1
|
Chen L, Wei C, Liu Y, Liao M, Wang J, Chen J, Yang P, Li L, Xie C, Lin M, Zhang Z, Zheng Y. Development of an optimized RPA-PfAgo detection system for MTHFR C677T polymorphism genotyping. Gene 2024; 922:148544. [PMID: 38734187 DOI: 10.1016/j.gene.2024.148544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 04/10/2024] [Accepted: 05/08/2024] [Indexed: 05/13/2024]
Abstract
This study introduces an efficient RPA-PfAgo detection system for the MTHFR C677T polymorphism, proposing a potential strategy to simplify the genotyping process. By optimizing recombinase polymerase amplification (RPA) with Pyrococcus furiosus Argonaute (PfAgo) nucleases, we achieved DNA amplification at a constant temperature. The assay was fine-tuned through meticulous primer and guide DNA selection, with optimal conditions established at 2.0 µL of MgAc, a reaction temperature of 42 °C, and a 10-minute reaction time for RPA. Further optimization of the PfAgo cleavage assay revealed the ideal concentrations of MnCl2, guide DNA, molecular beacon probes, the PfAgo enzyme, and the RPA product to maximize sensitivity and specificity. Clinical validation of 20 samples showed 100% concordance with Sanger sequencing, confirming the method's precision. The RPA-PfAgo system is a promising tool for on-site genotyping, with broad applications in personalized medicine and disease prevention.
Collapse
Affiliation(s)
- Lianghui Chen
- Reproductive Medicine, Guangxi Medical and Health Key Discipline Construction Project, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, China; Industrial College of Biomedicine and Health Industry, Youjiang Medical University for Nationalities, Baise 533000, China
| | - Cheng Wei
- Reproductive Medicine, Guangxi Medical and Health Key Discipline Construction Project, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, China; Industrial College of Biomedicine and Health Industry, Youjiang Medical University for Nationalities, Baise 533000, China
| | - Yaqun Liu
- School of Life Sciences and Food Technology, Hanshan Normal University, Chaozhou 521041, China; Guangdong Hybribio Biotech Co., Ltd., Chaozhou 521041, China; Guangdong Taiantang Pharmaceutical Co., Ltd., Shantou 515000, China.
| | - Meihua Liao
- Reproductive Medicine, Guangxi Medical and Health Key Discipline Construction Project, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, China; Industrial College of Biomedicine and Health Industry, Youjiang Medical University for Nationalities, Baise 533000, China
| | - Jialin Wang
- School of Life Sciences and Food Technology, Hanshan Normal University, Chaozhou 521041, China
| | - Jiaqi Chen
- School of Life Sciences and Food Technology, Hanshan Normal University, Chaozhou 521041, China
| | - Peikui Yang
- School of Life Sciences and Food Technology, Hanshan Normal University, Chaozhou 521041, China
| | - Liejun Li
- Guangdong Hybribio Biotech Co., Ltd., Chaozhou 521041, China
| | - Chengsong Xie
- Guangdong Taiantang Pharmaceutical Co., Ltd., Shantou 515000, China
| | - Min Lin
- Industrial College of Biomedicine and Health Industry, Youjiang Medical University for Nationalities, Baise 533000, China; School of Life Sciences and Food Technology, Hanshan Normal University, Chaozhou 521041, China
| | - Zhenxia Zhang
- School of Life Sciences and Food Technology, Hanshan Normal University, Chaozhou 521041, China
| | - Yuzhong Zheng
- Industrial College of Biomedicine and Health Industry, Youjiang Medical University for Nationalities, Baise 533000, China; School of Life Sciences and Food Technology, Hanshan Normal University, Chaozhou 521041, China.
| |
Collapse
|
2
|
Krasheninina OA, Novopashina DS, Apartsin EK, Venyaminova AG. Recent Advances in Nucleic Acid Targeting Probes and Supramolecular Constructs Based on Pyrene-Modified Oligonucleotides. Molecules 2017; 22:E2108. [PMID: 29189716 PMCID: PMC6150046 DOI: 10.3390/molecules22122108] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 11/28/2017] [Accepted: 11/28/2017] [Indexed: 12/17/2022] Open
Abstract
In this review, we summarize the recent advances in the use of pyrene-modified oligonucleotides as a platform for functional nucleic acid-based constructs. Pyrene is of special interest for the development of nucleic acid-based tools due to its unique fluorescent properties (sensitivity of fluorescence to the microenvironment, ability to form excimers and exciplexes, long fluorescence lifetime, high quantum yield), ability to intercalate into the nucleic acid duplex, to act as a π-π-stacking (including anchoring) moiety, and others. These properties of pyrene have been used to construct novel sensitive fluorescent probes for the sequence-specific detection of nucleic acids and the discrimination of single nucleotide polymorphisms (SNPs), aptamer-based biosensors, agents for binding of double-stranded DNAs, and building blocks for supramolecular complexes. Special attention is paid to the influence of the design of pyrene-modified oligonucleotides on their properties, i.e., the structure-function relationships. The perspectives for the applications of pyrene-modified oligonucleotides in biomolecular studies, diagnostics, and nanotechnology are discussed.
Collapse
Affiliation(s)
- Olga A Krasheninina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
| | - Darya S Novopashina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
| | - Evgeny K Apartsin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
| | - Alya G Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
| |
Collapse
|
3
|
Kholodar SA, Novopashina DS, Meschaninova MI, Venyaminova AG. Multipyrene tandem probes for point mutations detection in DNA. J Nucleic Acids 2013; 2013:860457. [PMID: 24455205 PMCID: PMC3886547 DOI: 10.1155/2013/860457] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Accepted: 11/11/2013] [Indexed: 01/26/2023] Open
Abstract
Here we report design, synthesis and characterization of highly sensitive, specific and stable in biological systems fluorescent probes for point mutation detection in DNA. The tandems of 3'- and 5'-mono- and bis-pyrene conjugated oligo(2'-O-methylribonucleotides), protected by 3'-"inverted" thymidine, were constructed and their potential as new instruments for genetic diagnostics was studied. Novel probes have been shown to exhibit an ability to form stable duplexes with DNA target due to the stabilizing effect of multiple pyrene units at the junction. The relationship between fluorescent properties of developed probes, the number of pyrene residues at the tandem junction, and the location of point mutation has been studied. On the basis of the data obtained, we have chosen the probes possessing the highest fluorescence intensity along with the best mismatch discrimination and deletion and insertion detection ability. Application of developed probes for detection of polymorphism C677T in MTHFR gene has been demonstrated on model systems.
Collapse
Affiliation(s)
- Svetlana A. Kholodar
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Avenue 8, Novosibirsk 630090, Russia
| | - Darya S. Novopashina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Avenue 8, Novosibirsk 630090, Russia
| | - Mariya I. Meschaninova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Avenue 8, Novosibirsk 630090, Russia
| | - Alya G. Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Avenue 8, Novosibirsk 630090, Russia
| |
Collapse
|
4
|
Boutorine AS, Novopashina DS, Krasheninina OA, Nozeret K, Venyaminova AG. Fluorescent probes for nucleic Acid visualization in fixed and live cells. Molecules 2013; 18:15357-97. [PMID: 24335616 PMCID: PMC6270009 DOI: 10.3390/molecules181215357] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 11/20/2013] [Accepted: 12/05/2013] [Indexed: 12/13/2022] Open
Abstract
This review analyses the literature concerning non-fluorescent and fluorescent probes for nucleic acid imaging in fixed and living cells from the point of view of their suitability for imaging intracellular native RNA and DNA. Attention is mainly paid to fluorescent probes for fluorescence microscopy imaging. Requirements for the target-binding part and the fluorophore making up the probe are formulated. In the case of native double-stranded DNA, structure-specific and sequence-specific probes are discussed. Among the latest, three classes of dsDNA-targeting molecules are described: (i) sequence-specific peptides and proteins; (ii) triplex-forming oligonucleotides and (iii) polyamide oligo(N-methylpyrrole/N-methylimidazole) minor groove binders. Polyamides seem to be the most promising targeting agents for fluorescent probe design, however, some technical problems remain to be solved, such as the relatively low sequence specificity and the high background fluorescence inside the cells. Several examples of fluorescent probe applications for DNA imaging in fixed and living cells are cited. In the case of intracellular RNA, only modified oligonucleotides can provide such sequence-specific imaging. Several approaches for designing fluorescent probes are considered: linear fluorescent probes based on modified oligonucleotide analogs, molecular beacons, binary fluorescent probes and template-directed reactions with fluorescence probe formation, FRET donor-acceptor pairs, pyrene excimers, aptamers and others. The suitability of all these methods for living cell applications is discussed.
Collapse
Affiliation(s)
- Alexandre S. Boutorine
- Muséum National d’Histoire Naturelle, CNRS, UMR 7196, INSERM, U565, 57 rue Cuvier, B.P. 26, Paris Cedex 05, F-75231, France; E-Mail:
| | - Darya S. Novopashina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk 630090, Russia; E-Mails: (D.S.N.); (O.A.K.); (A.G.V.)
| | - Olga A. Krasheninina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk 630090, Russia; E-Mails: (D.S.N.); (O.A.K.); (A.G.V.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova Str., 2, Novosibirsk 630090, Russia
| | - Karine Nozeret
- Muséum National d’Histoire Naturelle, CNRS, UMR 7196, INSERM, U565, 57 rue Cuvier, B.P. 26, Paris Cedex 05, F-75231, France; E-Mail:
| | - Alya G. Venyaminova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk 630090, Russia; E-Mails: (D.S.N.); (O.A.K.); (A.G.V.)
| |
Collapse
|