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Hu B, Wang Y, Sun S, Luo G, Zhang S, Zhang J, Chen L, Huang Z. Specificity Enhancement of Deoxyribonucleic Acid Polymerization for Sensitive Nucleic Acid Detection. Anal Chem 2020; 92:15872-15879. [PMID: 33236629 DOI: 10.1021/acs.analchem.0c03223] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Specificity of DNA polymerization plays a critical role in DNA replication and storage of genetic information. Likewise, biotechnological applications, such as nucleic acid detection, DNA amplification, and gene cloning, require high specificity in DNA synthesis catalyzed by DNA polymerases. However, errors in DNA polymerization (such as mis-incorporation and mis-priming) can significantly jeopardize the specificity. Herein, we report our discovery that the specificity of DNA enzymatic synthesis can be substantially enhanced (up to 100-fold higher) by attenuating DNA polymerase kinetics via the phosphorothioate dNTPs. This specificity enhancement allows convenient and sensitive nucleic acid detection, polymerization, PCR, and gene cloning with complex systems (such as human cDNA and genomic DNA). Further, we found that the specificity enhancement offered higher sensitivity (up to 50-fold better) for detecting nucleic acids, such as COVID-19 viral RNAs. Our findings have revealed a simple and convenient strategy for facilitating specificity and sensitivity of nucleic acid detection, amplification, and gene cloning.
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Affiliation(s)
- Bei Hu
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, P. R. China
| | - Yitao Wang
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, P. R. China
| | - Shichao Sun
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, P. R. China
| | - Guangcheng Luo
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, P. R. China
| | - Shun Zhang
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, P. R. China
| | - Jun Zhang
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, P. R. China
| | - Lu Chen
- Szostak-CDHT Institute for Large Nucleic Acids, Chengdu 610041, Sichuan, P.R. China
| | - Zhen Huang
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, P. R. China.,Szostak-CDHT Institute for Large Nucleic Acids, Chengdu 610041, Sichuan, P.R. China
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2
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Ren XD, Liu DY, Guo HQ, Wang L, Zhao N, Su N, Wei K, Ren S, Qu XM, Dai XT, Huang Q. Sensitive detection of low-abundance in-frame deletions in EGFR exon 19 using novel wild-type blockers in real-time PCR. Sci Rep 2019; 9:8276. [PMID: 31164704 PMCID: PMC6547704 DOI: 10.1038/s41598-019-44792-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 05/24/2019] [Indexed: 01/29/2023] Open
Abstract
Epidermal growth factor receptor (EGFR) mutations are associated with response of tyrosine kinase inhibitors (TKIs) for patients with advanced non-small cell lung cancer (NSCLC). However, the existing methods for detection of samples having rare mutations(i.e. ~0.01%) have limits in terms of specificity, time consumption or cost. In the current study, novel wild-type blocking (WTB) oligonucleotides modified with phosphorothioate or inverted dT at the 5'-termini were designed to precisely detect 11 common deletion mutations in exon 19 of EGFR gene (E19del) using a WTB-PCR assay. And internal competitive leptin amplifications were further applied to enhance the specificity of the WTB-PCR system. Our results showed that WTB-PCR could completely block amplification of wild-type EGFR when 200 ng of DNA was used as template. Furthermore, the current WTB-PCR assay facilitated the detection of E19del mutations with a selectivity of 0.01% and sensitivity as low as a single copy. And, the results showed that the current WTB-PCR system exceeded detection limits afforded by the ARMS-PCR assay. In conclusion, the current WTB-PCR strategy represents a simple and cost-effective method to precisely detect various low-abundance deletion mutations.
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Affiliation(s)
- Xiao-Dong Ren
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, P.R. China
- Department of Laboratory Medicine, Institute of Surgery Research, Daping Hospital, Third Military Medical University (Army Medical University), Chongqing, 400042, P.R. China
| | - Ding-Yuan Liu
- Department of Pulmonology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, P.R. China
| | - Hai-Qin Guo
- Department of Pulmonology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, P.R. China
| | - Liu Wang
- Department of Laboratory Medicine, Institute of Surgery Research, Daping Hospital, Third Military Medical University (Army Medical University), Chongqing, 400042, P.R. China
| | - Na Zhao
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, P.R. China
| | - Ning Su
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, P.R. China
| | - Kun Wei
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, P.R. China
| | - Sai Ren
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, P.R. China
| | - Xue-Mei Qu
- Department of Laboratory Medicine, Institute of Surgery Research, Daping Hospital, Third Military Medical University (Army Medical University), Chongqing, 400042, P.R. China
| | - Xiao-Tian Dai
- Department of Pulmonology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, P.R. China.
| | - Qing Huang
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, P.R. China.
- Department of Laboratory Medicine, Institute of Surgery Research, Daping Hospital, Third Military Medical University (Army Medical University), Chongqing, 400042, P.R. China.
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3
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Tabraue-Chávez M, Luque-González MA, Marín-Romero A, Sánchez-Martín RM, Escobedo-Araque P, Pernagallo S, Díaz-Mochón JJ. A colorimetric strategy based on dynamic chemistry for direct detection of Trypanosomatid species. Sci Rep 2019; 9:3696. [PMID: 30842455 PMCID: PMC6403333 DOI: 10.1038/s41598-019-39946-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 01/29/2019] [Indexed: 11/15/2022] Open
Abstract
Leishmaniasis and Chagas disease are endemic in many countries, and re-emerging in the developed countries. A rapid and accurate diagnosis is important for early treatment for reducing the duration of infection as well as for preventing further potential health complications. In this work, we have developed a novel colorimetric molecular assay that integrates nucleic acid analysis by dynamic chemistry (ChemNAT) with reverse dot-blot hybridization in an array format for a rapid and easy discrimination of Leishmania major and Trypanosoma cruzi. The assay consists of a singleplex PCR step that amplifies a highly homologous DNA sequence which encodes for the RNA component of the large ribosome subunit. The amplicons of the two different parasites differ between them by single nucleotide variations, known as “Single Nucleotide Fingerprint” (SNF) markers. The SNF markers can be easily identified by naked eye using a novel micro Spin-Tube device "Spin-Tube", as each of them creates a specific spot pattern. Moreover, the direct use of ribosomal RNA without requiring the PCR pre-amplification step is also feasible, further increasing the simplicity of the assay. The molecular assay delivers sensitivity capable of identifying up to 8.7 copies per µL with single mismatch specificity. The Spin-Tube thus represents an innovative solution providing benefits in terms of time, cost, and simplicity, all of which are crucial for the diagnosis of infectious disease in developing countries.
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Affiliation(s)
- Mavys Tabraue-Chávez
- DestiNA Genomica S.L. Parque Tecnológico Ciencias de la Salud (PTS), Avenida de la Innovación 1, Edificio BIC, 18016, Armilla, Granada, Spain
| | - María Angélica Luque-González
- GENYO Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government. PTS Granada - Avenida de la Ilustración, 114- 18016, Granada, Spain.,Department Medicinal and Organic Chemistry, School of Pharmacy, University of Granada, Campus Cartuja s/n, 18071, Granada, Spain
| | - Antonio Marín-Romero
- DestiNA Genomica S.L. Parque Tecnológico Ciencias de la Salud (PTS), Avenida de la Innovación 1, Edificio BIC, 18016, Armilla, Granada, Spain.,GENYO Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government. PTS Granada - Avenida de la Ilustración, 114- 18016, Granada, Spain.,Department Medicinal and Organic Chemistry, School of Pharmacy, University of Granada, Campus Cartuja s/n, 18071, Granada, Spain
| | - Rosario María Sánchez-Martín
- GENYO Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government. PTS Granada - Avenida de la Ilustración, 114- 18016, Granada, Spain.,Department Medicinal and Organic Chemistry, School of Pharmacy, University of Granada, Campus Cartuja s/n, 18071, Granada, Spain
| | - Pablo Escobedo-Araque
- ECsens, CITIC-UGR, Department of Electronics and Computer Technology, University of Granada, Campus Aynadamar, 18071, Granada, Spain
| | - Salvatore Pernagallo
- DestiNA Genomica S.L. Parque Tecnológico Ciencias de la Salud (PTS), Avenida de la Innovación 1, Edificio BIC, 18016, Armilla, Granada, Spain. .,DestiNA Genomics Ltd., 7-11 Melville St, Edinburgh, EH3 7PE, United Kingdom.
| | - Juan José Díaz-Mochón
- DestiNA Genomica S.L. Parque Tecnológico Ciencias de la Salud (PTS), Avenida de la Innovación 1, Edificio BIC, 18016, Armilla, Granada, Spain. .,GENYO Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government. PTS Granada - Avenida de la Ilustración, 114- 18016, Granada, Spain. .,Department Medicinal and Organic Chemistry, School of Pharmacy, University of Granada, Campus Cartuja s/n, 18071, Granada, Spain.
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4
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Torkamaneh D, Boyle B, Belzile F. Efficient genome-wide genotyping strategies and data integration in crop plants. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:499-511. [PMID: 29352324 DOI: 10.1007/s00122-018-3056-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 01/12/2018] [Indexed: 05/21/2023]
Abstract
Next-generation sequencing (NGS) has revolutionized plant and animal research by providing powerful genotyping methods. This review describes and discusses the advantages, challenges and, most importantly, solutions to facilitate data processing, the handling of missing data, and cross-platform data integration. Next-generation sequencing technologies provide powerful and flexible genotyping methods to plant breeders and researchers. These methods offer a wide range of applications from genome-wide analysis to routine screening with a high level of accuracy and reproducibility. Furthermore, they provide a straightforward workflow to identify, validate, and screen genetic variants in a short time with a low cost. NGS-based genotyping methods include whole-genome re-sequencing, SNP arrays, and reduced representation sequencing, which are widely applied in crops. The main challenges facing breeders and geneticists today is how to choose an appropriate genotyping method and how to integrate genotyping data sets obtained from various sources. Here, we review and discuss the advantages and challenges of several NGS methods for genome-wide genetic marker development and genotyping in crop plants. We also discuss how imputation methods can be used to both fill in missing data in genotypic data sets and to integrate data sets obtained using different genotyping tools. It is our hope that this synthetic view of genotyping methods will help geneticists and breeders to integrate these NGS-based methods in crop plant breeding and research.
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Affiliation(s)
- Davoud Torkamaneh
- Département de Phytologie, Université Laval, Québec City, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC, Canada
| | - Brian Boyle
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC, Canada
| | - François Belzile
- Département de Phytologie, Université Laval, Québec City, QC, Canada.
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC, Canada.
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5
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Identification of Trypanosomatids by detecting Single Nucleotide Fingerprints using DNA analysis by dynamic chemistry with MALDI-ToF. Talanta 2017; 176:299-307. [PMID: 28917755 DOI: 10.1016/j.talanta.2017.07.059] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 07/18/2017] [Accepted: 07/20/2017] [Indexed: 01/09/2023]
Abstract
Protozoan parasites of the Trypanosomatidae family can cause devastating diseases in humans and animals, such as Human African Trypanosomiasis or Sleeping Sickness, Chagas disease and Leishmaniasis. Currently, there are molecular assays for detecting parasitic infections and their post-treatment monitoring based on nucleic acid amplification, but there are still certain limitations which limit the development of assays that can detect and discriminate between parasite infections with a single test. Here, we present the development of a novel molecular assay for the rapid identification of Trypanosomatids, integrating DNA analysis by dynamic chemistry in conjunction with Matrix-Assisted Laser Desorption Ionization - Time-of-Flight Mass Spectrometry (MALDI-ToF). Differentiation of Trypanosoma cruzi, Trypanosoma brucei and Leishmania spp. is now possible using a single reaction tube, and enables rapid identification of Trypanosomatids. The test is based on a singleplex PCR, using a specific primer pair that amplifies a 155 base pair segment of the 28S ribosomal RNA gene, within a conserved homology region of Trypanosomatidae species. Amplified fragments are analysed by dynamic chemistry using two abasic PNA probes and the four reactive nucleobases - containing an aldehyde functional group - with MALDI-ToF to identify unique molecular patterns created by each specie due to their single base differences (Single Nucleotide Fingerprint 'SNF') in this highly homologous region. This novel assay offers the possibility to expand routine diagnostic testing for Trypanosomatids, and monitoring of therapeutic responses to these infectious diseases.
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6
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Park JH, Jang H, Jung YK, Jung YL, Shin I, Cho DY, Park HG. A mass spectrometry-based multiplex SNP genotyping by utilizing allele-specific ligation and strand displacement amplification. Biosens Bioelectron 2017; 91:122-127. [DOI: 10.1016/j.bios.2016.10.065] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 10/23/2016] [Accepted: 10/24/2016] [Indexed: 01/21/2023]
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7
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Hou J, Liu X, Liu J. Detection of Single Nucleotide Polymorphism by RNase H-Cleavage Mediated Allele-Specific Extension Method. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.5504/bbeq.2012.0048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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8
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Single base extension reaction-based surface enhanced Raman spectroscopy for DNA methylation assay. Biosens Bioelectron 2012; 31:451-7. [DOI: 10.1016/j.bios.2011.11.014] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 11/07/2011] [Accepted: 11/08/2011] [Indexed: 12/23/2022]
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9
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Luk’yanova TA, Zaitseva MA, Karpov VA, Pozmogova GE. The synthesis and mass spectrometry of oligonucleotides bearing thiophosphoryl modifications of the predetermined localization. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2011. [DOI: 10.1134/s106816200801010x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Li J, Deng T, Chu X, Yang R, Jiang J, Shen G, Yu R. Rolling circle amplification combined with gold nanoparticle aggregates for highly sensitive identification of single-nucleotide polymorphisms. Anal Chem 2010; 82:2811-6. [PMID: 20192245 DOI: 10.1021/ac100336n] [Citation(s) in RCA: 181] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A highly sensitive and specific colorimetry-based rolling circle amplification (RCA) assay method for single-nucleotide polymorphism genotyping has been developed. A circular template is generated by ligation upon the recognition of a point mutation on DNA targets. An RCA amplification is then initiated using the circular template in the presence of Phi29 polymerase. The RCA product can be digested by a restricting endonuclease, and the cleaved DNA fragments can mediate the aggregation of gold nanoparticle-tagged DNA probes. This causes a colorimetric change of the solution as the indicator of the mutation occurrence, which can be detected using UV-vis spectroscopy or viewed by naked eyes. On the basis of the high amplification efficiency of Phi29 polymerase, a mutated target of approximately 70 fM can be detected in this assay. In addition, the protection of the circle template using phosphorothioated nucleotides allows the digestion reaction to be performed simultaneously in RCA. Moreover, DNA ligase offers high fidelity in distinguishing the mismatched bases at the ligation site, resulting in positive detection of mutant targets even when the ratio of the wild-type to the mutant is 10,000:1. The developed RCA-based colorimetric detection scheme was demonstrated for SNP typing of beta-thalassemia gene at position -28 in genomic DNA.
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Affiliation(s)
- Jishan Li
- State Key Laboratory of Chem/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
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11
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Wang Z, Sew PH, Chong SS, Lee CGL. Realtime exonuclease-mediated allelic discrimination (READ): a simple homogeneous genotyping assay for SNPs at the ABC gene loci. Pharmacogenomics 2010; 10:1995-2001. [PMID: 19958098 DOI: 10.2217/pgs.09.114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIMS Members of the ATP-binding-cassette transporter family are implicated in the traffic of drugs/xenobiotics. Several SNPs in these ATP-binding-cassette genes were previously identified to show evidence of recent positive selection. These recent positive selection SNPs may confer functional effects and account for variation in drug response. To facilitate association studies between these SNPs and drug response, we report the development of a homogeneous (realtime exonuclease-mediated allelic discrimination) assay to genotype these SNPs. MATERIALS & METHODS Realtime exonuclease-mediated allelic discrimination involves real-time PCR using a proof-reading enzyme and simultaneous genotype determination by product presence/absence as detected using SYBR Green I stain. RESULTS A total of 29 recent positive selection SNPs from 17 ATP-binding-cassette transporter genes were evaluated. Of the 777 eealtime exonuclease-mediated allelic discrimination assays, 773 genotypes (approximately 99.5%) were concordant with the Perlegen data and other genotyping methods. CONCLUSION Therefore, this simple, robust, rapid, cost-effective single-step, closed-tube assay with a scalable and automatable platform has potential applications in population genetic screening and association studies.
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Affiliation(s)
- Zihua Wang
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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12
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Pyshnaya IA, Vinogradova OA, Kabilov MR, Ivanova EM, Pyshnyi DV. Bridged oligonucleotides as molecular probes for investigation of enzyme-substrate interaction and allele-specific analysis of DNA. BIOCHEMISTRY (MOSCOW) 2010; 74:1009-20. [PMID: 19916912 DOI: 10.1134/s0006297909090090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The efficiency of enzymatic conversion of DNA complexes containing non-nucleotide inserts has been studied. T4 DNA ligase and Taq DNA polymerase have been included in the study as examples of widely used DNA-dependent enzymes. A series of substrate DNA complexes have been formed using native oligonucleotides and bridged ones bearing non-nucleotide inserts based on phosphodiesters of di-, tetra-, or hexaethylene glycol, 1,5-pentanediol, 1,10-decanediol, and 3-hydroxy-2(hydroxymethyl)-tetrahydrofuran. The perturbation in DNA located far from the site of the enzyme action had almost no influence on the substrate properties of the complex, while insertion near this site significantly deteriorated them. The use of a series of modified duplexes allows one to locate the position of the enzyme-binding site on DNA substrate with the accuracy of 1-2 nucleotides. The presence of a non-nucleotide insert in the complex has been also shown to enhance the efficiency of single mismatch discrimination upon both template-directed ligation and extension of oligonucleotides.
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Affiliation(s)
- I A Pyshnaya
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Novosibirsk, 630090, Russia
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13
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Zon G. Automated synthesis of phosphorus–sulfur analogs of nucleic acids—25 years on: potential therapeutic agents and proven utility in biotechnology. NEW J CHEM 2010. [DOI: 10.1039/b9nj00577c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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14
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Significance of stereochemistry of 3'-terminal phosphorothioate-modified primer in DNA polymerase-mediated chain extension. Mol Biotechnol 2008; 40:119-26. [PMID: 18769882 DOI: 10.1007/s12033-008-9096-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2008] [Accepted: 03/20/2008] [Indexed: 10/21/2022]
Abstract
Influence of stereochemistry of the 3'-terminal phosphorothioate (PS)-modified primers was studied in a single base extension (SBE) assay to evaluate any improvements in specificity. SBE reactions were catalyzed by members of the high fidelity Pfu family of DNA polymerases with (exo+) or without (exo-) 3' --> 5' exonucleolytic activity. The diastereomerically pure PS-labeled primers used in these studies were obtained either by the stereospecific chemical synthesis invented in our laboratory or by the more conventional ion-exchange chromatographic method for separation of a mixture of diastereomers (R(P) and S(P)). When the SBE reaction was performed in the presence of mispaired 2'-deoxyribonucleoside triphosphates (dNTPs), the "racemic" 3'-phosphorothioate primer mixture resulted in a lower level of 3' --> 5' exonuclease-mediated cleavage products in comparison to the SBE reactions carried out with the corresponding unmodified primer. When the diastereomerically pure RP 3'-phosphorothioate primer was examined, the results were largely the same as for the racemic 3'-phosphorothioate primer mixture. In contrast, a 3'-PS primer of S(P) configuration displayed significantly improved performance in the SBE reaction. This included the lack of 3' --> 5' proofreading products, less mispriming, and improved yield of incorporation of the correct nucleotide.
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15
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Xiao L, Zhang J, Yin Y, Chen C, Li K, Chang A, Sirois P. Molecular diagnosis of HIV and relevant novel technologies in mutation analysis. Biotechnol Adv 2008; 26:389-97. [DOI: 10.1016/j.biotechadv.2008.04.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2008] [Revised: 04/01/2008] [Accepted: 04/27/2008] [Indexed: 12/12/2022]
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16
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Grogan DW, Stengel KR. Recombination of synthetic oligonucleotides with prokaryotic chromosomes: substrate requirements of the Escherichia coli/lambdaRed and Sulfolobus acidocaldarius recombination systems. Mol Microbiol 2008; 69:1255-65. [PMID: 18631240 DOI: 10.1111/j.1365-2958.2008.06356.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In order to reveal functional properties of recombination involving short ssDNAs in hyperthermophilic archaea, we evaluated oligonucleotide-mediated transformation (OMT) in Sulfolobus acidocaldarius and Escherichia coli as a function of the molecular properties of the ssDNA substrates. Unmodified ssDNAs as short as 20-22 nt yielded recombinants in both organisms, as did longer DNAs forming as few as 2-5 base pairs on one side of the genomic mutation. The two OMT systems showed similar responses to certain end modifications of the oligonucleotides, but E. coli was found to require a 5' phosphate on 5'-limited ssDNA whereas this requirement was not evident in S. acidocaldarius. The ability of both E. coli and S. acidocaldarius to incorporate short, mismatched ssDNAs into their genomes raises questions about the biological significance of this capability, including its phylogenetic distribution among microorganisms and its impact on genome stability. These questions seem particularly relevant for S. acidocaldarius, as this archaeon has natural competence for OMT, encodes no MutSL homologues and thrives under environmental conditions that accelerate DNA decomposition.
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Affiliation(s)
- Dennis W Grogan
- Department of Biological Sciences, University of Cincinnati, 614 Rieveschl Hall, ML 0006, Cincinnati, OH 45221-0006, USA.
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17
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Tsang JCH, Charoenkwan P, Chow KCK, Jin Y, Wanapirak C, Sanguansermsri T, Lo YMD, Chiu RWK. Mass Spectrometry–Based Detection of Hemoglobin E Mutation by Allele-Specific Base Extension Reaction. Clin Chem 2007; 53:2205-9. [DOI: 10.1373/clinchem.2007.095133] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract
Background: The specific detection of a minor population of mutant DNA molecules requires methods of high specificity and sensitivity. While the single-allele base extension reaction (SABER) was shown to be useful for the detection of certain beta-thalassemia mutations, we encountered problems with false positivity during development of SABER for the noninvasive prenatal diagnosis of the hemoglobin E (HbE) disease. Systematic optimization resulted in an alternative protocol, the allele-specific base extension reaction (ASBER).
Methods: An artificial model was established by mixing genomic DNA of HbE carriers and normal individuals. Effects of terminator concentration and annealing temperature on the nonspecificity of SABER were then studied. The use of a single relevant terminator and the other 3 types of dideoxynucleotide as competing terminators were also compared in the development of the ASBER protocol. Thirteen cases of HbE-susceptible pregnancies were tested to compare the SABER and the ASBER protocols.
Results: Decreasing the single relevant terminator concentration and increasing the annealing temperature in SABER were found to improve specificity. The use of the other 3 types of dideoxynucleotide as competing terminators was shown to offer better detection sensitivity than a single terminator in ASBER. Genotyping results were all correctly determined by ASBER, except one false-negative detection (sensitivity: 80%, specificity: 100%).
Conclusions: An alternative mass spectrometry–based protocol for noninvasive prenatal diagnosis, ASBER, has been successfully developed to allow the detection of a minor DNA population with a point mutation.
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Affiliation(s)
- Jason CH Tsang
- Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR
| | | | - Katherine CK Chow
- Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR
| | | | | | | | - YM Dennis Lo
- Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR
| | - Rossa WK Chiu
- Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR
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18
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Abstract
Planar microfluidic devices have emerged as effective tools for the electrophoretic separation of a variety of different DNA inputs. The advancement of this miniaturized platform was inspired initially by demands placed on electrophoretic performance metrics by the human genome project and has provided a viable alternative to slab gel and even capillary formats due to its ability to offer high resolution separations of nucleic acid materials in a fraction of the time associated with its predecessors, consumption of substantially less sample and reagents while maintaining the ability to perform many separations in parallel for realizing ultra-high throughputs. Another compelling advantage of this separation platform is that it offers the potential for integrating front-end sample preprocessing steps onto the separation device eliminating the need for manual sample handling. This review aims to compile a recent survey of various electrophoretic separations using either glass or polymer-based microchips in the areas of genotyping and DNA sequencing as well as those involving the growing field of DNA-based forensics.
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Affiliation(s)
- Rondedrick Sinville
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA
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19
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Hu YJ, Li ZF, Diamond AM. Enhanced discrimination of single nucleotide polymorphism in genotyping by phosphorothioate proofreading allele-specific amplification. Anal Biochem 2007; 369:54-9. [PMID: 17631854 DOI: 10.1016/j.ab.2007.04.042] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2007] [Revised: 04/25/2007] [Accepted: 04/25/2007] [Indexed: 11/17/2022]
Abstract
There is a significant demand for sensitive, inexpensive, and flexible genotyping techniques that can be accomplished with reasonable throughput. Allele-specific amplification (ASA) has the advantage of combining the amplification and discrimination steps into a single reaction. However, mismatch amplification that occurs during traditional ASA limits its application for genotyping. Here, a modified ASA termed phosphorothioate proofreading allele-specific amplification (PP-ASA) is developed, for single nucleotide polymorphism (SNP) genotyping analysis. Using both 3' end phosphorothioate modification of primers and DNA polymerase with proofreading activity completely eliminated mismatch amplifications, therefore enhancing discrimination between alleles for genotyping. The conditions for PP-ASA were optimized for template concentration and amplification cycle number as both were found to be critical for accurate genotyping. The utility of PP-ASA was assessed using both plasmid and genomic DNAs as templates and validated by polymerase chain reaction (PCR)-restriction fragment length polymorphism analysis of 60 human DNA samples for two distinct SNPs. PP-ASA represents a reliable, flexible, and inexpensive assay for SNP genotyping; it could be integrated to chip- or PCR-array-based assays to improve the throughput and reduce the cost for SNP analyses.
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Affiliation(s)
- Ya Jun Hu
- Department of Human Nutrition, University of Illinois at Chicago, Chicago, IL 60612, USA.
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20
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So AP, Turner RFB, Haynes CA. Minimizing loss of sequence information in SAGE ditags by modulating the temperature dependent 3' --> 5' exonuclease activity of DNA polymerases on 3'-terminal isoheptyl amino groups. Biotechnol Bioeng 2006; 94:54-65. [PMID: 16552775 DOI: 10.1002/bit.20805] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Numerous steps are required to prepare a sequencing library for serial analysis of gene expression (or SAGE) from an original mRNA sample. The presence of inefficiencies, however, can lead to a cumulative loss of sample during processing which can yield a library of short sequence tags (SSTs) that represents only a minute fraction of the original starting sample, potentially compromising the quality of the analysis and necessitating relatively large amounts of starting material. We show here that commonly observed higher molecular weight (HMW) amplification products observed following the PCR amplification of ditags are a direct result of the presence of HMW ligation products created during ditag formation. Using model tags, we demonstrate that the formation of these HMW ligation products becomes permissible following the release of the 3'-terminal isoheptyl amine (3'-IHA) from the SST during the fill-in reaction with the Klenow fragment (KF) of DNA polymerase (DNAP) I and is mediated by its 3' --> 5' exonuclease activity. We further show that the incorporation of SSTs into HMW ligation products can lead to a loss of sequence information from SAGE analysis, potentially skewing sequencing results away from the true distribution in the original sample. By modifying fill-in conditions through the use of Vent DNAP at 12 degrees C and by including terminal phosphorothioate linkages within the SAGE adaptors to specifically inhibit exonucleolytic removal of the 3'-terminal amine, we are able to maximize the yield of ditags and bypass the need for gel purification via PAGE following PCR. The modifications described here, combined with the modifications described previously by our group for adaptor ligation, ensure that the full sequence information content in SSTs derived from the transcriptome is preserved in the pool of amplified ditags prior to the creation of a SAGE library.
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Affiliation(s)
- Austin P So
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z3
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21
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Fan X, Xu Y, Di Bisceglie AM. Efficient amplification and cloning of near full-length hepatitis C virus genome from clinical samples. Biochem Biophys Res Commun 2006; 346:1163-72. [PMID: 16793008 PMCID: PMC7092855 DOI: 10.1016/j.bbrc.2006.06.039] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2006] [Accepted: 06/02/2006] [Indexed: 11/27/2022]
Abstract
Long RT-PCR (LRP) amplification of RNA templates is sometimes difficult compared to long PCR of DNA templates. Among RNA templates, hepatitis C virus (HCV) represents an excellent example to challenge the potential of LRP technology due to its extensive secondary structures and its difficulty to be readily cultured in vitro. The only source for viral genome amplification is clinical samples in which HCV is usually present at low titers. We have created a comprehensive optimization protocol that allows robust amplification of a 9.1 kb fragment of HCV, followed by efficient cloning into a novel vector. Detailed analyses indicate the lack of potential LRP-mediated recombination and the preservation of viral diversity. Thus, our LRP protocol could be applied for the amplification of other difficult RNA templates and may facilitate RNA virus research such as linked viral mutations and reverse genetics.
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Affiliation(s)
- Xiaofeng Fan
- Division of Gastroenterology and Hepatology, Saint Louis University Liver Center, Department of Internal Medicine, Saint Louis University School of Medicine, St. Louis, MO 63110, USA.
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22
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Lee HJ, Wark AW, Corn RM. Creating advanced multifunctional biosensors with surface enzymatic transformations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2006; 22:5241-50. [PMID: 16732647 PMCID: PMC2515861 DOI: 10.1021/la060223o] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
This paper summarizes our recent work on the coupling of surface enzyme chemistry and bioaffinity interactions on biopolymer microarrays for the creation of multiplexed biosensors with enhanced selectivity and sensitivity. The surface sensitive techniques of surface plasmon resonance imaging (SPRI) and surface plasmon fluorescence spectroscopy (SPFS) are used to detect the surface enzymatic transformations in real time. Three specific examples of novel coupled surface bioaffinity/surface enzymatic processes are demonstrated: (i) a surface enzymatic amplification method utilizing the enzyme ribonuclease H (RNase H) in conjunction with RNA microarrays that permits the ultrasensitive direct detection of genomic DNA at a concentration of 1 fM without labeling or PCR amplification, (ii) the use of RNA-DNA ligation chemistry to create renewable RNA microarrays from single stranded DNA microarrays, and (iii) the application of T7 RNA polymerase for the on-chip replication of RNA from double stranded DNA microarray elements. In addition, a simple yet powerful theoretical framework that includes the contributions of both enzyme adsorption and surface enzyme kinetics is used to quantitate surface enzyme reactivity. This model is successfully applied to SPRI and SPFS measurements of surface hydrolysis reactions of RNase H and Exonuclease III (Exo III) on oligonucleotide microarrays.
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Affiliation(s)
- Hye Jin Lee
- Department of Chemistry, University of California-Irvine, Irvine, California 92697, USA
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23
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Lu DD, Chen SH, Zhang W, Liang QD, Wang SQ. Sequence confirmation of synthetic phosphorothioate oligodeoxynucleotides using Sanger sequencing reactions in combination with mass spectrometry. Anal Biochem 2005; 345:81-9. [PMID: 16102718 DOI: 10.1016/j.ab.2005.06.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2005] [Revised: 06/23/2005] [Accepted: 06/28/2005] [Indexed: 11/16/2022]
Abstract
A protocol relying on Sanger sequencing reactions in combination with mass spectrometry (MS) for sequence confirmation of antisense phosphorothioate oligodeoxynucleotides is described. In this procedure, synthetic phosphorothioate oligodeoxynucleotides are used as reverse primers for extension of matched templates with enough length (approximately 150-300 bp) for well-established Sanger sequencing. Because the complementary strand of modified primer is used directly for sequencing primer extension, the base order shown in the sequencing result is reversely complementary to phosphorothioate oligodeoxynucleotide. This sequencing method can be applied not only to phosphorothioate oligodeoxynucleotides with different lengths (13-21 mer) and base composition but also to sequences with bases' switch, deletion, or insertion. In addition, modified primers incorporate the 5' end of polymerase chain reaction (PCR) products conveying the characters of phosphorothioate modification. The method requires only common reagents and instruments and so is better suited to routine sequence analysis in quality control of phosphorothioate antisense drugs.
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Affiliation(s)
- Dan-Dan Lu
- Beijing Institute of Radiation Medicine, Beijing 100850, People's Republic of China
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24
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Zhang J, Li K, Pardinas JR, Sommer SS, Yao KT. Proofreading genotyping assays mediated by high fidelity exo+ DNA polymerases. Trends Biotechnol 2005; 23:92-6. [PMID: 15661346 DOI: 10.1016/j.tibtech.2004.12.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA polymerases with 3'-5' proofreading function mediate high fidelity DNA replication but their application for mutation detection was almost completely neglected before 1998. The obstacle facing the use of exo(+) polymerases for mutation detection could be overcome by primer-3'-termini modification, which has been tested using allele-specific primers with 3' labeling, 3' exonuclease-resistance and 3' dehydroxylation modifications. Accordingly, three new types of single nucleotide polymorphism (SNP) assays have been developed to carry out genome-wide genotyping making use of the fidelity advantage of exo(+) polymerases. Such SNP assays might also provide a novel approach for re-sequencing and de novo sequencing. These new mutation detection assays are widely adaptable to a variety of platforms, including real-time PCR, multi-well plate and microarray technologies. Application of exo(+) polymerases to genetic analysis could accelerate the pace of personalized medicine.
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Affiliation(s)
- Jia Zhang
- SNP Institute, North District of the School, Nanhua University, Hengyang, Hunan, 421001, China
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25
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Fang S, Lee HJ, Wark AW, Kim HM, Corn RM. Determination of Ribonuclease H Surface Enzyme Kinetics by Surface Plasmon Resonance Imaging and Surface Plasmon Fluorescence Spectroscopy. Anal Chem 2005; 77:6528-34. [PMID: 16223236 DOI: 10.1021/ac051283m] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The kinetics of the ribonuclease H (RNase H) surface hydrolysis of RNA-DNA heteroduplexes formed on DNA microarrays was studied using a combination of real-time surface plasmon resonance imaging (SPRI) and surface plasmon fluorescence spectroscopy (SPFS). Time-dependent SPRI and SPFS data at various enzyme concentrations were quantitatively analyzed using a simple model that couples diffusion, enzyme adsorption, and surface enzyme kinetics. This model is characterized by a set of three rate constants, enzyme adsorption (k(a)), enzyme desorption (k(d)), enzyme catalysis (k(cat)), and one dimensionless diffusion parameter (beta). Values of k(a) = 3.15 (+/-0.20) x 10(6) M(-1).s(-1), k(d) = 0.10 (+/-0.05) s(-1), and k(cat) = 0.95 (+/-0.10) s(-1) were determined from fitting all of the SPRI and SPFS data sets. One of the most interesting kinetic parameters is the surface RNase H hydrolysis reaction rate constant (k(cat)), which was found to be approximately 10 times slower than that observed in solution, but approximately 100 times faster than that recently observed for the exonuclease III surface hydrolysis of double-stranded DNA microarrays (k(cat) = 0.009 s(-1)). Moreover, the surface coverage of the intermediate enzyme-substrate complex (ES) was found to be extremely small during the course of the reaction because k(cat) is much larger than the product of k(a) and the bulk enzyme concentration.
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Affiliation(s)
- Shiping Fang
- Department of Chemistry, University of California-Irvine, Irvine, California 92697, USA
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26
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Special-Purpose Modifications and Immobilized Functional Nucleic Acids for Biomolecular Interactions. Top Curr Chem (Cham) 2005. [DOI: 10.1007/b136673] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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27
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Lin-Ling C, Zhang J, Sommer SS, Li K. Single-base discrimination mediated by proofreading inert allele specific Primers. BMB Rep 2005; 38:24-7. [PMID: 15715942 DOI: 10.5483/bmbrep.2005.38.1.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The role of 3' exonuclease excision in DNA polymerization was evaluated for primer extension using inert allele specific primers with exonuclease-digestible ddNMP at their 3' termini. Efficient primer extension was observed in amplicons where the inert allele specific primers and their corresponding templates were mismatched. However, no primer-extended products were yielded by matched amplicons with inert primers. As a control, polymerase without proofreading activity failed to yield primer-extended products from inert primers regardless of whether the primers and templates were matched or mismatched. These data indicated that activation was undertaken for the inert allele specific primers through mismatch proofreading. Complementary to our previously developed SNP-operated on/off switch, in which DNA polymerization only occurs in matched amplicon, this new mutation detection assay mediated by exo(+) DNA polymerases has immediate applications in SNP analysis independently or in combination of the two assays.
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28
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Li K, Zhang J, Chen L, Sommer SS. Superb nucleotide discrimination by a novel on/off switch for DNA polymerization and its applications. Mol Biotechnol 2005; 29:93-100. [PMID: 15699566 DOI: 10.1385/mb:29:2:093] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
With the use of polymerases having 3' to 5' exonuclease activity and 3' phosphorothioate-modified allele-specific primers, we recently devised a SNP-operated on/off switch controlling DNA polymerization. One advantage of this novel on/off switch is its adaptability to arrayed primer extension. To further expand its application in genetic analysis, this new on/off switch was evaluated in discrimination of the match/mismatch status of single nucleotides upstream from the primer 3' terminal. A set of seven amplicons was developed with the templates differing from each other by a single nucleotide. Using this set of amplicons, the new on/off switch was shown to be able to efficiently discriminate single nucleotide polymorphisms from the primer 3' terminus to the -6 position from the primer 3' terminus. These data, illustrating the broad single nucleotide discrimination ability of this novel on/off switch, explain why the SNP-operated on/off switch is powerful in SNP analysis, and also indicate useful applications to genetic analysis additional to SNP assay. First, these data broaden the application of the novel on/off switch in the analysis of mutations other than SNPs. Second, it raises a nucleotide-walking algorithm suitable for de novo array-based sequencing analysis.
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Affiliation(s)
- Kai Li
- SNP Institute, Hengyang, Hunan, China.
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29
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Lee HJ, Wark AW, Goodrich TT, Fang S, Corn RM. Surface enzyme kinetics for biopolymer microarrays: a combination of Langmuir and Michaelis-Menten concepts. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2005; 21:4050-4057. [PMID: 15835973 DOI: 10.1021/la046822h] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Real-time surface plasmon resonance (SPR) imaging measurements of surface enzymatic reactions on DNA microarrays are analyzed using a kinetics model that couples the contributions of both enzyme adsorption and surface enzyme reaction kinetics. For the case of a 1:1 binding of an enzyme molecule (E) to a surface-immobilized substrate (S), the overall enzymatic reaction can be described in terms of classical Langmuir adsorption and Michaelis-Menten concepts and three rate constants: enzyme adsorption (k(a)), enzyme desorption (k(d)) and enzyme catalysis (k(cat)). In contrast to solution enzyme kinetics, the amount of enzyme in solution is in excess as compared to the amount of substrate on the surface. Moreover, the surface concentration of the intermediary enzyme-substrate complex (ES) is not constant with time, but goes to zero as the reaction is completed. However, kinetic simulations show that the fractional surface coverage of ES on the remaining unreacted sites does reach a steady-state value throughout the course of the surface reaction. This steady-state value approaches the Langmuir equilibrium value for cases where k(a)[E] >> k(cat). Experiments using the 3' --> 5' exodeoxyribonuclease activity of Exonuclease III on double-stranded DNA microarrays as a function of temperature and enzyme concentration are used to demonstrate how this model can be applied to quantitatively analyze the SPR imaging data.
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Affiliation(s)
- Hye Jin Lee
- Department of Chemistry, University of California-Irvine, Irvine, CA 92697, USA
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30
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Yang HL, Jiang HJ, Fang WY, Xu YY, Li K, Zhang J, Liao DF, He FC. High fidelity PCR with an off/on switch mediated by proofreading polymerases combining with phosphorothioate-modified primer. Biochem Biophys Res Commun 2005; 328:265-72. [PMID: 15670779 DOI: 10.1016/j.bbrc.2004.12.159] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2004] [Indexed: 11/22/2022]
Abstract
In the initial report, introducing a single phosphorothioate modification at the very 3' terminus of the oligodeoxynucleotide primer has been shown to effectively protect the oligodeoxynucleotide degradation due to the 3' exonuclease activity. In this study, we reported a novel finding that phosphorothioate modification at the 3' end of primers could not only effectively prevent the primer from degradation, but could also mediate an off-switch extension by Pfu polymerase when primers also carry single or multiple mismatched bases located in the first eight bases of the 3' terminus. This suggests that the combination of 3' phosphorothioate-modified primers with exo+ polymerases such as Pfu constituted an on/off switch, which allows perfectly matched primers to be extended but not mismatched primers. Furthermore, we found that polymerases with different fidelities showed different efficiencies in turning off mismatched-primer mediated extension. So we described here a SYBR green-based real-time quantitative PCR assay for the detection of abundance level of gene expression that did not require fluorescently labeled gene-specific probes or complicated primer combinations. The emergence of real-time quantitative RT-PCR technology is thus suited for a diverse application with a need for high-throughput methods to detect and quantify different gene expressions by way of simplicity, versatility, and accuracy, and thus could complement global microarray-based expression profiling strategies.
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Affiliation(s)
- Hui-Ling Yang
- SNP Institute, Institute of Pharmacy and Pharmacology, Nanhua University, Hengyang 421001, Hunan, China
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31
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Liao DF, Chen LL, Peng CY, Zhang J, Li K. Exo+ proofreading polymerases mediate genetic analysis and its application in biomedical studies. Acta Pharmacol Sin 2005; 26:302-6. [PMID: 15715925 DOI: 10.1111/j.1745-7254.2005.00056.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Polymerases with a proofreading function in their internal 3' to 5' exonuclease possess high fidelity for DNA replication both in vivo and in vitro. The obstacle facing Exo+ polymerases for single nucleotide polymorphism (SNP) detection could be bypassed by using primer-3'-termini modification. This hypothesis has been well tested using three types of modified allele specific primers with: 3' labeling, 3' to 5' exonuclease resistance, and 3' dehydroxylation. Accordingly, three new SNP assaying methods have been developed to carry out genome-wide genotyping, taking advantage of the enzymatic properties of Exo+ polymerases. These new mutation detection assays are widely adaptable to a variety of platforms, including multi-well plate and microarray technologies. Application of Exo+ polymerases to genetic analysis, including genotyping that is mostly relevant to pharma-cogenetics, high-fidelity gene expression profiling, rare mutation detection and mutation load assay, will help to accelerate the pace of personalized medicine. In this review paper, we will first introduce three new assays that we have recently developed, and then describe a number of their applications in pharmacogenetics and in other biomedical studies.
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Affiliation(s)
- Duan-fang Liao
- Division of Pharmacogenomics, SNP Institute, School of Life Science, Nanhua University, Hengyang 421001, China
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32
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Zhang J, Li K. New performance from an old member: SNP assay and de novo sequencing mediated by exo+ DNA polymerases. BMB Rep 2004; 37:269-74. [PMID: 15469706 DOI: 10.5483/bmbrep.2004.37.3.269] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
DNA polymerases without the 3' exonuclease function (exo(-) pol) have been widely used in sequencing and SNP genotyping. As a major player that expedited the coming of the postgenomic era, exo(-) polymerases worked remarkably well in the Human Genome Sequencing Project. However, it has become a challenge for this class of polymerases to efficiently screen the large number of SNPs that are found in the human genome. For more than three decades it has been recognized that polymerase fidelity varied according to the presence of proofreading activity that is mediated by its internal 3' exonuclease. Polymerases with proofreading function are famous for their high fidelity in DNA replication both in vivo and in vitro, but this well-known class of polymerases has been almost completely neglected in genetic analysis in the postgenomic era. We speculate that exo(+) polymerases may exhibit higher nucleotide identification ability when compared to exo- polymerases for an in vitro genetic analysis. With the application of exo(+) polymerases in SNP assays, a novel mechanism for the maintenance of DNA replication, the on/off switch, was discovered. Two new SNP assays have been developed to carry out genome-wide genotyping, taking advantage of the enzymatic properties of exo(+) polymerases. Furthermore, the on/off switch mechanism embodies a powerful nucleotide identification ability, which can be used to discriminate the bases that are upstream of the 3' terminus, and thus defines a new concept in de novo sequencing technology. Application of exo(+) polymerases to genetic analysis, and especially SNP assays, will greatly accelerate the pace to personalized medicine.
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33
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Twist CR, Winson MK, Rowland JJ, Kell DB. Single-nucleotide polymorphism detection using nanomolar nucleotides and single-molecule fluorescence. Anal Biochem 2004; 327:35-44. [PMID: 15033508 DOI: 10.1016/j.ab.2003.12.023] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2003] [Indexed: 11/23/2022]
Abstract
We have exploited three methods for discriminating single-nucleotide polymorphisms (SNPs) by detecting the incorporation or otherwise of labeled dideoxy nucleotides at the end of a primer chain using single-molecule fluorescence detection methods. Good discrimination of incorporated vs free nucleotide may be obtained in a homogeneous assay (without washing steps) via confocal fluorescence correlation spectroscopy or by polarization anisotropy obtained from confocal fluorescence intensity distribution analysis. Moreover, the ratio of the fluorescence intensities on each polarization channel may be used directly to discriminate the nucleotides incorporated. Each measurement took just a few seconds and was done in microliter volumes with nanomolar concentrations of labeled nucleotides. Since the confocal volumes interrogated are approximately 1fL and the reaction volume could easily be lowered to nanoliters, the possibility of SNP analysis with attomoles of reagents opens up a route to very rapid and inexpensive SNP detection. The method was applied with success to the detections of SNPs that are known to occur in the BRCA1 and CFTR genes.
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Affiliation(s)
- Charles R Twist
- Institute of Biological Sciences, Cledwyn Building, University of Wales, Aberystwyth SY23 3DD, Wales, UK
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34
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King GC, Di Giusto DA, Wlassoff WA, Giesebrecht S, Flening E, Tyrelle GD. Proofreading genotyping assays and electrochemical detection of SNPs. Hum Mutat 2004; 23:420-5. [PMID: 15108272 DOI: 10.1002/humu.20034] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The use of proofreading DNA polymerases in genotyping assays offers the prospect of improved performance. To this end, we have recently used compatible DNA polymerases, protected primers, and substrates to implement proofreading single base extension (P-SBE) and proofreading allele-specific extension (PRASE) assays. Key aspects of the P-SBE and related proofreading assay formats are described here. For transduction of genotyping reactions into physical signals, electrochemical SBE implementations may offer simple, inexpensive assays in electrode array or electrophoretic formats. We have developed electrochemically-labeled nucleotides and electrode detection methods with a view to these applications. Detection of electrochemically-labeled SBE products on an oligonucleotide-modified gold electrode surface is demonstrated.
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Affiliation(s)
- Garry C King
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia.
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35
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Di Giusto DA, Wlassoff WA, Giesebrecht S, Gooding JJ, King GC. Multipotential electrochemical detection of primer extension reactions on DNA self-assembled monolayers. J Am Chem Soc 2004; 126:4120-1. [PMID: 15053597 DOI: 10.1021/ja0319036] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Electroactive nucleoside triphosphates ("electrotides") have been incorporated into primers by DNA polymerase and detected on oligonucleotide surface-assembled monolayers. Four electrotides bearing three different electroactive moieties-ferrocene, vinylferrocene, and anthraquinone-are detected in four alternative formats.
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Affiliation(s)
- Daniel A Di Giusto
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales 2052, Australia
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36
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Di Giusto DA, King GC. Strong positional preference in the interaction of LNA oligonucleotides with DNA polymerase and proofreading exonuclease activities: implications for genotyping assays. Nucleic Acids Res 2004; 32:e32. [PMID: 14973328 PMCID: PMC373430 DOI: 10.1093/nar/gnh036] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The effect of locked nucleic acid (LNA) modification position upon representative DNA polymerase and exonuclease activities has been examined for potential use in primer extension genotyping applications. For the 3'-->5' exonuclease activities of four proofreading DNA polymerases (Vent, Pfu, Klenow fragment and T7 DNA polymerase) as well as exonuclease III, an LNA at the terminal (L-1) position of a primer is found to provide partial protection against the exonucleases of the two family B polymerases only. In contrast, an LNA residue at the penultimate (L-2) position generates essentially complete nuclease resistance. The polymerase active sites of these enzymes also display a distinct preference. An L-1 LNA modification has modest effects upon poly merization, but an L-2 LNA group slows dTTP incorporation somewhat while virtually abolishing extension with ddTTP or acyTTP terminators, even with A488L Vent DNA polymerase engineered for terminator incorporation. These observations on active site preference have been utilized to demonstrate two novel assays: exonuclease-mediated single base extension (E-SBE) and proofreading allele-specific extension (PRASE). We show that a model PRASE genotyping reaction with L-2 LNA primers offers greater specificity than existing non-proofreading assays, whether or not the non-proofreading reaction employs LNA-modified primers.
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Affiliation(s)
- Daniel A Di Giusto
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
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