The overall objective of this work is to develop methods that can provide mechanistic information about the ways in which the chemical functionality of a nearby surface affects nucleic acid base- pairing and hybridization, and to use these methods to understand how surface chemistry can be used to control DNA self-assembly. DNA-based biomedical nanotechnologies rely directly on Watson-Crick base-pairing to achieve molecular recognition capable of directing self-assembly for a variety of diagnostic and targeting applications. While base-pairing in the solution phase is relatively well-understood, in many DNA nanotechnologies, base-pairing/hybridization is intended to occur in the vicinity of one or more interfaces/surfaces that may promote competitive non- specific interactions with nucleic acids due to the particular vicinal surface chemistry. A better understanding of surface effects on hybridization will ultimately lead to improvements in a wide range of DNA-based technologies. In particular, it will enable the design and preparation of improved surface-modification strategies. We propose to develop advanced single-molecule tracking methods using total internal reflection fluorescence microscopy (TIRFM) with single-molecule resolution, where resonance energy transfer (RET) is used to obtain simultaneous conformational information. This approach can identify direct molecule-by-molecule correlations between conformation and dynamic interfacial events (e.g. adsorption/desorption, interfacial mobility, conformational fluctuations, hybridization), providing mechanistic understanding of how vicinal surface chemistry affects both specific and non-specific DNA interactions. These methods will be used to study DNA dynamics and base- pairing on model surfaces that represent the most important examples of competing non-covalent interactions. This two-year plan focuses on understanding the interfacial dynamic behavior of (1) oligonucleotides that can self-hybridize to form stem-loop secondary structures, and (2) complementary oligonucleotide pairs.

Public Health Relevance

DNA hybridization, the specific recognition of a DNA sequence by its complementary sequence, is the fundamental enabling phenomenon underlying a wide range of biomedical nanotechnologies, including molecular diagnostics, gene delivery, DNA sequencing, and many others. In these technologies, DNA molecules are required to exhibit specific recognition in the presence of foreign surfaces and materials that can interfere due to competitive chemical interactions. This work involves the development of novel single-molecule microscopy methods that will lead to a detailed understanding of these competitive interactions, permitting the design of improved materials and technologies.

National Institute of Health (NIH)
National Institute of Biomedical Imaging and Bioengineering (NIBIB)
Exploratory/Developmental Grants (R21)
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Nanotechnology Study Section (NANO)
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Conroy, Richard
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University of Colorado at Boulder
Engineering (All Types)
Schools of Engineering
United States
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Monserud, Jon H; Schwartz, Daniel K (2014) Mechanisms of surface-mediated DNA hybridization. ACS Nano 8:4488-99
Kastantin, Mark; Schwartz, Daniel K (2013) DNA hairpin stabilization on a hydrophobic surface. Small 9:933-41
Monserud, Jon H; Schwartz, Daniel K (2012) Effects of molecular size and surface hydrophobicity on oligonucleotide interfacial dynamics. Biomacromolecules 13:4002-11