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Eze NA, Milam VT. Quantitative Analysis of In Situ Locked Nucleic Acid and DNA Competitive Displacement Events on Microspheres. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:6871-6881. [PMID: 35617467 DOI: 10.1021/acs.langmuir.2c00220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Synthetic analogues of natural oligonucleotides known as locked nucleic acids (LNAs) offer superior nuclease resistance and cytocompatibility for numerous scenarios ranging from in vitro detection to intracellular imaging of nucleic acids. While recognized as stronger hybridization partners than equivalent DNA residues, quantitative analysis of LNA hybridization activity is lacking, especially with respect to competitive displacement of the original hybridization partner by another oligonucleotide. In the current study, we perform in situ measurements of toehold-mediated competitive displacement of soluble, fluorescently labeled primary targets from probe strands immobilized on microspheres using high throughput flow cytometry. Both LNA-DNA hybrid sequences and pure DNA sequences are employed as the immobilized strands, as soluble, fluorescently labeled 9-base-long primary targets, and as unlabeled 15-base-long secondary or competitive targets. In addition to comparing chemically substituted and unsubstituted sequences, we explore the effects of mismatched primary targets and the location of the toehold segment within the primary duplexes on the resulting displacement profiles. The primary duplex or double-stranded probe (dsprobe) systems implemented here exhibited varying responses to unlabeled secondary targets ranging from surprisingly modest primary target displacement activity despite the presence of a six base-long nucleotide toehold segment at the dsprobe free end to distinctive displacement profiles sensitive to LNA substitutions and the placement of the toehold segment closer to the microsphere surface.
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Houston JP, Yang Z, Sambrano J, Li W, Nichani K, Vacca G. Overview of Fluorescence Lifetime Measurements in Flow Cytometry. Methods Mol Biol 2018; 1678:421-446. [PMID: 29071689 DOI: 10.1007/978-1-4939-7346-0_18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The focus of this chapter is time-resolved flow cytometry, which is broadly defined as the ability to measure the timing of fluorescence decay from excited fluorophores that pass through cytometers or high-throughput cell counting and cell sorting instruments. We focus on this subject for two main reasons: first, to discuss the nuances of hardware and software modifications needed for these measurements because currently, there are no widespread time-resolved cytometers nor a one-size-fits-all approach; and second, to summarize the application space for fluorescence lifetime-based cell counting/sorting owing to the recent increase in the number of investigators interested in this approach. Overall, this chapter is structured into three sections: (1) theory of fluorescence decay kinetics, (2) modern time-resolved flow cytometry systems, and (3) cell counting and sorting applications. These commentaries are followed by conclusions and discussion about new directions and opportunities for fluorescence lifetime measurements in flow cytometry.
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Affiliation(s)
- Jessica P Houston
- Department of Chemical & Materials Engineering, New Mexico State University, MSC, PO Box 30001, Las Cruces, NM, 88003, USA.
| | - Zhihua Yang
- Department of Chemical & Materials Engineering, New Mexico State University, MSC, PO Box 30001, Las Cruces, NM, 88003, USA
| | - Jesse Sambrano
- Department of Chemical & Materials Engineering, New Mexico State University, MSC, PO Box 30001, Las Cruces, NM, 88003, USA
| | - Wenyan Li
- Department of Chemical & Materials Engineering, New Mexico State University, MSC, PO Box 30001, Las Cruces, NM, 88003, USA
| | - Kapil Nichani
- Department of Chemical & Materials Engineering, New Mexico State University, MSC, PO Box 30001, Las Cruces, NM, 88003, USA
| | - Giacomo Vacca
- Kinetic River Corp., 897, Independence Avenue, Suite 4A, Mountain View, CA, 94043-2357, USA
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Yuan B. Sensitivity of fluorophore-quencher labeled microbubbles to externally applied static pressure. Med Phys 2009; 36:3455-69. [PMID: 19746779 DOI: 10.1118/1.3158734] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
A fluorophore-quencher (F-Q) labeled microbubble system is proposed as a sensor for measuring externally applied static pressure distribution in a tumor. To quantify the sensitivity of such an F-Q bubble system to the externally applied pressure, a model describing bubble response to the static pressure was derived. Additionally, a model connecting the fluorescence lifetime and bubble radius was developed for the basic F-Q bubble system. The sensitivity is quantified based on these models given typical parameters. Results show that it is possible to resolve as low as 1 mm Hg pressure variation when both the F-Q bubble system and the measurement system are optimized. Strategies for optimizing an F-Q bubble system are discussed.
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Affiliation(s)
- Baohong Yuan
- Department of Biomedical Engineering, Catholic University of America, Washington, DC 20064, USA.
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Fang S, Guan Y, Blatchley ER, Shen C, Bergstrom DE. Conjugation of (E)-5-[2-(Methoxycarbonyl)ethenyl]cytidine to Hydrophilic Microspheres: Development of a Mobile Microscale UV Light Actinometer. Bioconjug Chem 2008; 19:592-7. [PMID: 18266312 DOI: 10.1021/bc700336x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shiyue Fang
- School of Civil Engineering, Purdue University, West Lafayette, Indiana 47907-2051, Birck Nanotechnology Center, Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Cancer Center, Purdue University, West Lafayette, Indiana 47907, and The Walther Cancer Institute, Indianapolis, Indiana 46208
| | - Yousheng Guan
- School of Civil Engineering, Purdue University, West Lafayette, Indiana 47907-2051, Birck Nanotechnology Center, Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Cancer Center, Purdue University, West Lafayette, Indiana 47907, and The Walther Cancer Institute, Indianapolis, Indiana 46208
| | - Ernest R. Blatchley
- School of Civil Engineering, Purdue University, West Lafayette, Indiana 47907-2051, Birck Nanotechnology Center, Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Cancer Center, Purdue University, West Lafayette, Indiana 47907, and The Walther Cancer Institute, Indianapolis, Indiana 46208
| | - Chengyue Shen
- School of Civil Engineering, Purdue University, West Lafayette, Indiana 47907-2051, Birck Nanotechnology Center, Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Cancer Center, Purdue University, West Lafayette, Indiana 47907, and The Walther Cancer Institute, Indianapolis, Indiana 46208
| | - Donald E. Bergstrom
- School of Civil Engineering, Purdue University, West Lafayette, Indiana 47907-2051, Birck Nanotechnology Center, Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Cancer Center, Purdue University, West Lafayette, Indiana 47907, and The Walther Cancer Institute, Indianapolis, Indiana 46208
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