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Kato K, Okami J, Nakamura H, Honma K, Sato Y, Nakamura S, Kukita Y, Nakatsuka SI, Higashiyama M. Analytical Performance of a Highly Sensitive System to Detect Gene Variants Using Next-Generation Sequencing for Lung Cancer Companion Diagnostics. Diagnostics (Basel) 2023; 13:diagnostics13081476. [PMID: 37189577 DOI: 10.3390/diagnostics13081476] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/15/2023] [Accepted: 04/17/2023] [Indexed: 05/17/2023] Open
Abstract
The recent increase in the number of molecular targeted agents for lung cancer has led to the demand for the simultaneous testing of multiple genes. Although gene panels using next-generation sequencing (NGS) are ideal, conventional panels require a high tumor content, and biopsy samples often do not meet this requirement. We developed a new NGS panel, called compact panel, characterized by high sensitivity, with detection limits for mutations of 0.14%, 0.20%, 0.48%, 0.24%, and 0.20% for EGFR exon 19 deletion, L858R, T790M, BRAF V600E, and KRAS G12C, respectively. Mutation detection also had a high quantitative ability, with correlation coefficients ranging from 0.966 to 0.992. The threshold for fusion detection was 1%. The panel exhibited good concordance with the approved tests. The identity rates were as follows: EGFR positive, 100% (95% confidence interval, 95.5-100); EGFR negative, 90.9 (82.2-96.3); BRAF positive, 100 (59.0-100); BRAF negative, 100 (94.9-100); KRAS G12C positive, 100 (92.7-100); KRAS G12C negative, 100 (93.0-100); ALK positive, 96.7 (83.8-99.9); ALK negative, 98.4 (97.2-99.2); ROS1 positive, 100 (66.4-100); ROS1 negative, 99.0 (94.6-100); MET positive, 98.0 (89.0-99.9); MET negative 100 (92.8-100); RET positive, 93.8 (69.8-100); RET negative, 100 (94.9-100). The analytical performance showed that the panel could handle various types of biopsy samples obtained by routine clinical practice without requiring strict pathological monitoring, as in the case of conventional NGS panels.
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Affiliation(s)
- Kikuya Kato
- Laboratory of Medical Genomics, Nara Institute of Science and Technology, Nara 630-0192, Japan
| | - Jiro Okami
- Department of General Thoracic Surgery, Osaka International Cancer Institute, Osaka 540-0008, Japan
| | - Harumi Nakamura
- Laboratory of Genomic Pathology, Osaka International Cancer Institute, Osaka 540-0008, Japan
| | - Keiichiro Honma
- Department of Diagnostic Pathology and Cytology, Osaka International Cancer Institute, Osaka 540-0008, Japan
| | | | - Seiji Nakamura
- Laboratory of Medical Genomics, Nara Institute of Science and Technology, Nara 630-0192, Japan
| | - Yoji Kukita
- Laboratory of Medical Genomics, Nara Institute of Science and Technology, Nara 630-0192, Japan
- Laboratory of Genomic Pathology, Osaka International Cancer Institute, Osaka 540-0008, Japan
| | - Shin-Ichi Nakatsuka
- Department of Diagnostic Pathology and Cytology, Osaka International Cancer Institute, Osaka 540-0008, Japan
| | - Masahiko Higashiyama
- Department of General Thoracic Surgery, Osaka International Cancer Institute, Osaka 540-0008, Japan
- Department of Thoracic Surgery, Higashiosaka City Medical Center, Osaka 578-8588, Japan
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2
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Erickson S, Paulson J, Brown M, Hahn W, Gil J, Barron-Montenegro R, Moreno-Switt AI, Eisenberg M, Nguyen MM. Isolation and engineering of a Listeria grayi bacteriophage. Sci Rep 2021; 11:18947. [PMID: 34556683 PMCID: PMC8460666 DOI: 10.1038/s41598-021-98134-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 09/03/2021] [Indexed: 01/02/2023] Open
Abstract
The lack of bacteriophages capable of infecting the Listeria species, Listeria grayi, is academically intriguing and presents an obstacle to the development of bacteriophage-based technologies for Listeria. We describe the isolation and engineering of a novel L. grayi bacteriophage, LPJP1, isolated from farm silage. With a genome over 200,000 base pairs, LPJP1 is the first and only reported jumbo bacteriophage infecting the Listeria genus. Similar to other Gram-positive jumbo phages, LPJP1 appeared to contain modified base pairs, which complicated initial attempts to obtain genomic sequence using standard methods. Following successful sequencing with a modified approach, a recombinant of LPJP1 encoding the NanoLuc luciferase was engineered using homologous recombination. This luciferase reporter bacteriophage successfully detected 100 stationary phase colony forming units of both subspecies of L. grayi in four hours. A single log phase colony forming unit was also sufficient for positive detection in the same time period. The recombinant demonstrated complete specificity for this particular Listeria species and did not infect 150 non-L. grayi Listeria strains nor any other bacterial genus. LPJP1 is believed to be the first reported lytic bacteriophage of L. grayi as well as the only jumbo bacteriophage to be successfully engineered into a luciferase reporter.
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Affiliation(s)
- Stephen Erickson
- Laboratory Corporation of America Holdings, New Brighton, MN, 55112, USA.
| | - John Paulson
- Laboratory Corporation of America Holdings, New Brighton, MN, 55112, USA
| | - Matthew Brown
- Laboratory Corporation of America Holdings, Burlington, NC, 27215, USA
| | - Wendy Hahn
- Laboratory Corporation of America Holdings, New Brighton, MN, 55112, USA
| | - Jose Gil
- Laboratory Corporation of America Holdings, Los Angeles, CA, 90062, USA
| | - Rocío Barron-Montenegro
- Escuela de Medicina Veterinaria, Facultad de Agronomía e Ingeniería Forestal, Facultad de Ciencias Biológicas, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile.,Millennium Initiative for Collaborative Research on Bacteria Resistance (MICROB-R), Santiago, Chile
| | - Andrea I Moreno-Switt
- Escuela de Medicina Veterinaria, Facultad de Agronomía e Ingeniería Forestal, Facultad de Ciencias Biológicas, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile.,Millennium Initiative for Collaborative Research on Bacteria Resistance (MICROB-R), Santiago, Chile
| | - Marcia Eisenberg
- Laboratory Corporation of America Holdings, Burlington, NC, 27215, USA
| | - Minh M Nguyen
- Laboratory Corporation of America Holdings, New Brighton, MN, 55112, USA
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3
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Archaeal DNA Polymerase-B as a DNA Template Guardian: Links between Polymerases and Base/Alternative Excision Repair Enzymes in Handling the Deaminated Bases Uracil and Hypoxanthine. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2016; 2016:1510938. [PMID: 27721668 PMCID: PMC5045986 DOI: 10.1155/2016/1510938] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 08/01/2016] [Indexed: 02/03/2023]
Abstract
In Archaea repair of uracil and hypoxanthine, which arise by deamination of cytosine and adenine, respectively, is initiated by three enzymes: Uracil-DNA-glycosylase (UDG, which recognises uracil); Endonuclease V (EndoV, which recognises hypoxanthine); and Endonuclease Q (EndoQ), (which recognises both uracil and hypoxanthine). Two archaeal DNA polymerases, Pol-B and Pol-D, are inhibited by deaminated bases in template strands, a feature unique to this domain. Thus the three repair enzymes and the two polymerases show overlapping specificity for uracil and hypoxanthine. Here it is demonstrated that binding of Pol-D to primer-templates containing deaminated bases inhibits the activity of UDG, EndoV, and EndoQ. Similarly Pol-B almost completely turns off EndoQ, extending earlier work that demonstrated that Pol-B reduces catalysis by UDG and EndoV. Pol-B was observed to be a more potent inhibitor of the enzymes compared to Pol-D. Although Pol-D is directly inhibited by template strand uracil, the presence of Pol-B further suppresses any residual activity of Pol-D, to near-zero levels. The results are compatible with Pol-D acting as the replicative polymerase and Pol-B functioning primarily as a guardian preventing deaminated base-induced DNA mutations.
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4
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Abellón-Ruiz J, Waldron KJ, Connolly BA. Archaeoglobus Fulgidus DNA Polymerase D: A Zinc-Binding Protein Inhibited by Hypoxanthine and Uracil. J Mol Biol 2016; 428:2805-13. [PMID: 27320386 PMCID: PMC4942837 DOI: 10.1016/j.jmb.2016.06.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 04/28/2016] [Accepted: 06/13/2016] [Indexed: 02/03/2023]
Abstract
Archaeal family-D DNA polymerases (Pol-D) comprise a small (DP1) proofreading subunit and a large (DP2) polymerase subunit. Pol-D is one of the least studied polymerase families, and this publication investigates the enzyme from Archaeoglobus fulgidus (Afu Pol-D). The C-terminal region of DP2 contains two conserved cysteine clusters, and their roles are investigated using site-directed mutagenesis. The cluster nearest the C terminus is essential for polymerase activity, and the cysteines are shown to serve as ligands for a single, critical Zn(2+) ion. The cysteines farthest from the C terminal were not required for activity, and a role for these amino acids has yet to be defined. Additionally, it is shown that Afu Pol-D activity is slowed by the template strand hypoxanthine, extending previous results that demonstrated inhibition by uracil. Hypoxanthine was a weaker inhibitor than uracil. Investigations with isolated DP2, which has a measurable polymerase activity, localised the deaminated base binding site to this subunit. Uracil and hypoxanthine slowed Afu Pol-D "in trans", that is, a copied DNA strand could be inhibited by a deaminated base in the alternate strand of a replication fork. The error rate of Afu Pol-D, measured in vitro, was 0.24×10(-5), typical for a polymerase that has been proposed to carry out genome replication in the Archaea. Deleting the 3'-5' proofreading exonuclease activity reduced fidelity twofold. The results presented in this publication considerably increase our knowledge of Pol-D.
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Affiliation(s)
- Javier Abellón-Ruiz
- Institute for Cell and Molecular Biology, University of Newcastle, Newcastle upon Tyne NE2 4HH, UK
| | - Kevin J Waldron
- Institute for Cell and Molecular Biology, University of Newcastle, Newcastle upon Tyne NE2 4HH, UK
| | - Bernard A Connolly
- Institute for Cell and Molecular Biology, University of Newcastle, Newcastle upon Tyne NE2 4HH, UK.
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Elshawadfy AM, Keith BJ, Ee Ooi H, Kinsman T, Heslop P, Connolly BA. DNA polymerase hybrids derived from the family-B enzymes of Pyrococcus furiosus and Thermococcus kodakarensis: improving performance in the polymerase chain reaction. Front Microbiol 2014; 5:224. [PMID: 24904539 PMCID: PMC4034419 DOI: 10.3389/fmicb.2014.00224] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 04/28/2014] [Indexed: 11/20/2022] Open
Abstract
The polymerase chain reaction (PCR) is widely applied across the biosciences, with archaeal Family-B DNA polymerases being preferred, due to their high thermostability and fidelity. The enzyme from Pyrococcus furiosus (Pfu-Pol) is more frequently used than the similar protein from Thermococcus kodakarensis (Tkod-Pol), despite the latter having better PCR performance. Here the two polymerases have been comprehensively compared, confirming that Tkod-Pol: (1) extends primer-templates more rapidly; (2) has higher processivity; (3) demonstrates superior performance in normal and real time PCR. However, Tkod-Pol is less thermostable than Pfu-Pol and both enzymes have equal fidelities. To understand the favorable properties of Tkod-Pol, hybrid proteins have been prepared. Single, double and triple mutations were used to site arginines, present at the “forked-point” (the junction of the exonuclease and polymerase channels) of Tkod-Pol, at the corresponding locations in Pfu-Pol, slightly improving PCR performance. The Pfu-Pol thumb domain, responsible for double-stranded DNA binding, has been entirely replaced with that from Tkod-Pol, again giving better PCR properties. Combining the “forked-point” and thumb swap mutations resulted in a marked increase in PCR capability, maintenance of high fidelity and retention of the superior thermostability associated with Pfu-Pol. However, even the arginine/thumb swap mutant falls short of Tkod-Pol in PCR, suggesting further improvement within the Pfu-Pol framework is attainable. The significance of this work is the observation that improvements in PCR performance are easily attainable by blending elements from closely related archaeal polymerases, an approach that may, in future, be extended by using more polymerases from these organisms.
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Affiliation(s)
- Ashraf M Elshawadfy
- Institute of Cell and Molecular Biosciences, University of Newcastle Newcastle upon Tyne, UK
| | - Brian J Keith
- Institute of Cell and Molecular Biosciences, University of Newcastle Newcastle upon Tyne, UK
| | - H'Ng Ee Ooi
- Institute of Cell and Molecular Biosciences, University of Newcastle Newcastle upon Tyne, UK
| | - Thomas Kinsman
- Institute of Cell and Molecular Biosciences, University of Newcastle Newcastle upon Tyne, UK
| | - Pauline Heslop
- Institute of Cell and Molecular Biosciences, University of Newcastle Newcastle upon Tyne, UK
| | - Bernard A Connolly
- Institute of Cell and Molecular Biosciences, University of Newcastle Newcastle upon Tyne, UK
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6
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Richardson TT, Gilroy L, Ishino Y, Connolly BA, Henneke G. Novel inhibition of archaeal family-D DNA polymerase by uracil. Nucleic Acids Res 2013; 41:4207-18. [PMID: 23408858 PMCID: PMC3627576 DOI: 10.1093/nar/gkt083] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Archaeal family-D DNA polymerase is inhibited by the presence of uracil in DNA template strands. When the enzyme encounters uracil, following three parameters change: DNA binding increases roughly 2-fold, the rate of polymerization slows by a factor of ≈ 5 and 3'-5' proof-reading exonuclease activity is stimulated by a factor of ≈ 2. Together these changes result in a significant decrease in polymerization activity and a reduction in net DNA synthesis. Pol D appears to interact with template strand uracil irrespective of its distance ahead of the replication fork. Polymerization does not stop at a defined location relative to uracil, rather a general decrease in DNA synthesis is observed. 'Trans' inhibition, the slowing of Pol D by uracil on a DNA strand not being replicated is also observed. It is proposed that Pol D is able to interact with uracil by looping out the single-stranded template, allowing simultaneous contact of both the base and the primer-template junction to give a polymerase-DNA complex with diminished extension ability.
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Affiliation(s)
- Tomas T Richardson
- Institute for Cell and Molecular Biosciences (ICaMB), Newcastle University, Newcastle upon Tyne NE2 4HH, UK
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7
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Richardson TT, Wu X, Keith BJ, Heslop P, Jones AC, Connolly BA. Unwinding of primer-templates by archaeal family-B DNA polymerases in response to template-strand uracil. Nucleic Acids Res 2013; 41:2466-78. [PMID: 23303790 PMCID: PMC3575838 DOI: 10.1093/nar/gks1364] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Archaeal family-B DNA polymerases bind tightly to deaminated bases and stall replication on encountering uracil in template strands, four bases ahead of the primer-template junction. Should the polymerase progress further towards the uracil, for example, to position uracil only two bases in front of the junction, 3′–5′ proof-reading exonuclease activity becomes stimulated, trimming the primer and re-setting uracil to the +4 position. Uracil sensing prevents copying of the deaminated base and permanent mutation in 50% of the progeny. This publication uses both steady-state and time-resolved 2-aminopurine fluorescence to show pronounced unwinding of primer-templates with Pyrococcus furiosus (Pfu) polymerase–DNA complexes containing uracil at +2; much less strand separation is seen with uracil at +4. DNA unwinding has long been recognized as necessary for proof-reading exonuclease activity. The roles of M247 and Y261, amino acids suggested by structural studies to play a role in primer-template unwinding, have been probed. M247 appears to be unimportant, but 2-aminopurine fluorescence measurements show that Y261 plays a role in primer-template strand separation. Y261 is also required for full exonuclease activity and contributes to the fidelity of the polymerase.
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Affiliation(s)
- Tomas T Richardson
- Institute of Cell and Molecular Biosciences (ICaMB), The University of Newcastle, Newcastle upon Tyne NE2 4HH, UK
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Gouge J, Ralec C, Henneke G, Delarue M. Molecular recognition of canonical and deaminated bases by P. abyssi family B DNA polymerase. J Mol Biol 2012; 423:315-36. [PMID: 22902479 DOI: 10.1016/j.jmb.2012.07.025] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 07/27/2012] [Accepted: 07/30/2012] [Indexed: 10/28/2022]
Abstract
Euryarchaeal polymerase B can recognize deaminated bases on the template strand, effectively stalling the replication fork 4nt downstream the modified base. Using Pyrococcus abyssi DNA B family polymerase (PabPolB), we investigated the discrimination between deaminated and natural nucleotide(s) by primer extension assays, electrophoretic mobility shift assays, and X-ray crystallography. Structures of complexes between the protein and DNA duplexes with either a dU or a dH in position +4 were solved at 2.3Å and 2.9Å resolution, respectively. The PabPolB is found in the editing mode. A new metal binding site has been uncovered below the base-checking cavity where the +4 base is flipped out; it is fully hydrated in an octahedral fashion and helps guide the strongly kinked template strand. Four other crystal structures with each of the canonical bases were also solved in the editing mode, and the presence of three nucleotides in the exonuclease site caused a shift in the coordination state of its metal A from octahedral to tetrahedral. Surprisingly, we find that all canonical bases also enter the base-checking pocket with very small differences in the binding geometry and in the calculated binding free energy compared to deaminated ones. To explain how this can lead to stalling of the replication fork, the full catalytic pathway and its branches must be taken into account, during which the base is checked several times. Our results strongly suggest a switch from elongation to editing modes right after nucleotide insertion when the modified base is at position +5.
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Affiliation(s)
- Jérôme Gouge
- Unité de Dynamique Structurale des Macromolécules, UMR 3528 du CNRS, Institut Pasteur, 25 rue du Dr Roux, 75015 Paris, France
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Fidelity in archaeal information processing. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2010; 2010. [PMID: 20871851 PMCID: PMC2943090 DOI: 10.1155/2010/960298] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2010] [Accepted: 07/12/2010] [Indexed: 12/30/2022]
Abstract
A key element during the flow of genetic information in living systems is fidelity. The accuracy of DNA replication influences the genome size as well as the rate of genome evolution. The large amount of energy invested in gene expression implies that fidelity plays a major role in fitness. On the other hand, an increase in fidelity generally coincides with a decrease in velocity. Hence, an important determinant of the evolution of life has been the establishment of a delicate balance between fidelity and variability. This paper reviews the current knowledge on quality control in archaeal information processing. While the majority of these processes are homologous in Archaea, Bacteria, and Eukaryotes, examples are provided of nonorthologous factors and processes operating in the archaeal domain. In some instances, evidence for the existence of certain fidelity mechanisms has been provided, but the factors involved still remain to be identified.
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Killelea T, Ghosh S, Tan SS, Heslop P, Firbank SJ, Kool ET, Connolly BA. Probing the interaction of archaeal DNA polymerases with deaminated bases using X-ray crystallography and non-hydrogen bonding isosteric base analogues. Biochemistry 2010; 49:5772-81. [PMID: 20527806 DOI: 10.1021/bi100421r] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Archaeal family-B DNA polymerases stall replication on encountering the pro-mutagenic bases uracil and hypoxanthine. This publication describes an X-ray crystal structure of Thermococcus gorgonarius polymerase in complex with a DNA containing hypoxanthine in the single-stranded region of the template, two bases ahead of the primer-template junction. Full details of the specific recognition of hypoxanthine are revealed, allowing a comparison with published data that describe uracil binding. The two bases are recognized by the same pocket, in the N-terminal domain, and make very similar protein-DNA interactions. Specificity for hypoxanthine (and uracil) arises from a combination of polymerase-base hydrogen bonds and shape fit between the deaminated bases and the pocket. The structure with hypoxanthine at position 2 explains the stimulation of the polymerase 3'-5' proofreading exonuclease, observed with deaminated bases at this location. A beta-hairpin element, involved in partitioning the primer strand between the polymerase and exonuclease active sites, inserts between the two template bases at the extreme end of the double-stranded DNA. This denatures the two complementary primer bases and directs the resulting 3' single-stranded extension toward the exonuclease active site. Finally, the relative importance of hydrogen bonding and shape fit in determining selectivity for deaminated bases has been examined using nonpolar isosteres. Affinity for both 2,4-difluorobenzene and fluorobenzimidazole, non-hydrogen bonding shape mimics of uracil and hypoxanthine, respectively, is strongly diminished, suggesting polar protein-base contacts are important. However, residual interaction with 2,4-difluorobenzene is seen, confirming a role for shape recognition.
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Affiliation(s)
- Tom Killelea
- Institute of Cell and Molecular Biosciences (ICaMB), The University of Newcastle, Newcastle upon Tyne NE2 4HH, UK
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