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Beard JW, Hunt SL, Evans A, Goenner C, Miller BL. Mimicking an in cellulo environment for enzyme-free paper-based nucleic acid tests at the point of care. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.27.582375. [PMID: 38464301 PMCID: PMC10925243 DOI: 10.1101/2024.02.27.582375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Point of care (PoC) nucleic acid amplification tests (NAATs) are a cornerstone of public health, providing the earliest and most accurate diagnostic method for many communicable diseases, such as HIV, in the same location the patient receives treatment. Communicable diseases disproportionately impact low-resource communities where NAATs are often unobtainable due to the resource intensive enzymes that drive the tests. Enzyme-free nucleic acid detection methods, such as hybridization chain reaction (HCR), use DNA secondary structures for self-driven amplification schemes producing large DNA nanostructures and capable of single molecule detection in cellulo. These thermodynamically driven DNA-based tests have struggled to penetrate the PoC diagnostic field due to their inadequate limits of detection or complex workflows. Here we present a proof-of-concept NAAT that combines HCR-based amplification of a target nucleic acid sequence with paper-based nucleic acid filtration and enrichment capable of detecting sub pM levels of synthetic DNA. We reconstruct the favorable hybridization conditions of an in cellulo reaction in vitro by incubating HCR in an evaporating, microvolume environment containing poly(ethylene glycol) as a crowding agent. We demonstrate that the kinetics and thermodynamics of DNA-DNA and DNA-RNA hybridization is enhanced by the dynamic evaporating environment and inclusion of crowding agents, bringing HCR closer to meeting PoC NAAT needs.
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Affiliation(s)
- Jeffrey W. Beard
- Department of Dermatology, University of Rochester, Rochester, NY 14627, USA
| | - Samuel L. Hunt
- Department of Dermatology, University of Rochester, Rochester, NY 14627, USA
| | - Alexander Evans
- Department of Biomedical Engineering, University of Rochester, Rochester, NY 14627, USA
| | - Coleman Goenner
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14627, USA
| | - Benjamin L. Miller
- Department of Dermatology, University of Rochester, Rochester, NY 14627, USA
- Department of Biomedical Engineering, University of Rochester, Rochester, NY 14627, USA
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14627, USA
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Lysne D, Hachigian T, Thachuk C, Lee J, Graugnard E. Leveraging Steric Moieties for Kinetic Control of DNA Strand Displacement Reactions. J Am Chem Soc 2023. [PMID: 37487322 PMCID: PMC10401717 DOI: 10.1021/jacs.3c04344] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
DNA strand displacement networks are a critical part of dynamic DNA nanotechnology and are proven primitives for implementing chemical reaction networks. Precise kinetic control of these networks is important for their use in a range of applications. Among the better understood and widely leveraged kinetic properties of these networks are toehold sequence, length, composition, and location. While steric hindrance has been recognized as an important factor in such systems, a clear understanding of its impact and role is lacking. Here, a systematic investigation of steric hindrance within a DNA toehold-mediated strand displacement network was performed through tracking kinetic reactions of reporter complexes with incremental concatenation of steric moieties near the toehold. Two subsets of steric moieties were tested with systematic variation of structures and reaction conditions to isolate sterics from electrostatics. Thermodynamic and coarse-grained computational modeling was performed to gain further insight into the impacts of steric hindrance. Steric factors yielded up to 3 orders of magnitude decrease in the reaction rate constant. This pronounced effect demonstrates that steric moieties can be a powerful tool for kinetic control in strand displacement networks while also being more broadly informative of DNA structural assembly in both DNA-based therapeutic and diagnostic applications that possess elements of steric hindrance through DNA functionalization with an assortment of chemistries.
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Affiliation(s)
- Drew Lysne
- Micron School of Materials Science and Engineering, Boise State University, 1910 University Dr., Boise, Idaho 83725, United States
| | - Tim Hachigian
- Micron School of Materials Science and Engineering, Boise State University, 1910 University Dr., Boise, Idaho 83725, United States
| | - Chris Thachuk
- Paul G Allen School of Computer Science and Engineering, University of Washington, Paul G. Allen Center, Box 352350, 185 E Stevens Way NE, Seattle, Washington 98195-2350, United States
| | - Jeunghoon Lee
- Micron School of Materials Science and Engineering, Boise State University, 1910 University Dr., Boise, Idaho 83725, United States
- Department of Chemistry and Biochemistry, Boise State University, 1910 University Dr., Boise, Idaho 83725, United States
| | - Elton Graugnard
- Micron School of Materials Science and Engineering, Boise State University, 1910 University Dr., Boise, Idaho 83725, United States
- Center for Advanced Energy Studies, Idaho Falls, Idaho 83401, United States
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Yun J, Lee JH. A highly selective and sensitive competitive aptasensor capable of quantifying thrombin elevated with side effects in severe COVID-19. J Pharm Biomed Anal 2022; 221:115076. [PMID: 36179502 PMCID: PMC9511899 DOI: 10.1016/j.jpba.2022.115076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/22/2022] [Accepted: 09/24/2022] [Indexed: 11/23/2022]
Abstract
To protect critical injury from blood clots with side effects in severe COVID-19, a highly selective and sensitive biosensor was developed for the quantification of trace levels of thrombin using the combination of a DNA aptamer (TBA) of thrombin and a complementary strand of TBA. TBA rapidly binds with thrombin, whereas it slowly binds with the complementary strand to form a double stranded DNA (dsDNA). SFC green intercalated into dsDNA cannot emit light in 1,1′-oxalyldiimidazole chemiluminescence (ODI-CL) reaction because high-energy intermediates formed from ODI-CL reaction cannot transfer energy to SFC trapped in dsDNA. However, SFC freely existing with the formation of G-quadruplex from the reaction of thrombin and TBA emits bright chemiluminescence because the high-energy intermediates can transfer energy to SFC (or camel) in solution. Thus, the brightness of light emitted in ODI-CL reaction was proportionally enhanced with the increase of thrombin in a sample due to the increase of G-quadruplex and reduction of dsDNA. The limit of detection (LOD) of the label free aptasensor operated with good linear calibration curve (10–320 mU/ml) was as low as 3 mU/ml (or 43 pM). Also, the biosensor was quantified trace levels of thrombin with good accuracy, precision, and reliability.
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Affiliation(s)
- Jaden Yun
- Luminescent MD, LLC, Hagerstown, MD 21742, United States; Phillips Exeter Academy, Exeter, NH 03833, United States
| | - Ji Hoon Lee
- Luminescent MD, LLC, Hagerstown, MD 21742, United States.
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Label-Free Homogeneous microRNA Detection in Cell Culture Medium Based on Graphene Oxide and Specific Fluorescence Quenching. NANOMATERIALS 2021; 11:nano11020368. [PMID: 33540562 PMCID: PMC7912907 DOI: 10.3390/nano11020368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/19/2021] [Accepted: 01/28/2021] [Indexed: 02/07/2023]
Abstract
Label-free homogeneous optical detection of low concentration of oligonucleotides using graphene oxide in complex solutions containing proteins remains difficult. We used a colloidal graphene oxide (GO) as a fluorescent probe quencher to detect microRNA-21 spiked-in cell culture medium, overcoming previously reported problematic aspects of protein interference with graphene oxide. We used a "turn off" assay for specific quenching-based detection of oligo DNA-microRNA hybridization in solution. A fluorescein conjugated 30-mer single-stranded DNA (ssDNA) probe was combined with a complementary synthetic microRNA (18 nucleotides) target. The probe-target hybridization was detected by specific quenching due to photoinduced electron transfer (PET). On the next step, GO captures and quenches the unhybridized probe by fluorescence resonance energy transfer (FRET) in the presence of cell culture medium supplemented with platelet lysate, 0.1% sodium dodecyl sulfate (SDS), 0.1% Triton X-100 and 50% formamide. This resulted in sensitive measurement of the specific probe-target complexes remaining in solution. The detection is linear in the range of 1 nM and 8 nM in a single 100 μL total volume assay sample containing 25% cell culture medium supplemented with platelet lysate. We highlight a general approach that may be adopted for microRNA target detection within complex physiological media.
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Yazdani M, Beiki Z, Jahanian A. RNA secondary structured logic gates for profiling the microRNA cancer biomarkers. IET Nanobiotechnol 2020; 14:181-190. [PMID: 32338625 PMCID: PMC8676559 DOI: 10.1049/iet-nbt.2019.0150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 10/09/2019] [Accepted: 11/20/2019] [Indexed: 04/05/2024] Open
Abstract
Deregulation of microRNAs expression is symptomatic of cancer disease and occurs before the awareness of cancer signs. Early detection of cancer disease can improve or drop the disease entirely. DNA computing is an emerging field of detecting microRNAs based on toehold-mediated strand displacement reactions, which is a more efficient method than the commonly used method like real-time PCR. Accuracy and cost of diagnostic applications are essential criteria that are achieved by using the DNA logic gates based on the DNA computing method. In this study, the authors proposed the multi-input liver cancer biosensor with the RNA secondary structure motifs as the computational module and two approaches are suggested.
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Affiliation(s)
- Mahsa Yazdani
- Faculty of Computer Science and Engineering, Shahid Beheshti University, G.C., Velenjak, Tehran 19839-63113, Iran
| | - Zohre Beiki
- Faculty of Computer Engineering, University of Isfahan, Isfahan, Iran
| | - Ali Jahanian
- Faculty of Computer Science and Engineering, Shahid Beheshti University, G.C., Velenjak, Tehran 19839-63113, Iran.
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Olson X, Kotani S, Padilla JE, Hallstrom N, Goltry S, Lee J, Yurke B, Hughes WL, Graugnard E. Availability: A Metric for Nucleic Acid Strand Displacement Systems. ACS Synth Biol 2017; 6:84-93. [PMID: 26875531 PMCID: PMC5259754 DOI: 10.1021/acssynbio.5b00231] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Indexed: 12/20/2022]
Abstract
DNA strand displacement systems have transformative potential in synthetic biology. While powerful examples have been reported in DNA nanotechnology, such systems are plagued by leakage, which limits network stability, sensitivity, and scalability. An approach to mitigate leakage in DNA nanotechnology, which is applicable to synthetic biology, is to introduce mismatches to complementary fuel sequences at key locations. However, this method overlooks nuances in the secondary structure of the fuel and substrate that impact the leakage reaction kinetics in strand displacement systems. In an effort to quantify the impact of secondary structure on leakage, we introduce the concepts of availability and mutual availability and demonstrate their utility for network analysis. Our approach exposes vulnerable locations on the substrate and quantifies the secondary structure of fuel strands. Using these concepts, a 4-fold reduction in leakage has been achieved. The result is a rational design process that efficiently suppresses leakage and provides new insight into dynamic nucleic acid networks.
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Affiliation(s)
- Xiaoping Olson
- Micron
School of Materials Science & Engineering, Department of Chemistry & Biochemistry, and Department of Electrical
& Computer Engineering, Boise State
University, 1910 University
Drive, Boise, Idaho 83725, United States
| | - Shohei Kotani
- Micron
School of Materials Science & Engineering, Department of Chemistry & Biochemistry, and Department of Electrical
& Computer Engineering, Boise State
University, 1910 University
Drive, Boise, Idaho 83725, United States
| | - Jennifer E. Padilla
- Micron
School of Materials Science & Engineering, Department of Chemistry & Biochemistry, and Department of Electrical
& Computer Engineering, Boise State
University, 1910 University
Drive, Boise, Idaho 83725, United States
| | - Natalya Hallstrom
- Micron
School of Materials Science & Engineering, Department of Chemistry & Biochemistry, and Department of Electrical
& Computer Engineering, Boise State
University, 1910 University
Drive, Boise, Idaho 83725, United States
| | - Sara Goltry
- Micron
School of Materials Science & Engineering, Department of Chemistry & Biochemistry, and Department of Electrical
& Computer Engineering, Boise State
University, 1910 University
Drive, Boise, Idaho 83725, United States
| | - Jeunghoon Lee
- Micron
School of Materials Science & Engineering, Department of Chemistry & Biochemistry, and Department of Electrical
& Computer Engineering, Boise State
University, 1910 University
Drive, Boise, Idaho 83725, United States
| | - Bernard Yurke
- Micron
School of Materials Science & Engineering, Department of Chemistry & Biochemistry, and Department of Electrical
& Computer Engineering, Boise State
University, 1910 University
Drive, Boise, Idaho 83725, United States
| | - William L. Hughes
- Micron
School of Materials Science & Engineering, Department of Chemistry & Biochemistry, and Department of Electrical
& Computer Engineering, Boise State
University, 1910 University
Drive, Boise, Idaho 83725, United States
| | - Elton Graugnard
- Micron
School of Materials Science & Engineering, Department of Chemistry & Biochemistry, and Department of Electrical
& Computer Engineering, Boise State
University, 1910 University
Drive, Boise, Idaho 83725, United States
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Song X, Eshra A, Dwyer C, Reif J. Renewable DNA seesaw logic circuits enabled by photoregulation of toehold-mediated strand displacement. RSC Adv 2017. [DOI: 10.1039/c7ra02607b] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
We propose a scalable design and verifications for photoregulated renewable DNA seesaw logic circuits, which can be repeatedly reset to reliably process new inputs. Synchronized control of complex DNA reaction networks could be achieved efficiently.
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Affiliation(s)
- Xin Song
- Department of Electrical and Computer Engineering
- Duke University
- Durham
- USA
| | - Abeer Eshra
- Department of Computer Science
- Duke University
- Durham
- USA
- Department of Computer Science and Engineering
| | - Chris Dwyer
- Department of Electrical and Computer Engineering
- Duke University
- Durham
- USA
- Department of Computer Science
| | - John Reif
- Department of Electrical and Computer Engineering
- Duke University
- Durham
- USA
- Department of Computer Science
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Oishi M, Sugiyama S. An Efficient Particle-Based DNA Circuit System: Catalytic Disassembly of DNA/PEG-Modified Gold Nanoparticle-Magnetic Bead Composites for Colorimetric Detection of miRNA. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:5153-5158. [PMID: 27483209 DOI: 10.1002/smll.201601741] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 06/27/2016] [Indexed: 05/07/2023]
Abstract
An efficient particle-based DNA circuit system for a new colorimetric miRNA assay is designed and devised based on a catalytic disassembly strategy through a target miRNA-triggered DNA circuit mechanism. The new particle-based DNA circuit system shows a rapid color change as well as significant improvement of sensitivity without need for other enzymes or instruments.
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Affiliation(s)
- Motoi Oishi
- Division of Materials Science, Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki, 305-8573, Japan.
| | - Satomi Sugiyama
- Division of Materials Science, Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki, 305-8573, Japan
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9
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Determining hydrodynamic forces in bursting bubbles using DNA nanotube mechanics. Proc Natl Acad Sci U S A 2015; 112:E6086-95. [PMID: 26504222 DOI: 10.1073/pnas.1424673112] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Quantifying the mechanical forces produced by fluid flows within the ocean is critical to understanding the ocean's environmental phenomena. Such forces may have been instrumental in the origin of life by driving a primitive form of self-replication through fragmentation. Among the intense sources of hydrodynamic shear encountered in the ocean are breaking waves and the bursting bubbles produced by such waves. On a microscopic scale, one expects the surface-tension-driven flows produced during bubble rupture to exhibit particularly high velocity gradients due to the small size scales and masses involved. However, little work has examined the strength of shear flow rates in commonly encountered ocean conditions. By using DNA nanotubes as a novel fluid flow sensor, we investigate the elongational rates generated in bursting films within aqueous bubble foams using both laboratory buffer and ocean water. To characterize the elongational rate distribution associated with a bursting bubble, we introduce the concept of a fragmentation volume and measure its form as a function of elongational flow rate. We find that substantial volumes experience surprisingly large flow rates: during the bursting of a bubble having an air volume of 10 mm(3), elongational rates at least as large as [Formula: see text] s(-1) are generated in a fragmentation volume of [Formula: see text] [Formula: see text]. The determination of the elongational strain rate distribution is essential for assessing how effectively fluid motion within bursting bubbles at the ocean surface can shear microscopic particles and microorganisms, and could have driven the self-replication of a protobiont.
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Affiliation(s)
- Anthony J. Genot
- Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
| | - Jonathan Bath
- Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
| | - Andrew J. Turberfield
- Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
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