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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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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