Fluorescence Blinking as an Output Signal for Biosensing

Roark, Brandon K.; Tan, Jenna A.; Ivanina, Anna V.; Chandler, Morgan; Castaneda, Jose; Kim, Ho Shin; Jawahar, Shriram; Viard, Mathias; Talic, Strahinja; Wustholz, Kristin L.; Yingling, Yaroslava G.; Jones, Marcus; Afonin, Kirill A.

doi:10.1021/acssensors.6b00352

Cited by 22 publications

(26 citation statements)

References 48 publications

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“…Nucleic acid-based nanoparticles (NANPs) [1,2,3,4,5,6,7,8,9,10,11,12,13] and other nucleic acid-based nanodevices [14,15,16,17] are an emerging research focus area in pharmacological and biological studies. NANPs can be designed and manipulated to produce a variety of different functionalized nanostructured scaffolds; the novel resultant structures require detailed characterization prior to further biomedical transition and in vivo studies [7,18,19,20,21,22].…”

Section: Introductionmentioning

confidence: 99%

Small-Angle Scattering as a Structural Probe for Nucleic Acid Nanoparticles (NANPs) in a Dynamic Solution Environment

et al. 2019

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Nucleic acid-based technologies are an emerging research focus area for pharmacological and biological studies because they are biocompatible and can be designed to produce a variety of scaffolds at the nanometer scale. The use of nucleic acids (ribonucleic acid (RNA) and/or deoxyribonucleic acid (DNA)) as building materials in programming the assemblies and their further functionalization has recently established a new exciting field of RNA and DNA nanotechnology, which have both already produced a variety of different functional nanostructures and nanodevices. It is evident that the resultant architectures require detailed structural and functional characterization and that a variety of technical approaches must be employed to promote the development of the emerging fields. Small-angle X-ray and neutron scattering (SAS) are structural characterization techniques that are well placed to determine the conformation of nucleic acid nanoparticles (NANPs) under varying solution conditions, thus allowing for the optimization of their design. SAS experiments provide information on the overall shapes and particle dimensions of macromolecules and are ideal for following conformational changes of the molecular ensemble as it behaves in solution. In addition, the inherent differences in the neutron scattering of nucleic acids, lipids, and proteins, as well as the different neutron scattering properties of the isotopes of hydrogen, combined with the ability to uniformly label biological macromolecules with deuterium, allow one to characterize the conformations and relative dispositions of the individual components within an assembly of biomolecules. This article will review the application of SAS methods and provide a summary of their successful utilization in the emerging field of NANP technology to date, as well as share our vision on its use in complementing a broad suite of structural characterization tools with some simulated results that have never been shared before.

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Section: Introductionmentioning

confidence: 99%

Small-Angle Scattering as a Structural Probe for Nucleic Acid Nanoparticles (NANPs) in a Dynamic Solution Environment

et al. 2019

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“…The unique features of DNA enable the organization of nanostructures into larger superstructures and macroscopic superlattices with well-defined orientations depending on their intrinsic architecture. 1,2 Current knowledge and experiences with DNA-organized supramolecular structures revolve around exploiting DNA-linked rigid nanostructures, 3,4 for example gold nanoparticles. 5,6 The rigidity of particles imparts directionality to hybridization interactions and the high-density of DNA strands on the surfaces act as 'valencies' to manipulate the stereo-organization precisely, either when DNA chains or DNA origami direct the organization, [7][8][9] or when steric hindrance induces formation of core-satellite structures.…”

Section: Introductionmentioning

confidence: 99%

DNA-directed arrangement of soft synthetic compartments and their behavior in vitro and in vivo

et al. 2020

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“…Previous studies with spiropyrans have primarily focused on tertiary structured short hairpin RNAs and their qualitative interactions as aptamers via surface plasmon resonance [27] and nanopores [28]. More recently, studies utilized spectral properties of gold nanoparticles and quantum dots to detect and quantify expression of specific RNA targets such as mRNAs [29,30], single-stranded RNAs (ssRNAs) [31,32], and short double-stranded RNAs (dsRNAs) [33]. However, they all used RNA probes that are complementary to the target RNAs and thus, their approach is limited to detecting just one or few RNA transcripts [34].…”

Section: Introductionmentioning

confidence: 99%

Spiropyran as a potential molecular diagnostic tool for double-stranded RNA detection

et al. 2019

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Background: Long double-stranded RNAs (dsRNAs) are duplex RNAs that can induce immune response when present in mammalian cells. These RNAs are historically associated with viral replication, but recent evidence suggests that human cells naturally encode endogenous dsRNAs that can regulate antiviral machineries in cellular contexts beyond immune response.Results: In this study, we use photochromic organic compound spiropyran to profile and quantitate dsRNA expression. We show that the open form of spiropyran, merocyanine, can intercalate between RNA base pairs, which leads to protonation and alteration in the spectral property of the compound. By quantifying the spectral change, we can detect and quantify dsRNA expression level, both synthetic and cellular. We further demonstrate that spiropyrans can be used as a molecular diagnostic tool to profile endogenously expressed dsRNAs. Particularly, we show that spiropyrans can robustly detect elevated dsRNA levels when colorectal cancer cells are treated with 5-aza-2′-deoxycytidine, an FDAapproved DNA-demethylating agent used for chemotherapy, thus demonstrating the use of spiropyran for predicting responsiveness to the drug treatment. Conclusion:As dsRNAs are signature of virus and accumulation of dsRNAs is implicated in various degenerative disease, our work establishes potential application of spiropyrans as a simple spectral tool to diagnose human disease based on dsRNA expression.

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Fluorescence Blinking as an Output Signal for Biosensing

Cited by 22 publications

References 48 publications

Small-Angle Scattering as a Structural Probe for Nucleic Acid Nanoparticles (NANPs) in a Dynamic Solution Environment

Small-Angle Scattering as a Structural Probe for Nucleic Acid Nanoparticles (NANPs) in a Dynamic Solution Environment

DNA-directed arrangement of soft synthetic compartments and their behavior in vitro and in vivo

Spiropyran as a potential molecular diagnostic tool for double-stranded RNA detection

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