD helicase studied by single-molecule manipulations

    8.5 Single-molecule FRET studies of the Rep helicase

    8.6 Problems

9  Topoisomerases

    9.1 Introduction to topoisomerases

    9.2 Bulk assays

    9.3 Single-molecule in vitro assays: type I topoisomerases

    9.4 Single-molecule in vitro assays: type II topoisomerases

    9.5 Single-molecule study of the coiling activity of gyrases

    9.6 In vivo studies of single topoIV localization and action in E.coli

10  Conclusions

References

Index