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Nam H, Lee E, Yang H, Lee K, Kwak T, Kim D, Kim H, Yang M, Yang Y, Son S, Nam YH, Minn I. PROMER technology: A new real-time PCR tool enabling multiplex detection of point mutation with high specificity and sensitivity. Biol Methods Protoc 2024; 9:bpae041. [PMID: 38938409 PMCID: PMC11208725 DOI: 10.1093/biomethods/bpae041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 05/21/2024] [Accepted: 06/02/2024] [Indexed: 06/29/2024] Open
Abstract
Real-time polymerase chain reaction (real-time PCR) is a powerful tool for the precise quantification of nucleic acids in various applications. In cancer management, the monitoring of circulating tumor DNA (ctDNA) from liquid biopsies can provide valuable information for precision care, including treatment selection and monitoring, prognosis, and early detection. However, the rare and heterogeneous nature of ctDNA has made its precise detection and quantification challenging, particularly for ctDNA containing hotspot mutations. We have developed a new real-time PCR tool, PROMER technology, which enables the precise and sensitive detection of ctDNA containing cancer-driven single-point mutations. The PROMER functions as both a PRObe and priMER, providing enhanced detection specificity. We validated PROMER technology using synthetic templates with known KRAS point mutations and demonstrated its sensitivity and linearity of quantification. Using genomic DNA from human cancer cells with mutant and wild-type KRAS, we confirmed that PROMER PCR can detect mutant DNA. Furthermore, we demonstrated the ability of PROMER technology to efficiently detect mutation-carrying ctDNA from the plasma of mice with human cancers. Our results suggest that PROMER technology represents a promising new tool for the precise detection and quantification of DNA containing point mutations in the presence of a large excess of wild-type counterpart.
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Affiliation(s)
- Hwanhee Nam
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, United States
| | - Esder Lee
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Hichang Yang
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Kyeyoon Lee
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Taeho Kwak
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Dain Kim
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Hyemin Kim
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Mihwa Yang
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Younjoo Yang
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Seungwan Son
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Young-Hyean Nam
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Il Minn
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, United States
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins Medical Institutions, Baltimore, MD 21287, United States
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2
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Li XY, Cui YX, Du YC, Tang AN, Kong DM. Isothermal cross-boosting extension–nicking reaction mediated exponential signal amplification for ultrasensitive detection of polynucleotide kinase. Analyst 2020; 145:3742-3748. [DOI: 10.1039/c9an02569c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
A novel nucleic acid-based isothermal signal amplification strategy, named cross-boosting extension–nicking reaction (CBENR) is developed and successfully used for rapid and ultrasensitive detection of polynucleotide kinase (PNK) activity.
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Affiliation(s)
- Xiao-Yu Li
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- Research Center for Analytical Sciences
- College of Chemistry
- Nankai University
| | - Yun-Xi Cui
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- Research Center for Analytical Sciences
- College of Chemistry
- Nankai University
| | - Yi-Chen Du
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- Research Center for Analytical Sciences
- College of Chemistry
- Nankai University
| | - An-Na Tang
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- Research Center for Analytical Sciences
- College of Chemistry
- Nankai University
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- Research Center for Analytical Sciences
- College of Chemistry
- Nankai University
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3
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Malfatti MC, Henneke G, Balachander S, Koh KD, Newnam G, Uehara R, Crouch RJ, Storici F, Tell G. Unlike the Escherichia coli counterpart, archaeal RNase HII cannot process ribose monophosphate abasic sites and oxidized ribonucleotides embedded in DNA. J Biol Chem 2019; 294:13061-13072. [PMID: 31300556 DOI: 10.1074/jbc.ra119.009493] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 07/05/2019] [Indexed: 12/12/2022] Open
Abstract
The presence of ribonucleoside monophosphates (rNMPs) in nuclear DNA decreases genome stability. To ensure survival despite rNMP insertions, cells have evolved a complex network of DNA repair mechanisms, in which the ribonucleotide excision repair pathway, initiated by type 2 RNase H (RNase HII/2), plays a major role. We recently demonstrated that eukaryotic RNase H2 cannot repair damage, that is, ribose monophosphate abasic (both apurinic or apyrimidinic) site (rAP) or oxidized rNMP embedded in DNA. Currently, it remains unclear why RNase H2 is unable to repair these modified nucleic acids having either only a sugar moiety or an oxidized base. Here, we compared the endoribonuclease specificity of the RNase HII enzymes from the archaeon Pyrococcus abyssi and the bacterium Escherichia coli, examining their ability to process damaged rNMPs embedded in DNA in vitro We found that E. coli RNase HII cleaves both rAP and oxidized rNMP sites. In contrast, like the eukaryotic RNase H2, P. abyssi RNase HII did not display any rAP or oxidized rNMP incision activities, even though it recognized them. Notably, the archaeal enzyme was also inactive on a mismatched rNMP, whereas the E. coli enzyme displayed a strong preference for the mispaired rNMP over the paired rNMP in DNA. On the basis of our biochemical findings and also structural modeling analyses of RNase HII/2 proteins from organisms belonging to all three domains of life, we propose that RNases HII/2's dual roles in ribonucleotide excision repair and RNA/DNA hydrolysis result in limited acceptance of modified rNMPs embedded in DNA.
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Affiliation(s)
- Matilde Clarissa Malfatti
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, 33100 Udine, Italy
| | - Ghislaine Henneke
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, F-29280 Plouzané, France
| | - Sathya Balachander
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Kyung Duk Koh
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Gary Newnam
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Ryo Uehara
- Ritsumeikan Global Innovation Research Organization, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan
| | - Robert J Crouch
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - Francesca Storici
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Gianluca Tell
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, 33100 Udine, Italy.
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Birien T, Thiel A, Henneke G, Flament D, Moalic Y, Jebbar M. Development of an Effective 6-Methylpurine Counterselection Marker for Genetic Manipulation in Thermococcus barophilus. Genes (Basel) 2018; 9:genes9020077. [PMID: 29414865 PMCID: PMC5852573 DOI: 10.3390/genes9020077] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 01/30/2018] [Accepted: 02/02/2018] [Indexed: 02/03/2023] Open
Abstract
A gene disruption system for Thermococcus barophilus was developed using simvastatin (HMG-CoA reductase encoding gene) for positive selection and 5-Fluoroorotic acid (5-FOA), a pyrF gene for negative selection. Multiple gene mutants were constructed with this system, which offers the possibility of complementation in trans, but produces many false positives (<80%). To significantly reduce the rate of false positives, we used another counterselective marker, 6-methylpurine (6-MP), a toxic analog of adenine developed in Thermococcus kodakarensis, consistently correlated with the TK0664 gene (encoding a hypoxanthine-guanine phosphoribosyl-transferase). We thus replaced pyrF by TK0664 on our suicide vector and tested T. barophilus strain sensitivity to 6-MP before and after transformation. Wild-Type (WT) T. barophilus is less sensitive to 6-MP than WT T. kodakarensis, and an increase of cell resistance was achieved after deletion of the T. barophilusTERMP_00517 gene homologous to T. kodakarensisTK0664. Results confirmed the natural resistance of T. barophilus to 6-MP and show that TK0664 can confer sensitivity. This new counterselection system vastly improves genetic manipulations in T. barophilus MP, with a strong decrease in false positives to <15%. Using this genetic tool, we have started to investigate the functions of several genes involved in genomic maintenance (e.g., polB and rnhB).
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Affiliation(s)
- Tiphaine Birien
- Université de Brest (UBO, UBL), Institut Universitaire Européen de la Mer (IUEM)-UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Rue Dumont d'Urville, F-29280 Plouzané, France.
- CNRS, IUEM-UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Rue Dumont d'Urville, F-29280 Plouzané, France.
- Ifremer, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Technopôle Pointe du diable, F-29280 Plouzané, France.
| | - Axel Thiel
- Université de Brest (UBO, UBL), Institut Universitaire Européen de la Mer (IUEM)-UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Rue Dumont d'Urville, F-29280 Plouzané, France.
- CNRS, IUEM-UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Rue Dumont d'Urville, F-29280 Plouzané, France.
- Ifremer, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Technopôle Pointe du diable, F-29280 Plouzané, France.
| | - Ghislaine Henneke
- Université de Brest (UBO, UBL), Institut Universitaire Européen de la Mer (IUEM)-UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Rue Dumont d'Urville, F-29280 Plouzané, France.
- CNRS, IUEM-UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Rue Dumont d'Urville, F-29280 Plouzané, France.
- Ifremer, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Technopôle Pointe du diable, F-29280 Plouzané, France.
| | - Didier Flament
- Université de Brest (UBO, UBL), Institut Universitaire Européen de la Mer (IUEM)-UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Rue Dumont d'Urville, F-29280 Plouzané, France.
- CNRS, IUEM-UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Rue Dumont d'Urville, F-29280 Plouzané, France.
- Ifremer, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Technopôle Pointe du diable, F-29280 Plouzané, France.
| | - Yann Moalic
- Université de Brest (UBO, UBL), Institut Universitaire Européen de la Mer (IUEM)-UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Rue Dumont d'Urville, F-29280 Plouzané, France.
- CNRS, IUEM-UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Rue Dumont d'Urville, F-29280 Plouzané, France.
- Ifremer, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Technopôle Pointe du diable, F-29280 Plouzané, France.
| | - Mohamed Jebbar
- Université de Brest (UBO, UBL), Institut Universitaire Européen de la Mer (IUEM)-UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Rue Dumont d'Urville, F-29280 Plouzané, France.
- CNRS, IUEM-UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Rue Dumont d'Urville, F-29280 Plouzané, France.
- Ifremer, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Technopôle Pointe du diable, F-29280 Plouzané, France.
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Minias AE, Brzostek AM, Minias P, Dziadek J. The deletion of rnhB in Mycobacterium smegmatis does not affect the level of RNase HII substrates or influence genome stability. PLoS One 2015; 10:e0115521. [PMID: 25603150 PMCID: PMC4300193 DOI: 10.1371/journal.pone.0115521] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 11/25/2014] [Indexed: 11/24/2022] Open
Abstract
RNase HII removes RNA from RNA/DNA hybrids, such as single ribonucleotides and RNA primers generated during DNA synthesis. Both, RNase HII substrates and RNase HII deficiency have been associated with genome instability in several organisms, and genome instability is a major force leading to the acquisition of drug resistance in bacteria. Understanding the mechanisms that underlie this phenomenon is one of the challenges in identifying efficient methods to combat bacterial pathogens. The aim of the present study was set to investigate the role of rnhB, presumably encoding RNase HII, in maintaining genome stability in the M. tuberculosis model organism Mycobacterium smegmatis. We performed gene replacement through homologous recombination to obtain mutant strains of Mycobacterium smegmatis lacking the rnhB gene. The mutants did not present an altered phenotype, according to the growth rate in liquid culture or susceptibility to hydroxyurea, and did not show an increase in the spontaneous mutation rate, determined using the Luria-Delbrück fluctuation test for streptomycin resistance in bacteria. The mutants also did not present an increase in the level of RNase HII substrates, measured as the level of alkaline degradation of chromosomal DNA or determined through immunodetection. We conclude that proteins other than RnhB proteins efficiently remove RNase HII substrates in M. smegmatis. These results highlight differences in the basic biology between Mycobacteria and eukaryotes and between different species of bacteria.
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Affiliation(s)
- Alina E. Minias
- Department of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
- Department of Microbiology, Biotechnology and Immunology, University of Lodz, Lodz, Poland
- * E-mail: (AM); (JD)
| | - Anna M. Brzostek
- Department of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
| | - Piotr Minias
- Department of Teacher Training and Biodiversity Studies, University of Lodz, Lodz, Poland
| | - Jaroslaw Dziadek
- Department of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
- * E-mail: (AM); (JD)
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Pluchon PF, Fouqueau T, Crezé C, Laurent S, Briffotaux J, Hogrel G, Palud A, Henneke G, Godfroy A, Hausner W, Thomm M, Nicolas J, Flament D. An extended network of genomic maintenance in the archaeon Pyrococcus abyssi highlights unexpected associations between eucaryotic homologs. PLoS One 2013; 8:e79707. [PMID: 24244547 PMCID: PMC3820547 DOI: 10.1371/journal.pone.0079707] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 09/24/2013] [Indexed: 11/18/2022] Open
Abstract
In Archaea, the proteins involved in the genetic information processing pathways, including DNA replication, transcription, and translation, share strong similarities with those of eukaryotes. Characterizations of components of the eukaryotic-type replication machinery complex provided many interesting insights into DNA replication in both domains. In contrast, DNA repair processes of hyperthermophilic archaea are less well understood and very little is known about the intertwining between DNA synthesis, repair and recombination pathways. The development of genetic system in hyperthermophilic archaea is still at a modest stage hampering the use of complementary approaches of reverse genetics and biochemistry to elucidate the function of new candidate DNA repair gene. To gain insights into genomic maintenance processes in hyperthermophilic archaea, a protein-interaction network centred on informational processes of Pyrococcus abyssi was generated by affinity purification coupled with mass spectrometry. The network consists of 132 interactions linking 87 proteins. These interactions give insights into the connections of DNA replication with recombination and repair, leading to the discovery of new archaeal components and of associations between eucaryotic homologs. Although this approach did not allow us to clearly delineate new DNA pathways, it provided numerous clues towards the function of new molecular complexes with the potential to better understand genomic maintenance processes in hyperthermophilic archaea. Among others, we found new potential partners of the replication clamp and demonstrated that the single strand DNA binding protein, Replication Protein A, enhances the transcription rate, in vitro, of RNA polymerase. This interaction map provides a valuable tool to explore new aspects of genome integrity in Archaea and also potentially in Eucaryotes.
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Affiliation(s)
- Pierre-François Pluchon
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- Université de Bretagne Occidentale, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- CNRS, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Thomas Fouqueau
- Lehrstuhl für Mikrobiologie, Universität Regensburg, Regensburg, Germany
| | - Christophe Crezé
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- Université de Bretagne Occidentale, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- CNRS, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Sébastien Laurent
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- Université de Bretagne Occidentale, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- CNRS, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Julien Briffotaux
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- Université de Bretagne Occidentale, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- CNRS, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Gaëlle Hogrel
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- Université de Bretagne Occidentale, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- CNRS, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Adeline Palud
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- Université de Bretagne Occidentale, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- CNRS, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Ghislaine Henneke
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- Université de Bretagne Occidentale, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- CNRS, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Anne Godfroy
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- Université de Bretagne Occidentale, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- CNRS, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Winfried Hausner
- Lehrstuhl für Mikrobiologie, Universität Regensburg, Regensburg, Germany
| | - Michael Thomm
- Lehrstuhl für Mikrobiologie, Universität Regensburg, Regensburg, Germany
| | - Jacques Nicolas
- IRISA-INRIA, Campus de Beaulieu, Rennes, France
- * E-mail: (DF); (JN)
| | - Didier Flament
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- Université de Bretagne Occidentale, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- CNRS, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- * E-mail: (DF); (JN)
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In vitro reconstitution of RNA primer removal in Archaea reveals the existence of two pathways. Biochem J 2012; 447:271-80. [PMID: 22849643 DOI: 10.1042/bj20120959] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Using model DNA substrates and purified recombinant proteins from Pyrococcus abyssi, I have reconstituted the enzymatic reactions involved in RNA primer elimination in vitro. In my dual-labelled system, polymerase D performed efficient strand displacement DNA synthesis, generating 5'-RNA flaps which were subsequently released by Fen1, before ligation by Lig1. In this pathway, the initial cleavage event by RNase HII facilitated RNA primer removal of Okazaki fragments. In addition, I have shown that polymerase B was able to displace downstream DNA strands with a single ribonucleotide at the 5'-end, a product resulting from a single cut in the RNA initiator by RNase HII. After RNA elimination, the combined activities of strand displacement DNA synthesis by polymerase B and flap cleavage by Fen1 provided a nicked substrate for ligation by Lig1. The unique specificities of Okazaki fragment maturation enzymes and replicative DNA polymerases strongly support the existence of two pathways in the resolution of RNA fragments.
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Dobosy JR, Rose SD, Beltz KR, Rupp SM, Powers KM, Behlke MA, Walder JA. RNase H-dependent PCR (rhPCR): improved specificity and single nucleotide polymorphism detection using blocked cleavable primers. BMC Biotechnol 2011; 11:80. [PMID: 21831278 PMCID: PMC3224242 DOI: 10.1186/1472-6750-11-80] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 08/10/2011] [Indexed: 12/13/2022] Open
Abstract
Background The polymerase chain reaction (PCR) is commonly used to detect the presence of nucleic acid sequences both in research and diagnostic settings. While high specificity is often achieved, biological requirements sometimes necessitate that primers are placed in suboptimal locations which lead to problems with the formation of primer dimers and/or misamplification of homologous sequences. Results Pyrococcus abyssi (P.a.) RNase H2 was used to enable PCR to be performed using blocked primers containing a single ribonucleotide residue which are activated via cleavage by the enzyme (rhPCR). Cleavage occurs 5'-to the RNA base following primer hybridization to the target DNA. The requirement of the primer to first hybridize with the target sequence to gain activity eliminates the formation of primer-dimers and greatly reduces misamplification of closely related sequences. Mismatches near the scissile linkage decrease the efficiency of cleavage by RNase H2, further increasing the specificity of the assay. When applied to the detection of single nucleotide polymorphisms (SNPs), rhPCR was found to be far more sensitive than standard allele-specific PCR. In general, the best discrimination occurs when the mismatch is placed at the RNA:DNA base pair. Conclusion rhPCR eliminates the formation of primer dimers and markedly improves the specificity of PCR with respect to off-target amplification. These advantages of the assay should find utility in challenging qPCR applications such as genotyping, high level multiplex assays and rare allele detection.
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Affiliation(s)
- Joseph R Dobosy
- Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA 5224, USA
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9
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Structure and function of a novel endonuclease acting on branched DNA substrates. Biochem Soc Trans 2011; 39:145-9. [PMID: 21265762 DOI: 10.1042/bst0390145] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Branched DNA structures that occur during DNA repair and recombination must be efficiently processed by structure-specific endonucleases in order to avoid cell death. In the present paper, we summarize our screen for new interaction partners for the archaeal replication clamp that led to the functional characterization of a novel endonuclease family, dubbed NucS. Structural analyses of Pyrococcus abyssi NucS revealed an unexpected binding site for ssDNA (single-stranded DNA) that directs, together with the replication clamp, the nuclease activity of this protein towards ssDNA-dsDNA (double-stranded DNA) junctions. Our studies suggest that understanding the detailed architecture and dynamic behaviour of the NucS (nuclease specific for ssDNA)-PCNA (proliferating-cell nuclear antigen) complex with DNA will be crucial for identification of its physiologically relevant activities.
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