1
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Yang Q, Ma N, He Y, Yu X, Yao B. Immobilized Palladium Nanoparticles on Phosphanamine-grafted Cellulose for Arylation of Uracil. CURRENT ORGANOCATALYSIS 2021. [DOI: 10.2174/2213337208666210816110719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
The synthesis of 5-arylation uracil nucleosides is an imperative challenge,
especially for the method of Suzuki reaction using N-unprotected uracil as materials, which holds
the potential to enhance the yield.
Objective:
The objective of the study was to find a more efficient catalyst to increase the yield of
aryluracils and aryluridines.
Methods:
We first constructed the phosphanamine-grafted cellulose (PAGC) from cellulose material.
Then, we prepared the nanocatalyst PAGC/Pd(0) through heating and reducing the mixture of
PAGC and Pa(OAc)2.
Results:
When using this nanocatalyst to catalyze the Suzuki reaction of 5-iodouracil or 5-iodouridine
and aryl heterocyclic boronic acids, the arylation yields have been significantly improved.
Conclusion:
This means that the resultant nanocatalyst exhibits a remarkable catalytic efficacy for
Suzuki arylation of 5-iodouracil and 5-iodouridine.
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Affiliation(s)
- Qian Yang
- School of Sciences, Xi`an University of Technology,Xi’an, 710054, China
| | - Na Ma
- School of Sciences, Xi`an University of Technology,Xi’an, 710054, China
| | - Yangqing He
- School of Sciences, Xi`an University of Technology,Xi’an, 710054, China
| | - Xiaojiao Yu
- School of Sciences, Xi`an University of Technology,Xi’an, 710054, China
| | - Binghua Yao
- School of Sciences, Xi`an University of Technology,Xi’an, 710054, China
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2
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Rausch C, Zhang P, Casas-Delucchi CS, Daiß JL, Engel C, Coster G, Hastert FD, Weber P, Cardoso MC. Cytosine base modifications regulate DNA duplex stability and metabolism. Nucleic Acids Res 2021; 49:12870-12894. [PMID: 34133727 PMCID: PMC8682791 DOI: 10.1093/nar/gkab509] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 05/26/2021] [Accepted: 06/03/2021] [Indexed: 12/14/2022] Open
Abstract
DNA base modifications diversify the genome and are essential players in development. Yet, their influence on DNA physical properties and the ensuing effects on genome metabolism are poorly understood. Here, we focus on the interplay of cytosine modifications and DNA processes. We show by a combination of in vitro reactions with well-defined protein compositions and conditions, and in vivo experiments within the complex networks of the cell that cytosine methylation stabilizes the DNA helix, increasing its melting temperature and reducing DNA helicase and RNA/DNA polymerase speed. Oxidation of methylated cytosine, however, reverts the duplex stabilizing and genome metabolic effects to the level of unmodified cytosine. We detect this effect with DNA replication and transcription proteins originating from different species, ranging from prokaryotic and viral to the eukaryotic yeast and mammalian proteins. Accordingly, lack of cytosine methylation increases replication fork speed by enhancing DNA helicase unwinding speed in cells. We further validate that this cannot simply be explained by altered global DNA decondensation, changes in histone marks or chromatin structure and accessibility. We propose that the variegated deposition of cytosine modifications along the genome regulates DNA helix stability, thereby providing an elementary mechanism for local fine-tuning of DNA metabolism.
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Affiliation(s)
- Cathia Rausch
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Peng Zhang
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany.,Center for Tissue Engineering and Stem Cell Research, Guizhou Medical University, Guiyang, Guizhou 550004, China
| | | | - Julia L Daiß
- Regensburg Center for Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Christoph Engel
- Regensburg Center for Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Gideon Coster
- Chester Beatty Laboratories, The Institute of Cancer Research, London SW3 6JB, UK
| | - Florian D Hastert
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Patrick Weber
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - M Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
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3
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Jakubovska J, Tauraite D, Birštonas L, Meškys R. N4-acyl-2'-deoxycytidine-5'-triphosphates for the enzymatic synthesis of modified DNA. Nucleic Acids Res 2019; 46:5911-5923. [PMID: 29846697 PMCID: PMC6158702 DOI: 10.1093/nar/gky435] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 05/08/2018] [Indexed: 02/06/2023] Open
Abstract
A huge diversity of modified nucleobases is used as a tool for studying DNA and RNA. Due to practical reasons, the most suitable positions for modifications are C5 of pyrimidines and C7 of purines. Unfortunately, by using these two positions only, one cannot expand a repertoire of modified nucleotides to a maximum. Here, we demonstrate the synthesis and enzymatic incorporation of novel N4-acylated 2′-deoxycytidine nucleotides (dCAcyl). We find that a variety of family A and B DNA polymerases efficiently use dCAcylTPs as substrates. In addition to the formation of complementary CAcyl•G pair, a strong base-pairing between N4-acyl-cytosine and adenine takes place when Taq, Klenow fragment (exo–), Bsm and KOD XL DNA polymerases are used for the primer extension reactions. In contrast, a proofreading phi29 DNA polymerase successfully utilizes dCAcylTPs but is prone to form CAcyl•A base pair under the same conditions. Moreover, we show that terminal deoxynucleotidyl transferase is able to incorporate as many as several hundred N4-acylated-deoxycytidine nucleotides. These data reveal novel N4-acylated deoxycytidine nucleotides as beneficial substrates for the enzymatic synthesis of modified DNA, which can be further applied for specific labelling of DNA fragments, selection of aptamers or photoimmobilization.
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Affiliation(s)
- Jevgenija Jakubovska
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Daiva Tauraite
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Lukas Birštonas
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
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4
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Wang Y, Ng N, Liu E, Lam CH, Perrin DM. Systematic study of constraints imposed by modified nucleoside triphosphates with protein-like side chains for use in in vitro selection. Org Biomol Chem 2018; 15:610-618. [PMID: 27942671 DOI: 10.1039/c6ob02335e] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Successful selection of modified DNAzymes depends on the potential for modified nucleoside triphosphates (dNTPs) to replace their unmodified counterparts in enzyme catalyzed primer extension reactions and, once incorporated, to serve as template bases for information transfer prior to PCR amplification. To date, the most densely modified DNAzymes have been selected from three modified dNTPs: 8-histaminyl-deoxyadenosine (dAimTP), 5-guanidinoallyl-deoxyuridine (dUgaTP), and 5-aminoallyl-deoxycytidine (dCaaTP) to provide several RNA-cleaving DNAzymes with greatly enhanced rate constants compared to unmodified counterparts. Here we report biophysical and enzymatic properties of these three modified nucleosides in the context of specific oligonucleotide sequences to understand how these three modified nucleobases function in combinatorial selection. The base-pairing abilities of oligonucleotides bearing one or three modified nucleosides were investigated by thermal denaturation studies and as templates for enzymatic polymerization with both modified and unmodified dNTPs. While we address certain shortcomings in the use of modified dNTPs, we also provide key evidence of faithful incorporation and enzymatic read-out, which strongly supports their continued use in in vitro selection.
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Affiliation(s)
- Yajun Wang
- Chemistry Department, UBC, 2036 Main Mall, Vancouver, BC, V6T-1Z1 Canada.
| | - Nicole Ng
- Chemistry Department, UBC, 2036 Main Mall, Vancouver, BC, V6T-1Z1 Canada.
| | - Erkai Liu
- Chemistry Department, UBC, 2036 Main Mall, Vancouver, BC, V6T-1Z1 Canada.
| | - Curtis H Lam
- Chemistry Department, UBC, 2036 Main Mall, Vancouver, BC, V6T-1Z1 Canada.
| | - David M Perrin
- Chemistry Department, UBC, 2036 Main Mall, Vancouver, BC, V6T-1Z1 Canada.
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5
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Tauraitė D, Jakubovska J, Dabužinskaitė J, Bratchikov M, Meškys R. Modified Nucleotides as Substrates of Terminal Deoxynucleotidyl Transferase. Molecules 2017; 22:molecules22040672. [PMID: 28441732 PMCID: PMC6154577 DOI: 10.3390/molecules22040672] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 04/10/2017] [Accepted: 04/19/2017] [Indexed: 11/30/2022] Open
Abstract
The synthesis of novel modified nucleotides and their incorporation into DNA sequences opens many possibilities to change the chemical properties of oligonucleotides (ONs), and, therefore, broaden the field of practical applications of modified DNA. The chemical synthesis of nucleotide derivatives, including ones bearing thio-, hydrazino-, cyano- and carboxy groups as well as 2-pyridone nucleobase-containing nucleotides was carried out. The prepared compounds were tested as substrates of terminal deoxynucleotidyl transferase (TdT). The nucleotides containing N4-aminocytosine, 4-thiouracil as well as 2-pyridone, 4-chloro- and 4-bromo-2-pyridone as a nucleobase were accepted by TdT, thus allowing enzymatic synthesis of 3’-terminally modified ONs. The successful UV-induced cross-linking of 4-thiouracil-containing ONs to TdT was carried out. Enzymatic post-synthetic 3’-modification of ONs with various photo- and chemically-reactive groups opens novel possibilities for future applications, especially in analysis of the mechanisms of polymerases and the development of photo-labels, sensors, and self-assembling structures.
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Affiliation(s)
- Daiva Tauraitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio al. 7, Vilnius LT-10257, Lithuania.
| | - Jevgenija Jakubovska
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio al. 7, Vilnius LT-10257, Lithuania.
| | - Julija Dabužinskaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio al. 7, Vilnius LT-10257, Lithuania.
| | - Maksim Bratchikov
- Department of Physiology, Biochemistry, Microbiology and Laboratory Medicine, Faculty of Medicine, Vilnius University, M. K. Čiurlionio g. 21, Vilnius LT-03101, Lithuania.
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio al. 7, Vilnius LT-10257, Lithuania.
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6
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Hottin A, Marx A. Structural Insights into the Processing of Nucleobase-Modified Nucleotides by DNA Polymerases. Acc Chem Res 2016; 49:418-27. [PMID: 26947566 DOI: 10.1021/acs.accounts.5b00544] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The DNA polymerase-catalyzed incorporation of modified nucleotides is employed in many biological technologies of prime importance, such as next-generation sequencing, nucleic acid-based diagnostics, transcription analysis, and aptamer selection by systematic enrichment of ligands by exponential amplification (SELEX). Recent studies have shown that 2'-deoxynucleoside triphosphates (dNTPs) that are functionalized with modifications at the nucleobase such as dyes, affinity tags, spin and redox labels, or even oligonucleotides are substrates for DNA polymerases, even if modifications of high steric demand are used. The position at which the modification is introduced in the nucleotide has been identified as crucial for retaining substrate activity for DNA polymerases. Modifications are usually attached at the C5 position of pyrimidines and the C7 position of 7-deazapurines. Furthermore, it has been shown that the nature of the modification may impact the efficiency of incorporation of a modified nucleotide into the nascent DNA strand by a DNA polymerase. This Account places functional data obtained in studies of the incorporation of modified nucleotides by DNA polymerases in the context of recently obtained structural data. Crystal structure analysis of a Thermus aquaticus (Taq) DNA polymerase variant (namely, KlenTaq DNA polymerase) in ternary complex with primer-template DNA and several modified nucleotides provided the first structural insights into how nucleobase-modified triphosphates are tolerated. We found that bulky modifications are processed by KlenTaq DNA polymerase as a result of cavities in the protein that enable the modification to extend outside the active site. In addition, we found that the enzyme is able to adapt to different modifications in a flexible manner and adopts different amino acid side-chain conformations at the active site depending on the nature of the nucleotide modification. Different "strategies" (i.e., hydrogen bonding, cation-π interactions) enable the protein to stabilize the respective protein-substrate complex without significantly changing the overall structure of the complex. Interestingly, it was also discovered that a modified nucleotide may be more efficiently processed by KlenTaq DNA polymerase when the 3'-primer terminus is also a modified nucleotide instead of a nonmodified natural one. Indeed, the modifications of two modified nucleotides at adjacent positions can interact with each other (i.e., by π-π interactions) and thereby stabilize the enzyme-substrate complex, resulting in more efficient transformation. Several studies have indicated that archeal DNA polymerases belonging to sequence family B are better suited for the incorporation of nucleobase-modified nucleotides than enzymes from family A. However, significantly less structural data are available for family B DNA polymerases. In order to gain insights into the preference for modified substrates by members of family B, we succeeded in obtaining binary structures of 9°N and KOD DNA polymerases bound to primer-template DNA. We found that the major groove of the archeal family B DNA polymerases is better accessible than in family A DNA polymerases. This might explain the observed superiority of family B DNA polymerases in polymerizing nucleotides that bear bulky modifications located in the major groove, such as modification at C5 of pyrimidines and C7 of 7-deazapurines. Overall, this Account summarizes our recent findings providing structural insight into the mechanism by which modified nucleotides are processed by DNA polymerases. It provides guidelines for the design of modified nucleotides, thus supporting future efforts based on the acceptance of modified nucleotides by DNA polymerases.
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Affiliation(s)
- Audrey Hottin
- Department
of Chemistry and
Konstanz Research School Chemical Biology University of Konstanz Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Andreas Marx
- Department
of Chemistry and
Konstanz Research School Chemical Biology University of Konstanz Universitätsstrasse 10, 78457 Konstanz, Germany
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7
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Khodursky A, Guzmán EC, Hanawalt PC. Thymineless Death Lives On: New Insights into a Classic Phenomenon. Annu Rev Microbiol 2015; 69:247-63. [PMID: 26253395 DOI: 10.1146/annurev-micro-092412-155749] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The primary mechanisms by which bacteria lose viability when deprived of thymine have been elusive for over half a century. Early research focused on stalled replication forks and the deleterious effects of uracil incorporation into DNA from thymidine-deficient nucleotide pools. The initiation of the replication cycle and origin-proximal DNA degradation during thymine starvation have now been quantified via whole-genome microarrays and other approaches. These advances have fostered innovative models and informative experiments in bacteria since this topic was last reviewed. Given that thymineless death is similar in mammalian cells and that certain antibacterial and chemotherapeutic drugs elicit thymine deficiency, a mechanistic understanding of this phenomenon might have valuable biomedical applications.
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Affiliation(s)
- Arkady Khodursky
- Biotechnology Institute and Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota 55108;
| | - Elena C Guzmán
- Departamento de Bioquímica Biología Molecular y Genética, Universidad de Extremadura, 06071 Badajoz, Spain;
| | - Philip C Hanawalt
- Department of Biology, Stanford University, Stanford, California 94305;
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8
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Abstract
To expand the chemical functionality of DNAzymes and aptamers, several new modified deoxyuridine triphosphates have been synthesized. An important precursor that enables this aim is 5-aminomethyl dUTP, whereby the pendent amine serves as a handle for further synthetic functionalization. Five functional groups were conjugated to 5-aminomethyl dUTP. Incorporation assays were performed on several templates that demand 2-5 sequential incorporation events using several commercially available DNA polymerases. It was found that Vent (exo-) DNA polymerase efficiently incorporates all five modified dUTPs. In addition, all nucleoside triphosphates were capable of supporting a double-stranded exponential PCR amplification. Modified PCR amplicons were PCR amplified into unmodified DNA and sequenced to verify that genetic information was conserved through incorporation, amplification, and reamplification. Overall these modified dUTPs represent new candidate substrates for use in selections using modified nucleotide libraries.
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9
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Hocek M. Synthesis of base-modified 2'-deoxyribonucleoside triphosphates and their use in enzymatic synthesis of modified DNA for applications in bioanalysis and chemical biology. J Org Chem 2014; 79:9914-21. [PMID: 25321948 DOI: 10.1021/jo5020799] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The synthesis of 2'-deoxyribonucleoside triphosphates (dNTPs) either by classical triphosphorylation of nucleosides or by aqueous cross-coupling reactions of halogenated dNTPs is discussed. Different enzymatic methods for synthesis of modified oligonucleotides and DNA by polymerase incorporation of modified nucleotides are summarized, and the applications in redox or fluorescent labeling, as well as in bioconjugations and modulation of interactions of DNA with proteins, are outlined.
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Affiliation(s)
- Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences & IOCB Research Center , Flemingovo nám. 2, CZ-16610 Prague 6, Czech Republic
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10
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Kuwahara M, Obika S. In vitro selection of BNA (LNA) aptamers. ARTIFICIAL DNA, PNA & XNA 2014; 4:39-48. [PMID: 24044051 DOI: 10.4161/adna.25786] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 07/17/2013] [Indexed: 01/03/2023]
Abstract
Recently, we achieved the first in vitro selection of 2'-O,4'-C-methylene bridged/locked nucleic acid (2',4'-BNA/LNA) aptamers. High-affinity thrombin-binding aptamers (TBAs) were obtained from DNA-based libraries containing 2'-O,4'-C-methylene-bridged/linked bicyclic ribonucleotides (B/L nucleotides) in the 5'-primer region, using the method of capillary electrophoresis systematic evolution of ligands by exponential enrichment (CE-SELEX). Furthermore, a similar selection protocol could provide TBAs that contain B/L nucleotides in both primer and random regions. We review technical challenges involved in the generation of various BNA libraries using analogs of B/L nucleoside-5'-triphosphate and polymerase variants and also discuss applications of these libraries to the selection of BNA (LNA) aptamers, as well as future prospects for their therapeutic and diagnostic uses.
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Affiliation(s)
- Masayasu Kuwahara
- Graduate School of Science and Technology; Gunma University; Gunma, Japan
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11
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Balintová J, Plucnara M, Vidláková P, Pohl R, Havran L, Fojta M, Hocek M. Benzofurazane as a New Redox Label for Electrochemical Detection of DNA: Towards Multipotential Redox Coding of DNA Bases. Chemistry 2013; 19:12720-31. [DOI: 10.1002/chem.201301868] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 06/18/2013] [Indexed: 12/24/2022]
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12
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Hollenstein M, Hipolito CJ, Lam CH, Perrin DM. Toward the combinatorial selection of chemically modified DNAzyme RNase A mimics active against all-RNA substrates. ACS COMBINATORIAL SCIENCE 2013; 15:174-82. [PMID: 23485334 DOI: 10.1021/co3001378] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The convenient use of SELEX and related combinatorial methods of in vitro selection provides a formidable gateway for the generation of DNA enzymes, especially in the context of improving their potential as gene therapeutic agents. Here, we report on the selection of DNAzyme 12-91, a modified nucleic acid catalyst adorned with imidazole, ammonium, and guanidinium groups that provide for efficient M(2+)-independent cleavage of an all-RNA target sequence (kobs = 0.06 min(-1)). While Dz12-91 was selected for intramolecular cleavage of an all-RNA target, it surprisingly cleaves a target containing a lone ribocytosine unit with even greater efficiency (kobs = 0.27 min(-1)) than Dz9-86 (kobs = 0.13 min(-1)). The sequence composition of Dz12-91 bears a marked resemblance to that of Dz9-86 (kobs = 0.0014 min(-1) with an all-RNA substrate) that was selected from the same library to cleave a target containing a single ribonucleotide. However, small alterations in the sequence composition have a profound impact on the substrate preference and catalytic properties. Indeed, Dz12-91 displays the highest known rate enhancement for the M(2+)-independent cleavage of all-RNA targets. Hence, Dz12-91 represents a step toward the generation of potentially therapeutically active DNAzymes and further underscores the usefulness of modified triphosphates in selection experiments.
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Affiliation(s)
- Marcel Hollenstein
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver BC, V6T
1Z1, Canada
| | - Christopher J. Hipolito
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver BC, V6T
1Z1, Canada
| | - Curtis H. Lam
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver BC, V6T
1Z1, Canada
| | - David M. Perrin
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver BC, V6T
1Z1, Canada
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13
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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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14
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Schoch J, Jäschke A. Synthesis and enzymatic incorporation of norbornene-modified nucleoside triphosphates for Diels–Alder bioconjugation. RSC Adv 2013. [DOI: 10.1039/c3ra40373d] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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15
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Kasahara Y, Kuwahara M. Artificial specific binders directly recovered from chemically modified nucleic acid libraries. J Nucleic Acids 2012; 2012:156482. [PMID: 23094139 PMCID: PMC3472525 DOI: 10.1155/2012/156482] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Accepted: 08/19/2012] [Indexed: 11/18/2022] Open
Abstract
Specific binders comprised of nucleic acids, that is, RNA/DNA aptamers, are attractive functional biopolymers owing to their potential broad application in medicine, food hygiene, environmental analysis, and biological research. Despite the large number of reports on selection of natural DNA/RNA aptamers, there are not many examples of direct screening of chemically modified nucleic acid aptamers. This is because of (i) the inferior efficiency and accuracy of polymerase reactions involving transcription/reverse-transcription of modified nucleotides compared with those of natural nucleotides, (ii) technical difficulties and additional time and effort required when using modified nucleic acid libraries, and (iii) ambiguous efficacies of chemical modifications in binding properties until recently; in contrast, the effects of chemical modifications on biostability are well studied using various nucleotide analogs. Although reports on the direct screening of a modified nucleic acid library remain in the minority, chemical modifications would be essential when further functional expansion of nucleic acid aptamers, in particular for medical and biological uses, is considered. This paper focuses on enzymatic production of chemically modified nucleic acids and their application to random screenings. In addition, recent advances and possible future research are also described.
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Affiliation(s)
- Yuuya Kasahara
- Graduate School of Engineering, Gunma University, 1-5-1 Tenjin-cho, Kiryu 376-8515, Japan
| | - Masayasu Kuwahara
- Graduate School of Engineering, Gunma University, 1-5-1 Tenjin-cho, Kiryu 376-8515, Japan
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16
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Kano C, Hanaoka F, Wang JY. Analysis of mice deficient in both REV1 catalytic activity and POLH reveals an unexpected role for POLH in the generation of C to G and G to C transversions during Ig gene hypermutation. Int Immunol 2012; 24:169-74. [DOI: 10.1093/intimm/dxr109] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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17
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Lam CH, Hipolito CJ, Hollenstein M, Perrin DM. A divalent metal-dependent self-cleaving DNAzyme with a tyrosine side chain. Org Biomol Chem 2011; 9:6949-54. [PMID: 21670811 DOI: 10.1039/c1ob05359k] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The enzymatic incorporation of a phenol-modified 2'-deoxyuridine triphosphate gave rise to a modified DNA library that was subsequently used in an in vitro selection for ribophosphodiester-cleaving DNAzymes in the presence of divalent zinc and magnesium cations. After 11 rounds of selection, cloning and sequencing resulted in 14 distinct sequences, the most active of which was Dz11-17PheO. Dz11-17PheO self-cleaved an embedded ribocytidine with an observed rate constant of 0.20 ± 0.02 min(-1) in the presence of 10 mM Mg(2+) and 1 mM Zn(2+) at room temperature. The activity was inhibited at low concentrations of Hg(2+) cations and somewhat higher concentrations of Eu(3+) cations.
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Affiliation(s)
- Curtis H Lam
- Chemistry Department, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
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Hocek M, Fojta M. Nucleobase modification as redox DNA labelling for electrochemical detection. Chem Soc Rev 2011; 40:5802-14. [PMID: 21625726 DOI: 10.1039/c1cs15049a] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Basic aspects of DNA electrochemistry with a strong focus on the use of modified nucleobases as redox probes for electrochemical bioanalysis are reviewed. Intrinsic electrochemical properties of nucleobases in combination with artificial redox-active nucleobase modifications are frequently applied in this field. Synthetic approaches (both chemical and enzymatic) to base-modified nucleic acids are briefly summarized and their applications in redox labelling are discussed. Finally, analytical applications including DNA hybridization, primer extension, PCR, SNP typing, DNA damage and DNA-protein interaction analysis are presented (critical review, 91 references).
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Affiliation(s)
- Michal Hocek
- Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Gilead Sciences & IOCB Research Center, Prague, Czech Republic.
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Kuwahara M, Takano Y, Kasahara Y, Nara H, Ozaki H, Sawai H, Sugiyama A, Obika S. Study on suitability of KOD DNA polymerase for enzymatic production of artificial nucleic acids using base/sugar modified nucleoside triphosphates. Molecules 2010; 15:8229-40. [PMID: 21076389 PMCID: PMC6259326 DOI: 10.3390/molecules15118229] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Revised: 11/06/2010] [Accepted: 11/10/2010] [Indexed: 01/26/2023] Open
Abstract
Recently, KOD and its related DNA polymerases have been used for preparing various modified nucleic acids, including not only base-modified nucleic acids, but also sugar-modified ones, such as bridged/locked nucleic acid (BNA/LNA) which would be promising candidates for nucleic acid drugs. However, thus far, reasons for the effectiveness of KOD DNA polymerase for such purposes have not been clearly elucidated. Therefore, using mutated KOD DNA polymerases, we studied here their catalytic properties upon enzymatic incorporation of nucleotide analogues with base/sugar modifications. Experimental data indicate that their characteristic kinetic properties enabled incorporation of various modified nucleotides. Among those KOD mutants, one achieved efficient successive incorporation of bridged nucleotides with a 2′-ONHCH2CH2-4′ linkage. In this study, the characteristic kinetic properties of KOD DNA polymerase for modified nucleoside triphosphates were shown, and the effectiveness of genetic engineering in improvement of the enzyme for modified nucleotide polymerization has been demonstrated.
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Affiliation(s)
- Masayasu Kuwahara
- Graduate School of Engineering, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan.
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Kuwahara M, Obika S, Nagashima JI, Ohta Y, Suto Y, Ozaki H, Sawai H, Imanishi T. Systematic analysis of enzymatic DNA polymerization using oligo-DNA templates and triphosphate analogs involving 2',4'-bridged nucleosides. Nucleic Acids Res 2008; 36:4257-65. [PMID: 18583360 PMCID: PMC2490744 DOI: 10.1093/nar/gkn404] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2008] [Revised: 06/07/2008] [Accepted: 06/09/2008] [Indexed: 11/16/2022] Open
Abstract
In order to systematically analyze the effects of nucleoside modification of sugar moieties in DNA polymerase reactions, we synthesized 16 modified templates containing 2',4'-bridged nucleotides and three types of 2',4'-bridged nucleoside-5'-triphospates with different bridging structures. Among the five types of thermostable DNA polymerases used, Taq, Phusion HF, Vent(exo-), KOD Dash and KOD(exo-), the KOD Dash and KOD(exo-) DNA polymerases could smoothly read through the modified templates containing 2'-O,4'-C-methylene-linked nucleotides at intervals of a few nucleotides, even at standard enzyme concentrations for 5 min. Although the Vent(exo-) DNA polymerase also read through these modified templates, kinetic study indicates that the KOD(exo-) DNA polymerase was found to be far superior to the Vent(exo-) DNA polymerase in accurate incorporation of nucleotides. When either of the DNA polymerase was used, the presence of 2',4'-bridged nucleotides on a template strand substantially decreased the reaction rates of nucleotide incorporations. The modified templates containing sequences of seven successive 2',4'-bridged nucleotides could not be completely transcribed by any of the DNA polymerases used; yields of longer elongated products decreased in the order of steric bulkiness of the modified sugars. Successive incorporation of 2',4'-bridged nucleotides into extending strands using 2',4'-bridged nucleoside-5'-triphospates was much more difficult. These data indicate that the sugar modification would have a greater effect on the polymerase reaction when it is adjacent to the elongation terminus than when it is on the template as well, as in base modification.
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Affiliation(s)
- Masayasu Kuwahara
- Department of Chemistry and Chemical Biology, Graduate School of Engineering, Gunma University, Gunma 376-8515, Japan.
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Hocek M, Fojta M. Cross-coupling reactions of nucleoside triphosphates followed by polymerase incorporation. Construction and applications of base-functionalized nucleic acids. Org Biomol Chem 2008; 6:2233-41. [PMID: 18563253 DOI: 10.1039/b803664k] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Construction of functionalized nucleic acids (DNA or RNA) via polymerase incorporation of modified nucleoside triphosphates is reviewed and selected applications of the modified nucleic acids are highlighted. The classical multistep approach for the synthesis of modified NTPs by triphosphorylation of modified nucleosides is compared to the novel approach consisting of direct aqueous cross-coupling reactions of unprotected halogenated nucleoside triphosphates. The combination of cross-coupling of NTPs with polymerase incorporation gives an efficient and straightforward two-step synthesis of modified nucleic acids. Primer extension using biotinylated templates followed by separation using streptavidine-coated magnetic beads and DNA duplex denaturation is used for preparation of modified single stranded oligonucleotides. Examples of using this approach for electrochemical DNA labelling and bioanalytical applications are given.
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Affiliation(s)
- Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic.
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