The Importance of Surfaces in Single-molecule Bioscience

Overview

Journal Mol Biosyst

Publisher Royal Society of Chemistry

Specialties Biochemistry
Molecular Biology

Date 2008 Apr 17

PMID 18414737

Citations 13

Authors

Mari-Liis Visnapuu

Daniel Duzdevich

Eric C Greene

Affiliations

Soon will be listed here.

Abstract

The last ten years have witnessed an explosion of new techniques that can be used to probe the dynamic behavior of individual biological molecules, leading to discoveries that would not have been possible with more traditional biochemical methods. A common feature among these single-molecule approaches is the need for the biological molecules to be anchored to a solid support surface. This must be done under conditions that minimize nonspecific adsorption without compromising the biological integrity of the sample. In this review we highlight why surface attachments are a critical aspect of many single-molecule studies and we discuss current methods for anchoring biomolecules. Finally, we provide a detailed description of a new method developed by our laboratory for anchoring and organizing hundreds of individual DNA molecules on a surface, allowing "high-throughput" studies of protein-DNA interactions at the single-molecule level.

Citing Articles

Single-molecule DNA-flow stretching assay as a versatile hybrid tool for investigating DNA-protein interactions.

Shehzad S, Kim H BMB Rep. 2024; 58(1):41-51.

PMID: 39701027 PMC: 11788529.

Advanced surface passivation for high-sensitivity studies of biomolecular condensates.

Yao R, Rosen M Proc Natl Acad Sci U S A. 2024; 121(22):e2403013121.

PMID: 38781207 PMC: 11145189. DOI: 10.1073/pnas.2403013121.

Oriented Soft DNA Curtains for Single-Molecule Imaging.

Kopu Stas A, Ivanovaite S, Rakickas T, Poceviciu Te E, Paksaite J, Karvelis T Langmuir. 2021; 37(11):3428-3437.

PMID: 33689355 PMC: 8280724. DOI: 10.1021/acs.langmuir.1c00066.

Improved Glass Surface Passivation for Single-Molecule Nanoarrays.

Cai H, Wind S Langmuir. 2016; 32(39):10034-10041.

PMID: 27622455 PMC: 5050166. DOI: 10.1021/acs.langmuir.6b02444.

An improved surface passivation method for single-molecule studies.

Hua B, Han K, Zhou R, Kim H, Shi X, Abeysirigunawardena S Nat Methods. 2014; 11(12):1233-6.

PMID: 25306544 PMC: 4245390. DOI: 10.1038/nmeth.3143.

References

Schnitzer M, Block S . Kinesin hydrolyses one ATP per 8-nm step. Nature. 1997; 388(6640):386-90. DOI: 10.1038/41111. View

Bianco P, Brewer L, Corzett M, Balhorn R, Yeh Y, Kowalczykowski S . Processive translocation and DNA unwinding by individual RecBCD enzyme molecules. Nature. 2001; 409(6818):374-8. DOI: 10.1038/35053131. View

Altman D, Sweeney H, Spudich J . The mechanism of myosin VI translocation and its load-induced anchoring. Cell. 2004; 116(5):737-49. DOI: 10.1016/s0092-8674(04)00211-9. View

Yildiz A, Tomishige M, Vale R, Selvin P . Kinesin walks hand-over-hand. Science. 2003; 303(5658):676-8. DOI: 10.1126/science.1093753. View

Sarkar A, Caamano S, Fernandez J . The elasticity of individual titin PEVK exons measured by single molecule atomic force microscopy. J Biol Chem. 2005; 280(8):6261-4. DOI: 10.1074/jbc.C400573200. View

Svoboda K, Schmidt C, Schnapp B, Block S . Direct observation of kinesin stepping by optical trapping interferometry. Nature. 1993; 365(6448):721-7. DOI: 10.1038/365721a0. View

van Oijen A . Honey, I shrunk the DNA: DNA length as a probe for nucleic-acid enzyme activity. Biopolymers. 2006; 85(2):144-53. DOI: 10.1002/bip.20624. View

Amitani I, Baskin R, Kowalczykowski S . Visualization of Rad54, a chromatin remodeling protein, translocating on single DNA molecules. Mol Cell. 2006; 23(1):143-8. DOI: 10.1016/j.molcel.2006.05.009. View

Ha T, Rasnik I, Cheng W, Babcock H, Gauss G, Lohman T . Initiation and re-initiation of DNA unwinding by the Escherichia coli Rep helicase. Nature. 2002; 419(6907):638-41. DOI: 10.1038/nature01083. View

10.

Ha T . Single-molecule fluorescence methods for the study of nucleic acids. Curr Opin Struct Biol. 2001; 11(3):287-92. DOI: 10.1016/s0959-440x(00)00204-9. View

11.

Asbury C, Fehr A, Block S . Kinesin moves by an asymmetric hand-over-hand mechanism. Science. 2003; 302(5653):2130-4. PMC: 1523256. DOI: 10.1126/science.1092985. View

12.

Wuite G, Smith S, Young M, Keller D, Bustamante C . Single-molecule studies of the effect of template tension on T7 DNA polymerase activity. Nature. 2000; 404(6773):103-6. DOI: 10.1038/35003614. View

13.

Greenleaf W, Block S . Single-molecule, motion-based DNA sequencing using RNA polymerase. Science. 2006; 313(5788):801. PMC: 1865524. DOI: 10.1126/science.1130105. View

14.

Strick T, Croquette V, Bensimon D . Single-molecule analysis of DNA uncoiling by a type II topoisomerase. Nature. 2000; 404(6780):901-4. DOI: 10.1038/35009144. View

15.

Cisse I, Okumus B, Joo C, Ha T . Fueling protein DNA interactions inside porous nanocontainers. Proc Natl Acad Sci U S A. 2007; 104(31):12646-50. PMC: 1937520. DOI: 10.1073/pnas.0610673104. View

16.

Fernandez J, Li H . Force-clamp spectroscopy monitors the folding trajectory of a single protein. Science. 2004; 303(5664):1674-8. DOI: 10.1126/science.1092497. View

17.

Koster D, Croquette V, Dekker C, Shuman S, Dekker N . Friction and torque govern the relaxation of DNA supercoils by eukaryotic topoisomerase IB. Nature. 2005; 434(7033):671-4. DOI: 10.1038/nature03395. View

18.

Sambongi Y, Iko Y, Tanabe M, Omote H, Ueda I, Yanagida T . Mechanical rotation of the c subunit oligomer in ATP synthase (F0F1): direct observation. Science. 1999; 286(5445):1722-4. DOI: 10.1126/science.286.5445.1722. View

19.

Lee J, Hite R, Hamdan S, Xie X, Richardson C, van Oijen A . DNA primase acts as a molecular brake in DNA replication. Nature. 2006; 439(7076):621-4. DOI: 10.1038/nature04317. View

20.

McKinney S, Freeman A, Lilley D, Ha T . Observing spontaneous branch migration of Holliday junctions one step at a time. Proc Natl Acad Sci U S A. 2005; 102(16):5715-20. PMC: 556122. DOI: 10.1073/pnas.0409328102. View