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8 - Atomic Force Microscopy and Detecting a DNA Biomarker of a Few Copies without Amplification

from Part III - Mapping DNA Molecules at the Single-Molecule Level

Published online by Cambridge University Press:  05 May 2022

Krishnarao Appasani
Affiliation:
GeneExpression Systems, Inc.
Raghu Kiran Appasani
Affiliation:
Psychiatrist, Neuroscientist, & Mental Health Advocate
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Summary

The term “biomarker,” a portmanteau of “biological marker,” has been defined by Hulka and colleagues (Hulka, 1990) as “cellular, biochemical or molecular alterations that are measurable in biological media such as human tissues, cells, or fluids.” In 1998, the definition was broadened as the National Institutes of Health Biomarkers Definitions Working Group defined a biomarker as “a characteristic that is objectively measured and evaluated as an indicator of normal biological processes, pathogenic processes, or pharmacologic responses to a therapeutic intervention” (Biomarkers Definition Working Group, 2001). In practice, the discovery and quantification of biomarkers require tools and technologies that help us predict and diagnose diseases; understand the cause, progression, and regression of diseases; and understand the outcomes of disease treatments. Different types of biomarkers have been used by generations of epidemiologists, physicians, and scientists to study all sorts of diseases. The importance of biomarkers in the diagnosis and management of cardiovascular diseases, infections, immunological and genetic disorders, and cancers is well known (Hulka, 1990; Perera and Weinstein, 2000).

Type
Chapter
Information
Single-Molecule Science
From Super-Resolution Microscopy to DNA Mapping and Diagnostics
, pp. 111 - 124
Publisher: Cambridge University Press
Print publication year: 2022

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References

Ando, T., Kodera, N., Takai, E., et al. (2001). A High-Speed Atomic Force Microscope for Studying Biological Macromolecules. Proceedings of the National Academy of Science, U.S.A., 98, 1246812472.CrossRefGoogle ScholarPubMed
Ando, T., Uchihashi, T., and Scheuring, S. (2014). Filming Biomolecular Processes by High-Speed Atomic Force Microscopy. Chemical Reviews, 114, 31203188.CrossRefGoogle ScholarPubMed
Archakov, A. I., Ivanov, Y. D., Lisitsa, A. V., and Zgoda, V. G. (2007). AFM Fishing Nanotechnology Is the Way to Reverse the Avogadro Number in Proteomics. Proteomics, 7 , 49.Google Scholar
Bailo, E. and Deckert, V. (2008). Tip-Enhanced Raman Spectroscopy of Single RNA Strands: Towards a Novel Direct-Sequencing Method. Angewandte Chemie International Edition, 47, 16581661.Google Scholar
Barrena, E., Kopta, S., Ogletree, D. F., Charych, D. H. , and Salmeron, M. (1999). Relationship between Friction and Molecular Structure: Alkylsilane Lubricant Films under Pressure. Physical Review Letters, 82, 28802883.CrossRefGoogle Scholar
Binnig, G. and Rohrer, H. (1982). Scanning Tunneling Microscopy. Helvetica Physica Acta, 55, 726735.Google Scholar
Binnig, G., Quate, C. F., and Gerber, C. (1986). Atomic force microscope, Physical Review Letters, 56, 930933.CrossRefGoogle ScholarPubMed
Biomarkers Definition Working Group (2001). Biomarkers and Surrogate Endpoints: Preferred Definitions and Conceptual Framework. Clinical Pharmacology and Therapeutics, 69, 8995.Google Scholar
Churnside, A. B., Sullan, R. M. A., Nguyen, D. M., et al. (2012). Routine and Timely Sub-picoNewton Force Stability and Precision for Biological Applications of Atomic Force Microscopy. Nano Letters, 12, 35573561.CrossRefGoogle ScholarPubMed
de Klein, A., van Kessel, A. G., Grosveld, G., et al. (1982). A Cellular Oncogene Is Translocated to the Philadelphia Chromosome in Chronic Myelocytic Leukaemia, Nature, 300, 765767.Google Scholar
Drake, B., Prater, C. B., Weisenhorn, A. L., et al. (1989). Imaging Crystals, Polymers, and Processes in Water with the Atomic Force Microscope. Science, 243, 15861589.CrossRefGoogle ScholarPubMed
Dufrêne, Y. F., Martinez-Martin, D., Medalsy, I., Alsteens, D., and Müller, D. J. (2013). Multiparametric Imaging of Biological Systems by Force-Distance Curve-Based AFM. Nature Methods, 10, 847854.Google Scholar
Dufrêne, Y. F., Ando, T., Garcia, R., et al. (2017). Imaging Modes of Atomic Force Microscopy for Application in Molecular and Cell Biology. Nature Nanotechnology, 12, 295307.Google Scholar
Eifert, A. and Kranz, C. (2014). Hyphenating Atomic Force Microscopy. Analytical Chemistry, 86, 51905200.CrossRefGoogle ScholarPubMed
Fernandez, J. M. and Li, H. B. (2004). Force-Clamp Spectroscopy Monitors the Folding Trajectory of a Single Protein. Science, 303, 16741678.CrossRefGoogle ScholarPubMed
Giessibl, F. J. (1995). Atomic-Resolution of the Silicon (111)-(7×7) Surface by Atomic Force Microscopy. Science, 267, 6871.Google Scholar
Greenleaf, W. J., and Block, S. M. (2006). Single-Molecule, Motion-Based DNA Sequencing Using RNA Polymerase. Science, 313, 801.CrossRefGoogle ScholarPubMed
Gruter, R. R., Voros, J., and Zambelli, T. (2013). FluidFM as a Lithography Tool in Liquid: Spatially Controlled Deposition of Fluorescent Nanoparticles. Nanoscale, 5, 10971104.CrossRefGoogle ScholarPubMed
Hansma, P. K., Cleveland, J. P., Radmacher, M., et al. (1994). Tapping Mode Atomic Force Microscopy in Liquids. Applied Physics Letters, 64, 17381740.Google Scholar
Hinterdorfer, P., Baumgartner, W., Gruber, H. J., Schilcher, K., and Schindler, H. (1996). Detection and Localization of Individual Antibody-Antigen Recognition Events by Atomic Force Microscopy. Proceedings of the National Academy of Science U. S. A., 93, 34773481.Google Scholar
Hoh, J. H., Lal, R., John, S. A., Revel, J. P., and Arnsdorf, M. F. (1991). Atomic Force Microscopy and Dissection of Gap-Junctions. Science, 253, 14051408.Google Scholar
Hughes, T., Janssen, J. W. G., Morgan, G., et al. (1990). False-Positive Results with PCR to Detect Leukaemia-Specific Transcript. Lancet, 335, 10371038.Google Scholar
Hulka, B. S. (1990). Overview of Biological Markers, In Hulka, B. S., Griffith, J. D., Wilcosky, T. C., eds., Biological Markers in Epidemiology. Oxford University Press, New York: 315.Google Scholar
Jacobs, B. K. M., Goetghebeur, E., and Clement, L. (2014). Impact of Variance Components on Reliability of Absolute Quantification Using Digital PCR. BMC Bioinformatics, 15, 283.CrossRefGoogle ScholarPubMed
Kim, Y., Kim, E-S., Lee, Y., et al. (2014). Reading Single DNA with DNA Polymerase Followed by Atomic Force Microscopy. Journal of the American Chemical Society, 136, 1375413760.Google Scholar
Kodera, N., Yamamoto, D., Ishikawa, R., and Ando, T. (2010). Video Imaging of Walking Myosin V by High-Speed Atomic Force Microscopy. Nature, 468, 7276.Google Scholar
Lee, Y., Kwon, S. H., Kim, Y., Lee, J. B., and Park, J. W. (2013). Mapping of Surface-Immobilized DNA with Force-Based Atomic Force Microscopy. Analytical Chemistry., 85, 40454050.Google Scholar
Lee, Y., Kim, Y., Lee, D., Roy, D., and Park, J. W. (2016). Quantification of Fewer than Ten Copies of a DNA Biomarker without Amplification or Labeling, Journal of the American Chemical Society, 138, 70757081.CrossRefGoogle ScholarPubMed
Marszalek, P. E., Li, H. B., and Fernandez, J. M. (2001). Fingerprinting Polysaccharides with Single-Molecule Atomic Force Microscopy. Nature Biotechnology, 19, 258262.Google Scholar
Medalsy, I., Hensen, U., and Müller, D. J. (2011). Imaging and Quantifying Chemical and Physical Properties of Native Proteins at Molecular Resolution by Force-Volume AFM. Angewandte Chemie International Edition, 50, 1210312108.Google Scholar
Neuman, K. C. and Nagy, A. (2008). Single-Molecule Force Spectroscopy: Optical Tweezers, Magnetic Tweezers and Atomic Force Microscopy. Nature Methods, 5, 491505.CrossRefGoogle ScholarPubMed
Perera, F. P. and Weinstein, I. B. (2000). Molecular Epidemiology: Recent Advances and Future Directions. Carcinogenesis, 21, 517524.Google Scholar
Puntheeranurak, T., Neundlinger, I. Kinne, R. K. H., and Hinterdorfer, P. (2011). Single-Molecule Recognition Force Spectroscopy of Transmembrane Transporters on Living Cells. Nature Protocols, 6, 14431452.CrossRefGoogle ScholarPubMed
Raab, A., Han, W. H., Badt, D., et al. (1999). Antibody Recognition Imaging by Force Microscopy. Nature Biotechnology, 17, 901905.Google Scholar
Roy, D. and Park, J. W. (2015). Spatially Nanoscale-Controlled Functional Surfaces toward Efficient Bioactive Platforms. Journal of Materials Chemistry B, 3, 51355149.Google Scholar
Sahin, O., Magonov, S., Su, C., Quate, C. F., and Solgaard, O. (2007). An Atomic Force Microscope Tip Designed to Measure Time-Varying Nanomechanical Forces. Nature Nanotechnology, 2, 507514.Google Scholar
Saini, S. (2016). PSA and Beyond: Alternative Prostate Cancer Biomarkers, Cell Oncology, 39, 97106.Google Scholar
Shan, Y. and Wang, H. (2015). The Structure and Function of Cell Membranes Examined by Atomic Force Microscopy and Single-Molecule Force Spectroscopy. Chemical Society Reviews, 44 , 36173638.CrossRefGoogle ScholarPubMed
Vogelstein, B. and Kinzler, K. W. (1999). Digital PCR, Proceedings of the National Academy of Science USA, 96, 92369241.CrossRefGoogle ScholarPubMed
Yersin, A., Hirling, H., Kasas, S., et al. (2007). Elastic Properties of the Cell Surface and Trafficking of Single AMPA Receptors in Living Hippocampal Neurons. Biophysical Journal, 92, 44824489.CrossRefGoogle ScholarPubMed

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