By the same authors

From the same journal

Probing DNA interactions with proteins using a single-molecule toolbox: inside the cell, in a test tube, and in a computer

Research output: Contribution to journalArticle

Standard

Probing DNA interactions with proteins using a single-molecule toolbox : inside the cell, in a test tube, and in a computer. / Wollman, Adam J.M.; Miller, Helen; Zhou, Zhaokun; Leake, Mark C.

In: Biochemical Society transactions, Vol. 43, No. 2, 01.04.2015, p. 139-145.

Research output: Contribution to journalArticle

Harvard

Wollman, AJM, Miller, H, Zhou, Z & Leake, MC 2015, 'Probing DNA interactions with proteins using a single-molecule toolbox: inside the cell, in a test tube, and in a computer', Biochemical Society transactions, vol. 43, no. 2, pp. 139-145. https://doi.org/10.1042/BST20140253

APA

Wollman, A. J. M., Miller, H., Zhou, Z., & Leake, M. C. (2015). Probing DNA interactions with proteins using a single-molecule toolbox: inside the cell, in a test tube, and in a computer. Biochemical Society transactions, 43(2), 139-145. https://doi.org/10.1042/BST20140253

Vancouver

Wollman AJM, Miller H, Zhou Z, Leake MC. Probing DNA interactions with proteins using a single-molecule toolbox: inside the cell, in a test tube, and in a computer. Biochemical Society transactions. 2015 Apr 1;43(2):139-145. https://doi.org/10.1042/BST20140253

Author

Wollman, Adam J.M. ; Miller, Helen ; Zhou, Zhaokun ; Leake, Mark C. / Probing DNA interactions with proteins using a single-molecule toolbox : inside the cell, in a test tube, and in a computer. In: Biochemical Society transactions. 2015 ; Vol. 43, No. 2. pp. 139-145.

Bibtex - Download

@article{820db8f6803843998795e50021d3aeaa,
title = "Probing DNA interactions with proteins using a single-molecule toolbox: inside the cell, in a test tube, and in a computer",
abstract = "DNA-interacting proteins have roles in multiple processes, many operating as molecular machines which undergo dynamic meta-stable transitions to bring about their biological function. To fully understand this molecular heterogeneity, DNA and the proteins that bind to it must ideally be interrogated at a single molecule level in their native in vivo environments, in a time-resolved manner, fast enough to sample the molecular transitions across the free-energy landscape. Progress has been made over the past decade in utilizing cutting-edge tools of the physical sciences to address challenging biological questions concerning the function and modes of action of several different proteins which bind to DNA. These physiologically relevant assays are technically challenging but can be complemented by powerful and often more tractable in vitro experiments which confer advantages of the chemical environment with enhanced detection signal-to-noise of molecular signatures and transition events. In the present paper, we discuss a range of techniques we have developed to monitor DNA–protein interactions in vivo, in vitro and in silico. These include bespoke single-molecule fluorescence microscopy techniques to elucidate the architecture and dynamics of the bacterial replisome and the structural maintenance of bacterial chromosomes, as well as new computational tools to extract single-molecule molecular signatures from live cells to monitor stoichiometry, spatial localization and mobility in living cells. We also discuss recent developments from our laboratory made in vitro, complementing these in vivo studies, which combine optical and magnetic tweezers to manipulate and image single molecules of DNA, with and without bound protein, in a new super-resolution fluorescence microscope.",
keywords = "DNA topology, Localization microscopy, Millisecond microscopy, Multidimensional microscopy, Slimfield, Photoblinking",
author = "Wollman, {Adam J.M.} and Helen Miller and Zhaokun Zhou and Leake, {Mark C.}",
note = "{\circledC} The Authors.",
year = "2015",
month = "4",
day = "1",
doi = "10.1042/BST20140253",
language = "English",
volume = "43",
pages = "139--145",
journal = "Biochemical Society transactions",
issn = "0300-5127",
publisher = "Portland Press Ltd.",
number = "2",

}

RIS (suitable for import to EndNote) - Download

TY - JOUR

T1 - Probing DNA interactions with proteins using a single-molecule toolbox

T2 - Biochemical Society transactions

AU - Wollman, Adam J.M.

AU - Miller, Helen

AU - Zhou, Zhaokun

AU - Leake, Mark C.

N1 - © The Authors.

PY - 2015/4/1

Y1 - 2015/4/1

N2 - DNA-interacting proteins have roles in multiple processes, many operating as molecular machines which undergo dynamic meta-stable transitions to bring about their biological function. To fully understand this molecular heterogeneity, DNA and the proteins that bind to it must ideally be interrogated at a single molecule level in their native in vivo environments, in a time-resolved manner, fast enough to sample the molecular transitions across the free-energy landscape. Progress has been made over the past decade in utilizing cutting-edge tools of the physical sciences to address challenging biological questions concerning the function and modes of action of several different proteins which bind to DNA. These physiologically relevant assays are technically challenging but can be complemented by powerful and often more tractable in vitro experiments which confer advantages of the chemical environment with enhanced detection signal-to-noise of molecular signatures and transition events. In the present paper, we discuss a range of techniques we have developed to monitor DNA–protein interactions in vivo, in vitro and in silico. These include bespoke single-molecule fluorescence microscopy techniques to elucidate the architecture and dynamics of the bacterial replisome and the structural maintenance of bacterial chromosomes, as well as new computational tools to extract single-molecule molecular signatures from live cells to monitor stoichiometry, spatial localization and mobility in living cells. We also discuss recent developments from our laboratory made in vitro, complementing these in vivo studies, which combine optical and magnetic tweezers to manipulate and image single molecules of DNA, with and without bound protein, in a new super-resolution fluorescence microscope.

AB - DNA-interacting proteins have roles in multiple processes, many operating as molecular machines which undergo dynamic meta-stable transitions to bring about their biological function. To fully understand this molecular heterogeneity, DNA and the proteins that bind to it must ideally be interrogated at a single molecule level in their native in vivo environments, in a time-resolved manner, fast enough to sample the molecular transitions across the free-energy landscape. Progress has been made over the past decade in utilizing cutting-edge tools of the physical sciences to address challenging biological questions concerning the function and modes of action of several different proteins which bind to DNA. These physiologically relevant assays are technically challenging but can be complemented by powerful and often more tractable in vitro experiments which confer advantages of the chemical environment with enhanced detection signal-to-noise of molecular signatures and transition events. In the present paper, we discuss a range of techniques we have developed to monitor DNA–protein interactions in vivo, in vitro and in silico. These include bespoke single-molecule fluorescence microscopy techniques to elucidate the architecture and dynamics of the bacterial replisome and the structural maintenance of bacterial chromosomes, as well as new computational tools to extract single-molecule molecular signatures from live cells to monitor stoichiometry, spatial localization and mobility in living cells. We also discuss recent developments from our laboratory made in vitro, complementing these in vivo studies, which combine optical and magnetic tweezers to manipulate and image single molecules of DNA, with and without bound protein, in a new super-resolution fluorescence microscope.

KW - DNA topology

KW - Localization microscopy

KW - Millisecond microscopy

KW - Multidimensional microscopy

KW - Slimfield

KW - Photoblinking

U2 - 10.1042/BST20140253

DO - 10.1042/BST20140253

M3 - Article

VL - 43

SP - 139

EP - 145

JO - Biochemical Society transactions

JF - Biochemical Society transactions

SN - 0300-5127

IS - 2

ER -