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Xu J, Han X, Xu W, Liu J, Zhu A, Song D, Long F. Development of a hybridization chain reaction-powered lab-on-fiber device for ultrafast point-of-care testing of circulating tuor DNA in whole blood. Talanta 2023; 259:124475. [PMID: 37004394 DOI: 10.1016/j.talanta.2023.124475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 03/04/2023] [Accepted: 03/19/2023] [Indexed: 03/30/2023]
Abstract
Circulating tumor DNA (ctDNA) demonstrates great promise in the guidance of prognostication, diagnosis, and surveillance of cancers, which highlights the need for rapid and sensitive point-of-care testing (POCT) technologies. Hybridization chain reaction (HCR)-based optical biosensors provide excellent solutions due to their prominent features. However, the requirement of a sophisticated and expensive optical readout device, relatively long detection time, and heating hold back their scalability and clinical applications. Here, an innovative HCR-powered lab-on-fiber device (HCR-LOFD) was developed for rapid on-site detection of ctDNA with high sensitivity, specificity, and reproducibility. A LOFD with a compact all-fiber optical structure was constructed for the fluorescence detection of the HCR system. Combining HCR, fluorescence energy resonant transfer, and the evanescent wave fluorescence principle, HCR-LOFD achieved the quantitative detection of KRAS G12D, the 12th amino acid from glycine (Gly) mutated aspartate (Asp) and the most common mutation of KARS, in 5 min at room temperature based on end-point detection mode or real-time fluorescence detection mode. This new assay platform was also successfully applied for the direct detection of KRAS G12D in whole blood with simple dilution. The application of HCR-LOFD not only greatly simplifies the complexity of optical readout devices and improves their scalability but also potentially serves as a sample-to-answer solution for the detection of biomarkers in limited medical resource regions.
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Kumari R, Lim JW, Sullivan MR, Malampy R, Baush C, Smolina I, Robin H, Demidov VV, Ugolini GS, Auclair JR, Konry T. A Novel Rolling Circle Amplification-Based Detection of SARS-CoV-2 with Multi-Region Padlock Hybridization. Diagnostics (Basel) 2022; 12:diagnostics12092252. [PMID: 36140653 PMCID: PMC9497765 DOI: 10.3390/diagnostics12092252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/09/2022] [Accepted: 09/11/2022] [Indexed: 11/16/2022] Open
Abstract
SARS-CoV-2 has remained a global health burden, primarily due to the continuous evolution of different mutant strains. These mutations present challenges to the detection of the virus, as the target genes of qPCR, the standard diagnostic method, may possess sequence alterations. In this study, we develop an isothermal one-step detection method using rolling circle amplification (RCA) for SARS-CoV-2. This novel strategy utilizes a multi-padlock (MP-RCA) approach to detect viral-RNA via a simplified procedure with the reliable detection of mutated strains over other procedures. We designed 40 padlock-based probes to target different sequences across the SARS-CoV-2 genome. We established an optimal one-step isothermal reaction protocol utilizing a fluorescent output detected via a plate reader to test a variety of padlock combinations. This method was tested on RNA samples collected from nasal swabs and validated via PCR. S-gene target failure (SGTF)-mutated strains of SARS-CoV-2 were included. We demonstrated that the sensitivity of our assay was linearly proportional to the number of padlock probes used. With the 40-padlock combination the MP-RCA assay was able to correctly detect 45 out 55 positive samples (81.8% efficiency). This included 10 samples with SGTF mutations which we were able to detect as positive with 100% efficiency. We found that the MP-RCA approach improves the sensitivity of the MP-RCA assay, and critically, allows for the detection of SARS-CoV-2 variants with SGTF. Our method offers the simplicity of the reaction and requires basic equipment compared to standard qPCR. This method provides an alternative approach to overcome the challenges of detecting SARS-CoV-2 and other rapidly mutating viruses.
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Affiliation(s)
- Rajesh Kumari
- Department of Pharmaceutical Sciences, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
| | - Ji Won Lim
- Department of Pharmaceutical Sciences, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
| | - Matthew Ryan Sullivan
- Department of Pharmaceutical Sciences, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
| | - Rachel Malampy
- Life Science Testing Center, Northeastern University, Burlington, MA 01803, USA
| | - Connor Baush
- Life Science Testing Center, Northeastern University, Burlington, MA 01803, USA
| | | | - Howard Robin
- LJ Pathology Consultants, La Jolla, CA 92037, USA
| | - Vadim V. Demidov
- Biotechnology & Pharmaceuticals Group, Global Prior Art, Inc., Boston, MA 02109, USA
| | - Giovanni Stefano Ugolini
- Department of Pharmaceutical Sciences, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
| | | | - Tania Konry
- Department of Pharmaceutical Sciences, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
- Correspondence:
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Ravi Kumara GS, Pandith A, Seo YJ. Highly fluorescent morpholine naphthalimide deoxyuridine nucleotide for the detection of miRNA 24-3P through rolling circle amplification. Analyst 2021; 145:4777-4781. [PMID: 32478340 DOI: 10.1039/d0an00723d] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In this study we synthesized the nucleotide dUrkTP, a highly fluorescent naphthalimide deoxyuridine triphosphate that undergoes aggregation-induced emission (AIE). We incorporated and extended dUrkTP during the primer extension of DNA mediated by DNA polymerase, and also in the rolling circle amplification of DNA mediated by Phi29 polymerase. Accordingly, we could use this fluorescent nucleotide for the detection of microRNA 24-3P, a biomarker of porcine reproductive and respiratory syndrome virus. The direct labeling system obtained during rolling circle DNA amplification exhibited increased fluorescence, due to AIE of the dUrkTP residue upon gel formation, thereby allowing the detection of miRNA 24-3P. This direct labeling system facilitated the simple and inexpensive detection of miRNA 24-3P with high sensitivity (limit of detection: 3.58 fM) and selectivity.
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Affiliation(s)
| | - Anup Pandith
- Department of Chemistry, Jeonbuk National University, Jeonju 561-756, South Korea.
| | - Young Jun Seo
- Department of Chemistry, Jeonbuk National University, Jeonju 561-756, South Korea.
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Zingg JM, Daunert S. Trinucleotide Rolling Circle Amplification: A Novel Method for the Detection of RNA and DNA. Methods Protoc 2018. [PMCID: PMC6526412 DOI: 10.3390/mps1020015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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Hollenstein M. Generation of long, fully modified, and serum-resistant oligonucleotides by rolling circle amplification. Org Biomol Chem 2016; 13:9820-4. [PMID: 26273951 DOI: 10.1039/c5ob01540e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Rolling Circle Amplification (RCA) is an isothermal enzymatic method generating single-stranded DNA products consisting of concatemers containing multiple copies of the reverse complement of the circular template precursor. Little is known on the compatibility of modified nucleoside triphosphates (dN*TPs) with RCA, which would enable the synthesis of long, fully modified ssDNA sequences. Here, dNTPs modified at any position of the scaffold were shown to be compatible with rolling circle amplification, yielding long (>1 kb), and fully modified single-stranded DNA products. This methodology was applied for the generation of long, cytosine-rich synthetic mimics of telomeric DNA. The resulting modified oligonucleotides displayed an improved resistance to fetal bovine serum.
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Affiliation(s)
- Marcel Hollenstein
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
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Preus S, Wilhelmsson LM. Advances in quantitative FRET-based methods for studying nucleic acids. Chembiochem 2012; 13:1990-2001. [PMID: 22936620 DOI: 10.1002/cbic.201200400] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Indexed: 01/02/2023]
Abstract
Förster resonance energy transfer (FRET) is a powerful tool for monitoring molecular distances and interactions at the nanoscale level. The strong dependence of transfer efficiency on probe separation makes FRET perfectly suited for "on/off" experiments. To use FRET to obtain quantitative distances and three-dimensional structures, however, is more challenging. This review summarises recent studies and technological advances that have improved FRET as a quantitative molecular ruler in nucleic acid systems, both at the ensemble and at the single-molecule levels.
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Affiliation(s)
- Søren Preus
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
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Chang CC, Chen CC, Wei SC, Lu HH, Liang YH, Lin CW. Diagnostic devices for isothermal nucleic acid amplification. SENSORS (BASEL, SWITZERLAND) 2012; 12:8319-37. [PMID: 22969402 PMCID: PMC3436031 DOI: 10.3390/s120608319] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 05/29/2012] [Accepted: 06/07/2012] [Indexed: 11/23/2022]
Abstract
Since the development of the polymerase chain reaction (PCR) technique, genomic information has been retrievable from lesser amounts of DNA than previously possible. PCR-based amplifications require high-precision instruments to perform temperature cycling reactions; further, they are cumbersome for routine clinical use. However, the use of isothermal approaches can eliminate many complications associated with thermocycling. The application of diagnostic devices for isothermal DNA amplification has recently been studied extensively. In this paper, we describe the basic concepts of several isothermal amplification approaches and review recent progress in diagnostic device development.
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Affiliation(s)
- Chia-Chen Chang
- Institute of Biomedical Engineering, National Taiwan University, Taipei 10617, Taiwan.
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Linck L, Kapusta P, Resch-Genger U. Spectroscopic and photophysical properties of dUTP and internally DNA bound fluorophores for optimized signal detection in biological formats. Photochem Photobiol 2012; 88:867-75. [PMID: 22360746 DOI: 10.1111/j.1751-1097.2012.01119.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Efficient signal generation in DNA-based assays requires understanding of the influence of fluorophore's interactions on the spectroscopic properties. The resulting changes in fluorescence intensity, quantum yield, emission anisotropy, and fluorescence lifetime provide straightforward tools for the study of molecular dynamics and interaction between labels and nucleic acids. Searching for bright fluorescent reporters for rolling circle amplification (RCA) as efficient signal enhancement strategy for biological formats, we investigated the spectroscopic properties of seven dyes: cyanines, rhodamines, and BODIPYs. They spectrally resemble Cy3, the most frequently used fluorophore in biodetection formats, and are measured in six samples (free dye, dye-dUTP, internally labeled ssDNA and dsDNA-single- and triple-labeled) using steady-state and time-resolved fluorometry. Special emphasis was dedicated to characterizing the nature of the interaction of these fluorophores differing in dye class, charge, and rigidity. Our results suggest dye charge and structure as main factors governing the dye's interactions, with DY-555 and Cy3B presenting the best candidates for our envisaged signal amplification strategy. This label comparison underlines the importance of a proper understanding of structure-property relations and dye-biomolecule interactions for reporter choice and presents a road map towards the design and interpretation of experiments using these labels on DNA of known sequence.
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Affiliation(s)
- Lena Linck
- BAM Federal Institute for Materials Research and Testing, Berlin, Germany
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Hwang H, Kim H, Myong S. Protein induced fluorescence enhancement as a single molecule assay with short distance sensitivity. Proc Natl Acad Sci U S A 2011; 108:7414-8. [PMID: 21502529 PMCID: PMC3088603 DOI: 10.1073/pnas.1017672108] [Citation(s) in RCA: 188] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Single-molecule FRET has been widely used for monitoring protein-nucleic acids interactions. Direct visualization of the interactions, however, often requires a site-specific labeling of the protein, which can be circuitous and inefficient. In addition, FRET is insensitive to distance changes in the 0-3-nm range. Here, we report a systematic calibration of a single molecule fluorescence assay termed protein induced fluorescence enhancement. This method circumvents protein labeling and displays a marked distance dependence below the 4-nm distance range. The enhancement of fluorescence is based on the photophysical phenomenon whereby the intensity of a fluorophore increases upon proximal binding of a protein. Our data reveals that the method can resolve as small as a single base pair distance at the extreme vicinity of the fluorophore, where the enhancement is maximized. We demonstrate the general applicability and distance sensitivity using (a) a finely spaced DNA ladder carrying a restriction site for BamHI, (b) RNA translocation by DExH enzyme RIG-I, and (c) filament dynamics of RecA on single-stranded DNA. The high spatio-temporal resolution data and sensitivity to short distances combined with the ability to bypass protein labeling makes this assay an effective alternative or a complement to FRET.
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Affiliation(s)
- Helen Hwang
- Bioengineering Department, University of Illinois, Urbana‐Champaign, Urbana, IL 61801
- Medical Scholars Program, University of Illinois, Urbana‐Champaign, Urbana, IL 61801
| | - Hajin Kim
- Physics Department, University of Illinois, Urbana‐Champaign, Urbana, IL 61801; and
| | - Sua Myong
- Bioengineering Department, University of Illinois, Urbana‐Champaign, Urbana, IL 61801
- Institute for Genomic Biology, University of Illinois, Urbana‐Champaign, Urbana, IL 61801
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Stougaard M, Juul S, Andersen FF, Knudsen BR. Strategies for highly sensitive biomarker detection by Rolling Circle Amplification of signals from nucleic acid composed sensors. Integr Biol (Camb) 2011; 3:982-92. [DOI: 10.1039/c1ib00049g] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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