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Molecular-Scale Studies on Biopolymers Using Atomic Force Microscopy

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Book cover Polymer Therapeutics II

Part of the book series: Advances in Polymer Science ((POLYMER,volume 193))

Abstract

The atomic force microscope (AFM) is capable of acquiring a range of structural and physicochemical information on a wide range of biopolymers. The ability to achieve nanoscale resolution, coupled with the potential to image and manipulate real-time molecular-scale events, suggests that AFM is one of the most promising techniques available for the study of biopolymers. AFM offers the potential to obtain a wide range of both quantitative and qualitative information on biopolymers, ranging from their conformations in physiological buffers to the forces involved in bond cleavage. This review explores the most common modes of AFM operation including imaging (contact and tapping mode) and force spectroscopy. The application of these modes to biopolymer characterisation will be discussed, with an emphasis on key studies.

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Abbreviations

3-MPA:

3-Mercaptopropanoic acid

11-MUA:

11-Mercaptoundecanoic acid

AFM:

Atomic force microscope or atomic force microscopy

APTES:

3-Aminopropyltriethoxysilane (used to create AP-mica)

AP-mica:

APTES-mica

Bp:

Base pair(s)

BR:

Bacteriarhodopsin

BSA:

Bovine Serum Albumin

BSA-MPAD:

BSA conjugated with a mercaptopropanoic acid derivative of atarazine

CBH I:

An exoglucanase enzyme (a cellulase)

CMA:

Carboxymethylamylose

CM-AFM:

Contact mode AFM

CMC:

Carboxymethylcellulose

CNT:

Carbon nanotubes

Cryo-AFM:

Cryogenic atomic force microscopy

csA:

Glycoprotein contact site AS

DMSO:

Dimethylsulfoxide

dsDNA:

Double-stranded DNA

dsRNA:

Double-stranded RNA

EDC:

1-Ethyl-3-(3-dimethylaminopropyl)-carbodiimide

EDTA:

Ethylenediaminetetraacetic acid

EGII:

Endogluconase

EtBr:

Ethidium bromide

FDC:

Force--distance curve

HPI:

Hexagonally packed intermediate layer

Ig:

Immunoglobin

LT:

Large tectosquares

MoMLV:

Moloney murine leukaemia virus

MPADT:

mercaptopropanoic acid derivative of atarazine

NCM-AFM:

Noncontact mode AFM

NHS:

N-hydroxysulfosuccinamide

OT:

Optical tweezers

PAMAM:

Poly(amidoamine) (a type of dendrimer)

pBR322:

An E. coli DNA plasmid

PBS:

Phosphate-buffered saline

PEGylated:

Polyethylene-glycolated

PEI:

Polyethylenimine

PID:

Proportional-integral-differential

pLL:

poly-(l-lysine)

pLL-AsOR:

pLL-Asialoorosomucoid

pLL-g-pHPMA:

Polyhydroypropylmethacrylamide-graft-pLL

POPC:

Palmitoyl-oleoyl phosphatidylcholine

pRSVluc:

A luciferase plasmid

PVAL:

Poly(vinyl) alcohol

RH:

Relative humidity

RNAP:

RNA polymerase enzyme

SAM(s):

Self-assembled monolayers

SMFS:

Single molecule force spectroscopy

SPM:

Scanning probe microscope

ssRNA:

Single-stranded RNA

STM:

Scanning tunnelling microscope

Ti-O:

Titanium oxide

TM-AFM:

Tapping mode AFM

TMEV:

Theiler's murine encephalomyelitis virus

tRNA:

Transfer RNA

WLC:

Worm-like coil

YO:

Oxide yellow (a dye)

YO-PRO-1:

An intercalating dye based on YO

YOYO:

Dimerised YO

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Acknowledgments

The authors would like to thank Omar Wahab and Cãtãlin Fotea (University of Nottingham) for their scientific input. JE and YTAC would like to thank the BBSRC for their studentships.

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  1. Laboratory of Biophysics and Surface Analysis, School of Pharmacy, University of Nottingham, University Park, NG7 2RD, Nottingham, UK

    James S. Ellis, Stephanie Allen, Ya Tsz A. Chim, Clive J. Roberts, Saul J. B. Tendler & Martyn C. Davies

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  1. James S. Ellis
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  2. Stephanie Allen
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  3. Ya Tsz A. Chim
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  4. Clive J. Roberts
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Correspondence to Martyn C. Davies .

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Ronit Satchi-Fainaro Ruth Duncan

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Ellis, J.S., Allen, S., Chim, Y.T.A., Roberts, C.J., Tendler, S.J.B., Davies, M.C. Molecular-Scale Studies on Biopolymers Using Atomic Force Microscopy. In: Satchi-Fainaro, R., Duncan, R. (eds) Polymer Therapeutics II. Advances in Polymer Science, vol 193. Springer, Berlin, Heidelberg. https://doi.org/10.1007/12_027

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