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Sakhabutdinova AR, Garafutdinov RR. Mechanism of DNA multimerization caused by strand-displacement DNA polymerases. Anal Biochem 2025; 703:115876. [PMID: 40254165 DOI: 10.1016/j.ab.2025.115876] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2025] [Revised: 04/07/2025] [Accepted: 04/18/2025] [Indexed: 04/22/2025]
Abstract
It has been recently shown that for Bst DNA polymerase, the side isothermal amplification reaction named multimerization (MM) proceeds under certain conditions. MM hinders interpretation of amplification results and reduces the accuracy and reliability of DNA/RNA diagnostics. Here, the mechanism of MM caused by strand-displacement DNA polymerases is reported. The mechanism includes the following key stages: 1) envelopment of the enzyme globule by the synthesized DNA strand, facilitated by DNA breathing, 2) convergence of the 3'-ends of the DNA strands and pseudo-cyclic trigger DNA structure formation, 3) synthesis of the products with repeated motifs resulting in their expansion due to DNA slippage. Initiation of MM reaction occurs with extremely low probability, however, the resulting few trigger DNA structures are efficiently amplified and ultimately lead to the accumulation of nonspecific amplicons (multimers). Molecular models with certain steric and thermodynamic characteristics were used to confirm the proposed mechanism. The highest MM efficiency was observed for DNA templates and reaction conditions that facilitated DNA breathing, complete envelopment of the enzyme globule with DNA strands and convergence of their 3'-ends.
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Affiliation(s)
- Assol R Sakhabutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre, Russian Academy of Sciences, Prosp, Oktyabrya, 71, 450054, Ufa, Bashkortostan, Russia.
| | - Ravil R Garafutdinov
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre, Russian Academy of Sciences, Prosp, Oktyabrya, 71, 450054, Ufa, Bashkortostan, Russia.
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Negrón DA, Trivedi S, Tolli N, Ashford D, Melton G, Guertin S, Jennings K, Necciai BD, Sozhamannan S, Abramson BW. Loop-mediated isothermal amplification assays for the detection of antimicrobial resistance elements in Vibrio cholera. BMC Bioinformatics 2024; 25:384. [PMID: 39695927 DOI: 10.1186/s12859-024-06001-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2024] [Accepted: 11/26/2024] [Indexed: 12/20/2024] Open
Abstract
BACKGROUND The bacterium Vibrio cholerae causes diarrheal illness and can acquire genetic material leading to multiple drug resistance (MDR). Rapid detection of resistance-conferring mobile genetic elements helps avoid the prescription of ineffective antibiotics for specific strains. Colorimetric loop-mediated isothermal amplification (LAMP) assays provide a rapid and cost-effective means for detection at point-of-care since they do not require specialized equipment, require limited expertise to perform, and can take less than 30 min to perform in resource limited regions. LAMP output is a color change that can be viewed by eye, but it can be difficult to design primer sets, determine target specificity, and interpret subjective color changes. METHODS We developed an algorithm for the in silico design and evaluation of LAMP assays within the open-source PCR Signature Erosion Tool (PSET) and a computer vision application for the quantitative analysis of colorimetric outputs. First, Primer3 calculates LAMP primer sequence candidates with settings based on GC-content optimization. Next, PSET aligns the primer sequences of each assay against large sequence databases to calculate sufficient sequence similarity, coverage, and primer arrangement to the intended taxa, ultimately generating a confusion matrix. Finally, we tested assay candidates in the laboratory against synthetic constructs. RESULTS As an example, we generated new LAMP assays targeting drug resistance in V. cholerae and evaluated existing ones from the literature based on in silico target specificity and in vitro testing. Improvements in the design and testing of LAMP assays, with heightened target specificity and a simple analysis platform, increase utility for in-field applications. Overall, 9 of the 16 tested LAMP assays had positive signal through visual and computer vision-based detection methods developed here. Here we show LAMP assays tested on synthetic AMR gene targets for aph(6), varG, floR, qnrVC5, and almG, which allow for resistance to aminoglycosides, penicillins, carbapenems, phenicols, fluoroquinolones, and polymyxins respectively.
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Grants
- W911SR-22-C-0049 Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense (JPEO-CBRND)
- W911SR-22-C-0049 Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense (JPEO-CBRND)
- W911SR-22-C-0049 Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense (JPEO-CBRND)
- W911SR-22-C-0049 Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense (JPEO-CBRND)
- W911SR-22-C-0049 Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense (JPEO-CBRND)
- W911SR-22-C-0049 Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense (JPEO-CBRND)
- W911SR-22-C-0049 Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense (JPEO-CBRND)
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Affiliation(s)
| | - Shipra Trivedi
- Noblis, Inc., 2002 Edmund Halley Dr, Reston, VA, 20191, USA
| | | | - David Ashford
- Noblis ESI, 14425 Penrose Pl, Chantilly, VA, 20151, USA
| | | | | | | | - Bryan D Necciai
- Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense (JPEO-CBRND), Joint Project Lead for CBRND Enabling Biotechnologies (JPL CBRND EB), Frederick, MD, 21702, USA
| | - Shanmuga Sozhamannan
- Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense (JPEO-CBRND), Joint Project Lead for CBRND Enabling Biotechnologies (JPL CBRND EB), Frederick, MD, 21702, USA
- Joint Research and Development, Inc., Stafford, VA, 22556, USA
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Chen Y, Zhu Y, Peng C, Wang X, Wu J, Chen H, Xu J. A Point-of-Care Nucleic Acid Quantification Method by Counting Light Spots Formed by LAMP Amplicons on a Paper Membrane. BIOSENSORS 2024; 14:139. [PMID: 38534246 DOI: 10.3390/bios14030139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 03/06/2024] [Accepted: 03/07/2024] [Indexed: 03/28/2024]
Abstract
Nucleic acid quantification, allowing us to accurately know the copy number of target nucleic acids, is significant for diagnosis, food safety, agricultural production, and environmental protection. However, current digital quantification methods require expensive instruments or complicated microfluidic chips, making it difficult to popularize in the point-of-care detection. Paper is an inexpensive and readily available material. In this study, we propose a simple and cost-effective paper membrane-based digital loop-mediated isothermal amplification (LAMP) method for nucleic acid quantification. In the presence of DNA fluorescence dyes, the high background signals will cover up the amplicons-formed bright spots. To reduce the background fluorescence signals, a quencher-fluorophore duplex was introduced in LAMP primers to replace non-specific fluorescence dyes. After that, the amplicons-formed spots on the paper membrane can be observed; thus, the target DNA can be quantified by counting the spots. Take Vibrio parahaemolyticus DNA detection as an instance, a good linear relationship is obtained between the light spots and the copy numbers of DNA. The paper membrane-based digital LAMP detection can detect 100 copies target DNA per reaction within 30 min. Overall, the proposed nucleic acid quantification method has the advantages of a simple workflow, short sample-in and answer-out time, low cost, and high signal-to-noise, which is promising for application in resourced limited areas.
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Affiliation(s)
- Yanju Chen
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Yuanyuan Zhu
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Cheng Peng
- Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xiaofu Wang
- Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jian Wu
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Huan Chen
- Hangzhou Digital-Micro Biotech Co., Ltd., Hangzhou 311215, China
| | - Junfeng Xu
- Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
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