1
|
Palla M, Punthambaker S, Stranges B, Vigneault F, Nivala J, Wiegand D, Ayer A, Craig T, Gremyachinskiy D, Franklin H, Sun S, Pollard J, Trans A, Arnold C, Schwab C, Mcgaw C, Sarvabhowman P, Dalal D, Thai E, Amato E, Lederman I, Taing M, Kelley S, Qwan A, Fuller CW, Roever S, Church GM. Multiplex Single-Molecule Kinetics of Nanopore-Coupled Polymerases. ACS NANO 2021; 15:489-502. [PMID: 33370106 DOI: 10.1021/acsnano.0c05226] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
DNA polymerases have revolutionized the biotechnology field due to their ability to precisely replicate stored genetic information. Screening variants of these enzymes for specific properties gives the opportunity to identify polymerases with different features. We have previously developed a single-molecule DNA sequencing platform by coupling a DNA polymerase to an α-hemolysin pore on a nanopore array. Here, we use this approach to demonstrate a single-molecule method that enables rapid screening of polymerase variants in a multiplex manner. In this approach, barcoded DNA strands are complexed with polymerase variants and serve as templates for nanopore sequencing. Nanopore sequencing of the barcoded DNA reveals both the barcode identity and kinetic properties of the polymerase variant associated with the cognate barcode, allowing for multiplexed investigation of many polymerase variants in parallel on a single nanopore array. Further, we develop a robust classification algorithm that discriminates kinetic characteristics of the different polymerase mutants. As a proof of concept, we demonstrate the utility of our approach by screening a library of ∼100 polymerases to identify variants for potential applications of biotechnological interest. We anticipate our screening method to be broadly useful for applications that require polymerases with altered physical properties.
Collapse
Affiliation(s)
- Mirkó Palla
- Harvard Medical School, Department of Genetics, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, United States
| | - Sukanya Punthambaker
- Harvard Medical School, Department of Genetics, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, United States
| | - Benjamin Stranges
- Harvard Medical School, Department of Genetics, Boston, Massachusetts 02115, United States
| | - Frederic Vigneault
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, United States
| | - Jeff Nivala
- Harvard Medical School, Department of Genetics, Boston, Massachusetts 02115, United States
| | - Daniel Wiegand
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, United States
| | - Aruna Ayer
- Roche Sequencing Solutions, Santa Clara, California 95050, United States
| | - Timothy Craig
- Roche Sequencing Solutions, Santa Clara, California 95050, United States
| | | | - Helen Franklin
- Roche Sequencing Solutions, Santa Clara, California 95050, United States
| | - Shaw Sun
- Roche Sequencing Solutions, Santa Clara, California 95050, United States
| | - James Pollard
- Roche Sequencing Solutions, Santa Clara, California 95050, United States
| | - Andrew Trans
- Roche Sequencing Solutions, Santa Clara, California 95050, United States
| | - Cleoma Arnold
- Roche Sequencing Solutions, Santa Clara, California 95050, United States
| | - Charles Schwab
- Roche Sequencing Solutions, Santa Clara, California 95050, United States
| | - Colin Mcgaw
- Roche Sequencing Solutions, Santa Clara, California 95050, United States
| | | | - Dhruti Dalal
- Roche Sequencing Solutions, Santa Clara, California 95050, United States
| | - Eileen Thai
- Roche Sequencing Solutions, Santa Clara, California 95050, United States
| | - Evan Amato
- Roche Sequencing Solutions, Santa Clara, California 95050, United States
| | - Ilya Lederman
- Roche Sequencing Solutions, Santa Clara, California 95050, United States
| | - Meng Taing
- Roche Sequencing Solutions, Santa Clara, California 95050, United States
| | - Sara Kelley
- Roche Sequencing Solutions, Santa Clara, California 95050, United States
| | - Adam Qwan
- Roche Sequencing Solutions, Santa Clara, California 95050, United States
| | - Carl W Fuller
- Roche Sequencing Solutions, Santa Clara, California 95050, United States
- Columbia University, Center for Genome Technology and Biomolecular Engineering, Department of Chemical Engineering, New York, New York 10027, United States
| | - Stefan Roever
- Roche Sequencing Solutions, Santa Clara, California 95050, United States
| | - George M Church
- Harvard Medical School, Department of Genetics, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, United States
| |
Collapse
|
2
|
Aloisi CMN, Nilforoushan A, Ziegler N, Sturla SJ. Sequence-Specific Quantitation of Mutagenic DNA Damage via Polymerase Amplification with an Artificial Nucleotide. J Am Chem Soc 2020; 142:6962-6969. [PMID: 32196326 PMCID: PMC7192524 DOI: 10.1021/jacs.9b11746] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
![]()
DNA mutations can result from replication
errors due to different
forms of DNA damage, including low-abundance DNA adducts induced by
reactions with electrophiles. The lack of strategies to measure DNA
adducts within genomic loci, however, limits our understanding of
chemical mutagenesis. The use of artificial nucleotides incorporated
opposite DNA adducts by engineered DNA polymerases offers a potential
basis for site-specific detection of DNA adducts, but the availability
of effective artificial nucleotides that insert opposite DNA adducts
is extremely limited, and furthermore, there has been no report of
a quantitative strategy for determining how much DNA alkylation occurs
in a sequence of interest. In this work, we synthesized an artificial
nucleotide triphosphate that is selectively inserted opposite O6-carboxymethyl-guanine DNA by an engineered
polymerase and is required for DNA synthesis past the adduct. We characterized
the mechanism of this enzymatic process and demonstrated that the
artificial nucleotide is a marker for the presence and location in
the genome of O6-carboxymethyl-guanine.
Finally, we established a mass spectrometric method for quantifying
the incorporated artificial nucleotide and obtained a linear relationship
with the amount of O6-carboxymethyl-guanine
in the target sequence. In this work, we present a strategy to identify,
locate, and quantify a mutagenic DNA adduct, advancing tools for linking
DNA alkylation to mutagenesis and for detecting DNA adducts in genes
as potential diagnostic biomarkers for cancer prevention.
Collapse
Affiliation(s)
- Claudia M N Aloisi
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092 Zurich, Switzerland
| | - Arman Nilforoushan
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092 Zurich, Switzerland
| | - Nathalie Ziegler
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092 Zurich, Switzerland
| | - Shana J Sturla
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092 Zurich, Switzerland
| |
Collapse
|
3
|
Identification of Thermus aquaticus DNA polymerase variants with increased mismatch discrimination and reverse transcriptase activity from a smart enzyme mutant library. Sci Rep 2019; 9:590. [PMID: 30679705 PMCID: PMC6345897 DOI: 10.1038/s41598-018-37233-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 12/02/2018] [Indexed: 12/13/2022] Open
Abstract
DNA polymerases the key enzymes for several biotechnological applications. Obviously, nature has not evolved these enzymes to be compatible with applications in biotechnology. Thus, engineering of a natural scaffold of DNA polymerases may lead to enzymes improved for several applications. Here, we investigated a two-step approach for the design and construction of a combinatorial library of mutants of KlenTaq DNA polymerase. First, we selected amino acid sites for saturation mutagenesis that interact with the primer/template strands or are evolutionarily conserved. From this library, we identified mutations that little interfere with DNA polymerase activity. Next, these functionally active mutants were combined randomly to construct a second library with enriched sequence diversity. We reasoned that the combination of mutants that have minuscule effect on enzyme activity and thermostability, will result in entities that have an increased mutation load but still retain activity. Besides activity and thermostability, we screened the library for entities with two distinct properties. Indeed, we identified two different KlenTaq DNA polymerase variants that either exhibit increased mismatch extension discrimination or increased reverse transcription PCR activity, respectively.
Collapse
|
4
|
Abstract
DNA repair is now understood to play a key role in a variety of disease states, most notably cancer. Tools for studying DNA have typically relied on traditional biochemical methods which are often laborious and indirect. Efforts to study the biology and therapeutic relevance of DNA repair pathways can be limited by such methods. Recently, specific fluorescent probes have been developed to aid in the study of DNA repair. Fluorescent probes offer the advantage of being able to directly assay for DNA repair activity in a simple, mix-and-measure format. This review will summarize the distinct classes of probe designs and their potential utility in varied research and preclinical settings.
Collapse
Affiliation(s)
- David L. Wilson
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Eric T. Kool
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| |
Collapse
|
5
|
Aschenbrenner J, Werner S, Marchand V, Adam M, Motorin Y, Helm M, Marx A. Engineering of a DNA Polymerase for Direct m 6 A Sequencing. Angew Chem Int Ed Engl 2018; 57:417-421. [PMID: 29115744 PMCID: PMC5768020 DOI: 10.1002/anie.201710209] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Indexed: 12/16/2022]
Abstract
Methods for the detection of RNA modifications are of fundamental importance for advancing epitranscriptomics. N6 -methyladenosine (m6 A) is the most abundant RNA modification in mammalian mRNA and is involved in the regulation of gene expression. Current detection techniques are laborious and rely on antibody-based enrichment of m6 A-containing RNA prior to sequencing, since m6 A modifications are generally "erased" during reverse transcription (RT). To overcome the drawbacks associated with indirect detection, we aimed to generate novel DNA polymerase variants for direct m6 A sequencing. Therefore, we developed a screen to evolve an RT-active KlenTaq DNA polymerase variant that sets a mark for N6 -methylation. We identified a mutant that exhibits increased misincorporation opposite m6 A compared to unmodified A. Application of the generated DNA polymerase in next-generation sequencing allowed the identification of m6 A sites directly from the sequencing data of untreated RNA samples.
Collapse
Affiliation(s)
- Joos Aschenbrenner
- Department of Chemistry, Konstanz Research School Chemical BiologyUniversity of KonstanzUniversitätsstraße 1078457KonstanzGermany
| | - Stephan Werner
- Institute of Pharmacy and BiochemistryJohannes Gutenberg University MainzStaudingerweg 555128MainzGermany
| | - Virginie Marchand
- Laboratoire Ingénierie Moléculaire et Physiopathologie Articulaire, IMoPA, UMR7365 CNRS-ULBiopôle de L'Université de Lorraine9, Avenue de la Forêt de Haye54505Vandoeuvre-les-NancyFrance
| | - Martina Adam
- Department of Chemistry, Konstanz Research School Chemical BiologyUniversity of KonstanzUniversitätsstraße 1078457KonstanzGermany
| | - Yuri Motorin
- Laboratoire Ingénierie Moléculaire et Physiopathologie Articulaire, IMoPA, UMR7365 CNRS-ULBiopôle de L'Université de Lorraine9, Avenue de la Forêt de Haye54505Vandoeuvre-les-NancyFrance
| | - Mark Helm
- Institute of Pharmacy and BiochemistryJohannes Gutenberg University MainzStaudingerweg 555128MainzGermany
| | - Andreas Marx
- Department of Chemistry, Konstanz Research School Chemical BiologyUniversity of KonstanzUniversitätsstraße 1078457KonstanzGermany
| |
Collapse
|
6
|
Aschenbrenner J, Werner S, Marchand V, Adam M, Motorin Y, Helm M, Marx A. Entwicklung einer DNA-Polymerase für die direkte m6A-Sequenzierung. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201710209] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Joos Aschenbrenner
- Fachbereich Chemie, Konstanz Research School Chemical Biology; Universität Konstanz; Universitätsstraße 10 78457 Konstanz Deutschland
| | - Stephan Werner
- Institut für Pharmazie und Biochemie; Johannes Gutenberg-Universität Mainz; Staudingerweg 5 55128 Mainz Deutschland
| | - Virginie Marchand
- Laboratoire Ingénierie Moléculaire et Physiopathologie, Articulaire, IMoPA, UMR7365 CNRS-UL; Biopôle de L'Université de Lorraine; 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy Frankreich
| | - Martina Adam
- Fachbereich Chemie, Konstanz Research School Chemical Biology; Universität Konstanz; Universitätsstraße 10 78457 Konstanz Deutschland
| | - Yuri Motorin
- Laboratoire Ingénierie Moléculaire et Physiopathologie, Articulaire, IMoPA, UMR7365 CNRS-UL; Biopôle de L'Université de Lorraine; 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy Frankreich
| | - Mark Helm
- Institut für Pharmazie und Biochemie; Johannes Gutenberg-Universität Mainz; Staudingerweg 5 55128 Mainz Deutschland
| | - Andreas Marx
- Fachbereich Chemie, Konstanz Research School Chemical Biology; Universität Konstanz; Universitätsstraße 10 78457 Konstanz Deutschland
| |
Collapse
|
7
|
Chovancova P, Merk V, Marx A, Leist M, Kranaster R. Reverse-transcription quantitative PCR directly from cells without RNA extraction and without isothermal reverse-transcription: a 'zero-step' RT-qPCR protocol. Biol Methods Protoc 2017; 2:bpx008. [PMID: 32002469 PMCID: PMC6977950 DOI: 10.1093/biomethods/bpx008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 04/05/2017] [Accepted: 04/25/2017] [Indexed: 02/06/2023] Open
Abstract
We describe an ultra-rapid and sensitive method to quantify gene expression levels in
cultured cells. The procedure is based on reverse-transcription quantitative PCR (RT-qPCR)
directly from cells, without RNA extraction and without an isothermal
reverse-transcription step. Human neurons (Lund human mesencephalic cells) were lysed at
different stages of differentiation, and the lysates were used directly as template for
the combined RT-qPCR reaction. We detected a down-regulation of a proliferation marker and
an up-regulation of neuronal dopaminergic genes expression. We were able to detect the
reference gene target from as few as a single cell, demonstrating the application of the
method for efficient amplification from small cell numbers. The data were fully in line
with those obtained by the standard two-step RT-qPCR from the extracted total RNA. Our
‘zero-step’ RT-qPCR method proved to be simple and reliable with a total time from cell
lysis to the end of the qPCR as short as 1.5 h. It is therefore particularly suitable for
RT-qPCRs where large numbers of samples must be handled, or where data are required within
short time.
Collapse
Affiliation(s)
- Petra Chovancova
- In vitro Toxicology and Biomedicine, University of Konstanz, D-78457 Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Verena Merk
- myPOLS Biotec GmbH, D-78457 Konstanz, Germany
| | - Andreas Marx
- myPOLS Biotec GmbH, D-78457 Konstanz, Germany.,Department of Chemistry, University of Konstanz, D-78457 Konstanz, Germany
| | - Marcel Leist
- In vitro Toxicology and Biomedicine, University of Konstanz, D-78457 Konstanz, Germany
| | | |
Collapse
|
8
|
Aschenbrenner J, Marx A. Direct and site-specific quantification of RNA 2'-O-methylation by PCR with an engineered DNA polymerase. Nucleic Acids Res 2016; 44:3495-502. [PMID: 27016740 PMCID: PMC4856998 DOI: 10.1093/nar/gkw200] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 03/14/2016] [Indexed: 01/21/2023] Open
Abstract
Methylation of the 2′-hydroxyl-group of ribonucleotides is found in all major classes of RNA in eukaryotes and is one of the most abundant posttranscriptional modifications of stable RNAs. In spite of intense studies, the multiple functions of RNA 2′-O-methylation are still not understood. One major obstacle in the field are the technical demanding detection methods, which are typically laborious and do not always deliver unambiguous results. We present a thermostable KlenTaq DNA polymerase variant with significant reverse transcription activity that is able to discriminate 2′-O-methylated from unmethylated RNAs. The engineered enzyme catalyzes DNA synthesis from DNA as well as RNA templates and enables expeditious quantification of 2′-O-methylation of individual nucleotides directly from total RNA extracts by a simple qRT-PCR.
Collapse
Affiliation(s)
- Joos Aschenbrenner
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, D-78457 Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, D-78457 Konstanz, Germany
| |
Collapse
|
9
|
Aschenbrenner J, Drum M, Topal H, Wieland M, Marx A. Direct sensing of 5-methylcytosine by polymerase chain reaction. Angew Chem Int Ed Engl 2014; 53:8154-8. [PMID: 24923910 PMCID: PMC4499253 DOI: 10.1002/anie.201403745] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Indexed: 12/22/2022]
Abstract
The epigenetic control of genes by the methylation of cytosine resulting in 5-methylcytosine (5mC) has fundamental implications for human development and disease. Analysis of alterations in DNA methylation patterns is an emerging tool for cancer diagnostics and prognostics. Here we report that two thermostable DNA polymerases, namely the DNA polymerase KlenTaq derived from Thermus aquaticus and the KOD DNA polymerase from Thermococcus kodakaraensis, are able to extend 3'-mismatched primer strands more efficiently from 5 mC than from unmethylated C. This feature was advanced by generating a DNA polymerase mutant with further improved 5mC/C discrimination properties and its successful application in a novel methylation-specific PCR approach directly from untreated human genomic DNA.
Collapse
Affiliation(s)
- Joos Aschenbrenner
- Department of Chemistry, Konstanz Research School Chemical Biology, University of KonstanzUniversitätsstrasse 10, 78457 Konstanz (Germany)
| | - Matthias Drum
- Department of Chemistry, Konstanz Research School Chemical Biology, University of KonstanzUniversitätsstrasse 10, 78457 Konstanz (Germany)
| | - Hüsnü Topal
- Department of Chemistry, Konstanz Research School Chemical Biology, University of KonstanzUniversitätsstrasse 10, 78457 Konstanz (Germany)
| | - Markus Wieland
- Department of Chemistry, Konstanz Research School Chemical Biology, University of KonstanzUniversitätsstrasse 10, 78457 Konstanz (Germany)
| | - Andreas Marx
- Department of Chemistry, Konstanz Research School Chemical Biology, University of KonstanzUniversitätsstrasse 10, 78457 Konstanz (Germany)
| |
Collapse
|
10
|
Aschenbrenner J, Drum M, Topal H, Wieland M, Marx A. Detektion von 5-Methylcytosin in unbehandelter genomischer DNA durch Polymerasekettenreaktion. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201403745] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
|
11
|
Drum M, Kranaster R, Ewald C, Blasczyk R, Marx A. Variants of a Thermus aquaticus DNA polymerase with increased selectivity for applications in allele- and methylation-specific amplification. PLoS One 2014; 9:e96640. [PMID: 24800860 PMCID: PMC4011760 DOI: 10.1371/journal.pone.0096640] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 04/09/2014] [Indexed: 01/25/2023] Open
Abstract
The selectivity of DNA polymerases is crucial for many applications. For example, high discrimination between the extension of matched versus mismatched primer termini is desired for the detection of a single nucleotide variation at a particular locus within the genome. Here we describe the generation of thermostable mutants of the large fragment of Thermus aquaticus DNA polymerase (KlenTaq) with increased mismatch extension selectivity. In contrast to previously reported much less active KlenTaq mutants with mismatch discrimination abilities, many of the herein discovered mutants show conserved wild-type-like high activities. We demonstrate for one mutant containing the single amino acid exchange R660V the suitability for application in allele-specific amplifications directly from whole blood without prior sample purification. Also the suitability of the mutant for methylation specific amplification in the diagnostics of 5-methyl cytosines is demonstrated. Furthermore, the identified mutant supersedes other commercially available enzymes in human leukocyte antigen (HLA) analysis by sequence-specific primed polymerase chain reactions (PCRs).
Collapse
Affiliation(s)
- Matthias Drum
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Ramon Kranaster
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
- myPOLS Biotec, University of Konstanz, Konstanz, Germany
| | - Christina Ewald
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Rainer Blasczyk
- Institute for Transfusion Medicine, Hannover Medical School, Hannover, Germany
| | - Andreas Marx
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
- * E-mail:
| |
Collapse
|
12
|
Strittmatter T, Bareth B, Immel TA, Huhn T, Mayer TU, Marx A. Small Molecule Inhibitors of Human DNA Polymerase λ. ACS Chem Biol 2011; 6:314-9. [PMID: 21194240 DOI: 10.1021/cb100382m] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
To discover chemical probes to further under-stand the function of individual DNA polymerases, we established a generally applicable high-throughput screening. By applying this technique we discovered three novel inhibitor classes of human DNA polymerase λ (DNA Pol λ), a key enzyme to maintain the genetic integrity of the genome. The rhodanines, classified as an excellent drug scaffold, were found to be the most potent inhibitors for DNA Pol λ. Importantly, they are up to 10 times less active against the highly similar DNA polymerase β. We investigated basic structure activity relationships. Furthermore, the rhodanines showed pharmacological activity in two human cancer cell lines. So the here reported small molecules could serve as useful DNA Pol λ probes and might serve as starting point to develop novel therapeutic agents.
Collapse
Affiliation(s)
- Tobias Strittmatter
- Departments of Chemistry and Biology, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Bettina Bareth
- Departments of Chemistry and Biology, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Timo A. Immel
- Departments of Chemistry and Biology, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Thomas Huhn
- Departments of Chemistry and Biology, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Thomas U. Mayer
- Departments of Chemistry and Biology, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Andreas Marx
- Departments of Chemistry and Biology, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| |
Collapse
|