1
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Ouaray Z, Benner SA, Georgiadis MM, Richards NGJ. Building better polymerases: Engineering the replication of expanded genetic alphabets. J Biol Chem 2020; 295:17046-17059. [PMID: 33004440 PMCID: PMC7863901 DOI: 10.1074/jbc.rev120.013745] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 09/30/2020] [Indexed: 11/30/2022] Open
Abstract
DNA polymerases are today used throughout scientific research, biotechnology, and medicine, in part for their ability to interact with unnatural forms of DNA created by synthetic biologists. Here especially, natural DNA polymerases often do not have the "performance specifications" needed for transformative technologies. This creates a need for science-guided rational (or semi-rational) engineering to identify variants that replicate unnatural base pairs (UBPs), unnatural backbones, tags, or other evolutionarily novel features of unnatural DNA. In this review, we provide a brief overview of the chemistry and properties of replicative DNA polymerases and their evolved variants, focusing on the Klenow fragment of Taq DNA polymerase (Klentaq). We describe comparative structural, enzymatic, and molecular dynamics studies of WT and Klentaq variants, complexed with natural or noncanonical substrates. Combining these methods provides insight into how specific amino acid substitutions distant from the active site in a Klentaq DNA polymerase variant (ZP Klentaq) contribute to its ability to replicate UBPs with improved efficiency compared with Klentaq. This approach can therefore serve to guide any future rational engineering of replicative DNA polymerases.
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Affiliation(s)
- Zahra Ouaray
- School of Chemistry, Cardiff University, Park Place, Cardiff, United Kingdom
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Alachua, Florida, USA
| | - Millie M Georgiadis
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA.
| | - Nigel G J Richards
- School of Chemistry, Cardiff University, Park Place, Cardiff, United Kingdom; Foundation for Applied Molecular Evolution, Alachua, Florida, USA.
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2
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Chemical Modification of Aptamers for Increased Binding Affinity in Diagnostic Applications: Current Status and Future Prospects. Int J Mol Sci 2020; 21:ijms21124522. [PMID: 32630547 PMCID: PMC7350236 DOI: 10.3390/ijms21124522] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 06/19/2020] [Accepted: 06/22/2020] [Indexed: 12/13/2022] Open
Abstract
Aptamers are short single stranded DNA or RNA oligonucleotides that can recognize analytes with extraordinary target selectivity and affinity. Despite their promising properties and diagnostic potential, the number of commercial applications remains scarce. In order to endow them with novel recognition motifs and enhanced properties, chemical modification of aptamers has been pursued. This review focuses on chemical modifications, aimed at increasing the binding affinity for the aptamer's target either in a non-covalent or covalent fashion, hereby improving their application potential in a diagnostic context. An overview of current methodologies will be given, thereby distinguishing between pre- and post-SELEX (Systematic Evolution of Ligands by Exponential Enrichment) modifications.
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3
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Laos R, Lampropoulos C, Benner SA. The surprising pairing of 2-aminoimidazo[1,2-a][1,3,5]triazin-4-one, a component of an expanded DNA alphabet. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2019; 75:22-28. [PMID: 30601127 DOI: 10.1107/s2053229618016923] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 11/28/2018] [Indexed: 11/10/2022]
Abstract
Synthetic biologists demonstrate their command over natural biology by reproducing the behaviors of natural living systems on synthetic biomolecular platforms. For nucleic acids, this is being done stepwise, first by adding replicable nucleotides to DNA, and then removing its standard nucleotides. This challenge has been met in vitro with `six-letter' DNA and RNA, where the Watson-Crick pairing `concept' is recruited to increase the number of independently replicable nucleotides from four to six. The two nucleobases most successfully added so far are Z and P, which present a donor-donor-acceptor and an acceptor-acceptor-donor pattern, respectively. This pair of nucleobases are part of an `artificially expanded genetic information system' (AEGIS). The Z nucleobase has been already crystallized, characterized, and published in this journal [Matsuura et al. (2016). Acta Cryst. C72, 952-959]. More recently, variants of Taq polymerase have been crystallized with the pair P:Z trapped in the active site. Here we report the crystal structure of the nucleobase 2-aminoimidazo[1,2-a][1,3,5]triazin-4-one (trivially named P) as the monohydrate, C5H5N5O·H2O. The nucleobase P was crystallized from water and characterized by X-ray diffraction. Interestingly, the crystal structure shows two tautomers of P packed in a Watson-Crick fashion that cocrystallized in a 1:1 ratio.
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Affiliation(s)
- Roberto Laos
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Box 7, Alachua, FL 32615, USA
| | - Christos Lampropoulos
- Department of Chemistry, University of North Florida, 1 UNF Drive, Jacksonville, FL 32224, USA
| | - Steven A Benner
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Box 7, Alachua, FL 32615, USA
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4
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Kolganova NA, Vasiliskov VA, Kuznetsova VE, Shershov VE, Lapa SA, Guseinov TO, Spitsyn MA, Timofeev EN, Chudinov AV. Factors Affecting the Tailing of Blunt End DNA with Fluorescent Pyrimidine dNTPs. Mol Biotechnol 2018; 60:879-886. [PMID: 30244435 DOI: 10.1007/s12033-018-0124-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The transferase activity of non-proofreading DNA polymerases is a well-known phenomenon that has been utilized in cloning and sequencing applications. The non-templated addition of modified nucleotides at DNA blunt ends is a potentially useful feature of DNA polymerases that can be used for selective transformation of DNA 3' ends. In this paper, we characterized the tailing reaction at perfectly matched and mismatched duplex ends with Cy3- and Cy5-modified pyrimidine nucleotides. It was shown that the best DNA tailing substrate does not have a perfect Watson-Crick base pair at the end. Mismatched duplexes with a 3' dC were the most efficient in the Taq DNA polymerase-catalysed tailing reaction with a Cy5-modified dUTP. We further demonstrated that the arrangement of the dye residue relative to the nucleobase notably affects the outcome of the tailing reaction. A comparative study of labelled deoxycytidine and deoxyuridine nucleotides showed higher efficiency for dUTP derivatives. The non-templated addition of modified nucleotides by Taq polymerase at a duplex blunt end was generally complicated by the pyrophosphorolysis and 5' exonuclease activity of the enzyme.
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Affiliation(s)
- Natalia A Kolganova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, Moscow, Russia, 119991
| | - Vadim A Vasiliskov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, Moscow, Russia, 119991
| | - Viktoriya E Kuznetsova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, Moscow, Russia, 119991
| | - Valeriy E Shershov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, Moscow, Russia, 119991
| | - Sergey A Lapa
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, Moscow, Russia, 119991
| | - Timur O Guseinov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, Moscow, Russia, 119991
| | - Maksim A Spitsyn
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, Moscow, Russia, 119991
| | - Edward N Timofeev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, Moscow, Russia, 119991.
| | - Alexander V Chudinov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, Moscow, Russia, 119991
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5
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Karalkar NB, Benner SA. The challenge of synthetic biology. Synthetic Darwinism and the aperiodic crystal structure. Curr Opin Chem Biol 2018; 46:188-195. [PMID: 30098527 DOI: 10.1016/j.cbpa.2018.07.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 06/07/2018] [Accepted: 07/13/2018] [Indexed: 12/25/2022]
Abstract
'Grand Challenges' offer ways to discover flaws in existing theory without first needing to guess what those flaws are. Our grand challenge here is to reproduce the Darwinism of terran biology, but on molecular platforms different from standard DNA. Access to Darwinism distinguishes the living from the non-living state. However, theory suggests that any biopolymer able to support Darwinism must (a) be able to form Schrödinger's `aperiodic crystal', where different molecular components pack into a single crystal lattice, and (b) have a polyelectrolyte backbone. In 1953, the descriptive biology of Watson and Crick suggested DNA met Schrödinger's criertion, forming a linear crystal with geometrically similar building blocks supported on a polyelectrolye backbone. At the center of genetics were nucleobase pairs that fit into that crystal lattice by having both size complementarity and hydrogen bonding complementarity to enforce a constant geometry. This review covers experiments that show that by adhering to these two structural rules, the aperiodic crystal structure is maintained in DNA having 6 (or more) components. Further, this molecular system is shown to support Darwinism. Together with a deeper understanding of the role played in crystal formation by the poly-charged backbone and the intervening scaffolding, these results define how we might search for Darwinism, and therefore life, on Mars, Europa, Enceladus, and other watery lagoons in our Solar System.
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Affiliation(s)
- Nilesh B Karalkar
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, Box 7, Alachua, FL 32615, United States
| | - Steven A Benner
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, Box 7, Alachua, FL 32615, United States; Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, FL 32615, United States.
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6
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Tomori T, Nagaoka K, Takeshita L, Shiozawa T, Miyatake Y, Masaki Y, Sekine M, Seio K. Deoxynucleoside Triphosphate Containing Pyridazin-3-one Aglycon as a Thymidine Triphosphate Substitute for Primer Extension and Chain Elongation by Klenow Fragments. J Org Chem 2018; 83:8353-8363. [PMID: 29952565 DOI: 10.1021/acs.joc.8b00918] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Deoxynucleoside 5'-triphosphate was synthesized with 3-oxo-2 H-pyridazin-6-yl (PzO)-a uracil analogue lacking a 2-keto group-as the nucleobase. Theoretical analyses and hybridization experiments indicated that PzO recognizes adenine (A) for formation of a Watson-Crick base pair. Primer extension reactions using nucleoside 5'-triphosphate and the Klenow fragment revealed that the synthetic nucleoside 5'-triphosphate was incorporated into the 3' end of the primer through recognition of A in the template strand. Moreover, the 3'-nucleotide residue harboring PzO as the base was resistant to the 3'-exonuclease activity of Klenow fragment exo+. The primer bearing the PzO base at the 3' end could function in subsequent chain elongation. These properties of PzO were attributed to the presence of an endocyclic nitrogen atom at the position ortho to the glycosidic bond, which was presumed to form an H-bond with the amino acid residue of DNA polymerase for effective recognition of the 3' end of the primer for primer extension. These results provide a basis for designing new nucleobases by combining a nitrogen atom at the position ortho to the glycosidic bond and base-pairing sites for Watson-Crick hydrogen bonding.
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Affiliation(s)
- Takahito Tomori
- School of Life Science and Technology , Tokyo Institute of Technology , 4259 Nagatsuta , Midoriku, Yokohama 226-8501 , Japan
| | - Kento Nagaoka
- School of Life Science and Technology , Tokyo Institute of Technology , 4259 Nagatsuta , Midoriku, Yokohama 226-8501 , Japan
| | - Leo Takeshita
- School of Life Science and Technology , Tokyo Institute of Technology , 4259 Nagatsuta , Midoriku, Yokohama 226-8501 , Japan
| | - Takashi Shiozawa
- School of Life Science and Technology , Tokyo Institute of Technology , 4259 Nagatsuta , Midoriku, Yokohama 226-8501 , Japan
| | - Yuya Miyatake
- School of Life Science and Technology , Tokyo Institute of Technology , 4259 Nagatsuta , Midoriku, Yokohama 226-8501 , Japan
| | - Yoshiaki Masaki
- School of Life Science and Technology , Tokyo Institute of Technology , 4259 Nagatsuta , Midoriku, Yokohama 226-8501 , Japan
| | - Mitsuo Sekine
- School of Life Science and Technology , Tokyo Institute of Technology , 4259 Nagatsuta , Midoriku, Yokohama 226-8501 , Japan
| | - Kohji Seio
- School of Life Science and Technology , Tokyo Institute of Technology , 4259 Nagatsuta , Midoriku, Yokohama 226-8501 , Japan
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7
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Singh I, Kim MJ, Molt RW, Hoshika S, Benner SA, Georgiadis MM. Structure and Biophysics for a Six Letter DNA Alphabet that Includes Imidazo[1,2-a]-1,3,5-triazine-2(8H)-4(3H)-dione (X) and 2,4-Diaminopyrimidine (K). ACS Synth Biol 2017; 6:2118-2129. [PMID: 28752992 DOI: 10.1021/acssynbio.7b00150] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A goal of synthetic biology is to develop new nucleobases that retain the desirable properties of natural nucleobases at the same time as expanding the genetic alphabet. The nonstandard Watson-Crick pair between imidazo[1,2-a]-1,3,5-triazine-2(8H)-4(3H)-dione (X) and 2,4-diaminopyrimidine (K) does exactly this, pairing via complementary arrangements of hydrogen bonding in these two nucleobases, which do not complement any natural nucleobase. Here, we report the crystal structure of a duplex DNA oligonucleotide in B-form including two consecutive X:K pairs in GATCXK DNA determined as a host-guest complex at 1.75 Å resolution. X:K pairs have significant propeller twist angles, similar to those observed for A:T pairs, and a calculated hydrogen bonding pairing energy that is weaker than that of A:T. Thus, although inclusion of X:K pairs results in a duplex DNA structure that is globally similar to that of an analogous G:C structure, the X:K pairs locally and energetically more closely resemble A:T pairs.
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Affiliation(s)
- Isha Singh
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Myong-Jung Kim
- Foundation for Applied Molecular Evolution, and the Westheimer Institute of Science & Technology, 13709 Progress Boulevard, Box 7, Alachua, Florida 32615, United States
- Firebird Biomolecular
Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, Florida 32615, United States
| | - Robert W. Molt
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
- ENSCO, Inc., 4849 North Wickham Road, Melbourne, Florida 32940, United States
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution, and the Westheimer Institute of Science & Technology, 13709 Progress Boulevard, Box 7, Alachua, Florida 32615, United States
- Firebird Biomolecular
Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, Florida 32615, United States
| | - Steven A. Benner
- Foundation for Applied Molecular Evolution, and the Westheimer Institute of Science & Technology, 13709 Progress Boulevard, Box 7, Alachua, Florida 32615, United States
- Firebird Biomolecular
Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, Florida 32615, United States
| | - Millie M. Georgiadis
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
- Department
of Chemistry and Chemical Biology, Indiana University, Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
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8
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Malvezzi S, Angelov T, Sturla SJ. Minor Groove 3-Deaza-Adenosine Analogues: Synthesis and Bypass in Translesion DNA Synthesis. Chemistry 2016; 23:1101-1109. [PMID: 27862447 DOI: 10.1002/chem.201604289] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Indexed: 11/07/2022]
Abstract
Anticancer drugs that alkylate DNA in the minor groove may give rise to 3-alkyl-adenosine adducts that interfere with replication, inducing apoptosis in rapidly dividing cancer cells. However, translesion DNA synthesis (TLS) by polymerase enzymes (Pols) with the capacity to bypass DNA adducts may contribute to damage tolerance and drug resistance. 3-Alkyl-adenosine adducts are unstable and depurinate, which is a barrier to addressing chemical and enzymatic aspects of how they impact the progress of DNA Pols. To characterize structure-based relationships of 3-adenine alkylation relevant to cancer drugs on duplex stability and DNA Pol-catalyzed DNA synthesis, we synthesized stable 3-deaza-3-alkyl-adenosine analogues, including 3-deaza-3-phenethyl-adenosine and 3-deaza-3-methoxynaphthylethyl-adenosine, and incorporated them into oligonucleotides. A moderate reduction of duplex stability was observed on the basis of thermal denaturation data. Replication studies using purified Y-family human DNA Pols hPol η, κ, and ι indicated that these enzymes can perform TLS over the modified bases. hPol η had higher misincorporation rates when synthesizing opposite the modified bases compared with adenine, whereas hPol κ and ι maintained high fidelity. These results provide insight into how alterations in chemical structure reduce bypass of minor-groove adducts, and provide novel chemical probes for evaluating minor-groove DNA alkylation.
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Affiliation(s)
- Stefano Malvezzi
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, 8092, Zurich, Switzerland
| | - Todor Angelov
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, 8092, Zurich, Switzerland
| | - Shana J Sturla
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, 8092, Zurich, Switzerland
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9
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Abstract
Aptamers are nucleic acid-based scaffolds that can bind with high affinity to a variety of biological targets. Aptamers are identified from large DNA or RNA libraries through a process of directed molecular evolution (SELEX). Chemical modification of nucleic acids considerably increases the functional and structural diversity of aptamer libraries and substantially increases the affinity of the aptamers. Additionally, modified aptamers exhibit much greater resistance to biodegradation. The evolutionary selection of modified aptamers is conditioned by the possibility of the enzymatic synthesis and replication of non-natural nucleic acids. Wild-type or mutant polymerases and their non-natural nucleotide substrates that can support SELEX are highlighted in the present review. A focus is made on the efforts to find the most suitable type of nucleotide modifications and the engineering of new polymerases. Post-SELEX modification as a complementary method will be briefly considered as well.
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Affiliation(s)
- Sergey A Lapa
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
| | - Alexander V Chudinov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Edward N Timofeev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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10
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Kim HJ, Leal NA, Hoshika S, Benner SA. Ribonucleosides for an artificially expanded genetic information system. J Org Chem 2014; 79:3194-9. [PMID: 24597611 PMCID: PMC3985877 DOI: 10.1021/jo402665d] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
Rearranging hydrogen bonding groups
adds nucleobases to an artificially
expanded genetic information system (AEGIS), pairing orthogonally
to standard nucleotides. We report here a large-scale synthesis of
the AEGIS nucleotide carrying 2-amino-3-nitropyridin-6-one (trivially
Z) via Heck coupling and a hydroboration/oxidation sequence.
RiboZ is more stable against epimerization than its 2′-deoxyribo
analogue. Further, T7 RNA polymerase incorporates ZTP opposite its
Watson–Crick complement, imidazo[1,2-a]-1,3,5-triazin-4(8H)one (trivially P), laying grounds for using this “second-generation”
AEGIS Z:P pair to add amino acids encoded by mRNA.
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Affiliation(s)
- Hyo-Joong Kim
- Foundation for Applied Molecular Evolution (FfAME), 720 SW Second Avenue, Suite 201, Gainesville, Florida 32601, United States
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11
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Rankin KM, Sproviero M, Rankin K, Sharma P, Wetmore SD, Manderville RA. C8-heteroaryl-2'-deoxyguanosine adducts as conformational fluorescent probes in the NarI recognition sequence. J Org Chem 2012; 77:10498-508. [PMID: 23171213 DOI: 10.1021/jo302164c] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The optical, redox, and electronic properties of C(8)-heteroaryl-2'-deoxyguanosine (dG) adducts with C(8)-substituents consisting of furyl ((Fur)dG), pyrrolyl ((Pyr)dG), thienyl ((Th)dG), benzofuryl ((Bfur)dG), indolyl ((Ind)dG), and benzothienyl ((Bth)dG) are described. These adducts behave as fluorescent nucleobase probes with emission maxima from 379 to 419 nm and fluorescence quantum yields (Φ(fl)) in the 0.1-0.8 range in water at neutral pH. The probes exhibit quenched fluorescence with increased solvent viscosity and decreased solvent polarity. The (Fur)dG, (Bfur)dG, (Ind)dG, and (Bth)dG derivatives were incorporated into the G(3) position of the 12-mer oligonucleotide 5'-CTCG(1)G(2)CG(3)CCATC-3' that contains the recognition sequence of the NarI Type II restriction endonuclease. This sequence is widely used to study the biological activity (mutagenicity) of C(8)-arylamine-dG adducts with adduct conformation (anti vs syn) playing a critical role in the biological outcome. The modified NarI(X = (Fur)G, (Ind)G, (Bfur)G, or (Bth)G) oligonucleotides were hybridized to the complementary strand containing either C (NarI'(C)) or G (NarI'(G)) opposite the probe. The duplex structures were characterized by UV melting temperature analysis, fluorescence spectroscopy, collisional fluorescence quenching studies, and circular dichroism (CD). The emission of the probes showed sensitivity to the opposing base in the duplex, and suggested the utility of fluorescence spectroscopy to monitor probe conformation.
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Affiliation(s)
- Katherine M Rankin
- Department of Chemistry, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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12
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Xia S, Christian TD, Wang J, Konigsberg WH. Probing minor groove hydrogen bonding interactions between RB69 DNA polymerase and DNA. Biochemistry 2012; 51:4343-53. [PMID: 22571765 DOI: 10.1021/bi300416z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Minor groove hydrogen bonding (HB) interactions between DNA polymerases (pols) and N3 of purines or O2 of pyrimidines have been proposed to be essential for DNA synthesis from results obtained using various nucleoside analogues lacking the N3 or O2 contacts that interfered with primer extension. Because there has been no direct structural evidence to support this proposal, we decided to evaluate the contribution of minor groove HB interactions with family B pols. We have used RB69 DNA pol and 3-deaza-2'-deoxyadenosine (3DA), an analogue of 2-deoxyadenosine, which has the same HB pattern opposite T but with N3 replaced with a carbon atom. We then determined pre-steady-state kinetic parameters for the insertion of dAMP opposite dT using primer/templates (P/T)-containing 3DA. We also determined three structures of ternary complexes with 3DA at various positions in the duplex DNA substrate. We found that the incorporation efficiency of dAMP opposite dT decreased 10(2)-10(3)-fold even when only one minor groove HB interaction was missing. Our structures show that the HB pattern and base pair geometry of 3DA/dT is exactly the same as those of dA/dT, which makes 3DA an optimal analogue for probing minor groove HB interactions between a DNA polymerase and a nucleobase. In addition, our structures provide a rationale for the observed 10(2)-10(3)-fold decrease in the rate of nucleotide incorporation. The minor groove HB interactions between position n - 2 of the primer strand and RB69pol fix the rotomer conformations of the K706 and D621 side chains, as well as the position of metal ion A and its coordinating ligands, so that they are in the optinal orientation for DNA synthesis.
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Affiliation(s)
- Shuangluo Xia
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
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13
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Kim HJ, Chen F, Benner SA. Synthesis and Properties of 5-Cyano-Substituted Nucleoside Analog with a Donor–Donor–Acceptor Hydrogen-Bonding Pattern. J Org Chem 2012; 77:3664-9. [DOI: 10.1021/jo300230z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hyo-Joong Kim
- Foundation for Applied Molecular Evolution (FfAME), 720 SW Second Avenue,
Suite 201, Gainesville, Florida 32601, United States
- The Westheimer Institute for Science and Technology (TWIST), 720 SW
second Avenue, Suite 208, Gainesville, Florida 32601, United States
| | - Fei Chen
- Foundation for Applied Molecular Evolution (FfAME), 720 SW Second Avenue,
Suite 201, Gainesville, Florida 32601, United States
- The Westheimer Institute for Science and Technology (TWIST), 720 SW
second Avenue, Suite 208, Gainesville, Florida 32601, United States
- The CAS Key Laboratory of Genome
Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Steven A. Benner
- Foundation for Applied Molecular Evolution (FfAME), 720 SW Second Avenue,
Suite 201, Gainesville, Florida 32601, United States
- The Westheimer Institute for Science and Technology (TWIST), 720 SW
second Avenue, Suite 208, Gainesville, Florida 32601, United States
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14
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Jarchow-Choy SK, Krueger AT, Liu H, Gao J, Kool ET. Fluorescent xDNA nucleotides as efficient substrates for a template-independent polymerase. Nucleic Acids Res 2010; 39:1586-94. [PMID: 20947563 PMCID: PMC3045586 DOI: 10.1093/nar/gkq853] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Template independent polymerases, and terminal deoxynucleotidyl transferase (TdT) in particular, have been widely used in enzymatic labeling of DNA 3′-ends, yielding fluorescently-labeled polymers. The majority of fluorescent nucleotides used as TdT substrates contain tethered fluorophores attached to a natural nucleotide, and can be hindered by undesired fluorescence characteristics such as self-quenching. We previously documented the inherent fluorescence of a set of four benzo-expanded deoxynucleoside analogs (xDNA) that maintain Watson–Crick base pairing and base stacking ability; however, their substrate abilities for standard template-dependent polymerases were hampered by their large size. However, it seemed possible that a template-independent enzyme, due to lowered geometric constraints, might be less restrictive of nucleobase size. Here, we report the synthesis and study of xDNA nucleoside triphosphates, and studies of their substrate abilities with TdT. We find that this polymerase can incorporate each of the four xDNA monomers with kinetic efficiencies that are nearly the same as those of natural nucleotides, as measured by steady-state methods. As many as 30 consecutive monomers could be incorporated. Fluorescence changes over time could be observed in solution during the enzymatic incorporation of expanded adenine (dxATP) and cytosine (dxCTP) analogs, and after incorporation, when attached to a glass solid support. For (dxA)n polymers, monomer emission quenching and long-wavelength excimer emission was observed. For (dxC)n, fluorescence enhancement was observed in the polymer. TdT-mediated synthesis may be a useful approach for creating xDNA labels or tags on DNA, making use of the fluorescence and strong hybridization properties of the xDNA.
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15
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Vinogradova O, Pyshnyi D. Selectivity of Enzymatic Conversion of Oligonucleotide Probes during Nucleotide Polymorphism Analysis of DNA. Acta Naturae 2010; 2:36-53. [PMID: 22649627 PMCID: PMC3347538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The analysis of DNA nucleotide polymorphisms is one of the main goals of DNA diagnostics. DNA-dependent enzymes (DNA polymerases and DNA ligases) are widely used to enhance the sensitivity and reliability of systems intended for the detection of point mutations in genetic material. In this article, we have summarized the data on the selectiveness of DNA-dependent enzymes and on the structural factors in enzymes and DNA which influence the effectiveness of mismatch discrimination during enzymatic conversion of oligonucleotide probes on a DNA template. The data presented characterize the sensitivity of a series of DNA-dependent enzymes that are widely used in the detection of noncomplementary base pairs in nucleic acid substrate complexes. We have analyzed the spatial properties of the enzyme-substrate complexes. These properties are vital for the enzymatic reaction and the recognition of perfect DNA-substrates. We also discuss relevant approaches to increasing the selectivity of enzyme-dependent reactions. These approaches involve the use of modified oligonucleotide probes which "disturb" the native structure of the DNA-substrate complexes.
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Affiliation(s)
- O.A. Vinogradova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division, Russian Academy of Sciences
| | - D.V. Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division, Russian Academy of Sciences
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16
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Kuchta RD. Nucleotide Analogues as Probes for DNA and RNA Polymerases. CURRENT PROTOCOLS IN CHEMICAL BIOLOGY 2010; 2:111-124. [PMID: 21822500 PMCID: PMC3149870 DOI: 10.1002/9780470559277.ch090203] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Nucleotide analogues represent a major class of anti-cancer and anti-viral drugs, and provide an extremely powerful tool for dissecting the mechanisms of DNA and RNA polymerases. While the basic assays themselves are relatively straight-forward, a key issue is to appropriately design the studies to answer the mechanistic question of interest. This article addresses the major issues involved in designing these studies, and some of the potential difficulties that arise in interpreting the data. Examples are given both of the type of analogues typically used, the experimental approaches with different polymerases, and issues with data interpretation.
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Affiliation(s)
- Robert D Kuchta
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309
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17
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Ogata S, Takahashi M, Minakawa N, Matsuda A. Unnatural imidazopyridopyrimidine:naphthyridine base pairs: selective incorporation and extension reaction by Deep Vent (exo- ) DNA polymerase. Nucleic Acids Res 2009; 37:5602-9. [PMID: 19628664 PMCID: PMC2761277 DOI: 10.1093/nar/gkp611] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In our previous communication we reported the enzymatic recognition of unnatural imidazopyridopyrimidine:naphthyridine (Im:Na) base pairs, i.e. ImO(N):NaN(O) and ImN(O):NaO(N), using the Klenow fragment exo(-) [KF (exo(-))]. We describe herein the successful results of (i) improved enzymatic recognition for ImN(O):NaO(N) base pairs and (ii) further primer extension reactions after the Im:Na base pairs by Deep Vent DNA polymerase exo(-) [Deep Vent (exo(-))]. Since KF (exo(-)) did not catalyze primer extension reactions after the Im:Na base pair, we carried out a screening of DNA polymerases to promote the primer extension reaction as well as to improve the selectivity of base pair recognition. As a result, a family B DNA polymerase, especially Deep Vent (exo(-)), seemed most promising for this purpose. In the ImO(N):NaN(O) base pair, incorporation of NaN(O)TP against ImO(N) in the template was preferable to that of the natural dNTPs, while incorporation of dATP as well as dGTP competed with that of ImO(N)TP when NaN(O) was placed in the template. Thus, the selectivity of base pair recognition by Deep Vent (exo(-)) was less than that by KF (exo(-)) in the case of the ImO(N):NaN(O) base pair. On the other hand, incorporation of NaO(N)TP against ImN(O) in the template and that of ImN(O)TP against NaO(N) were both quite selective. Thus, the selectivity of base pair recognition was improved by Deep Vent (exo(-)) in the ImN(O):NaO(N) base pair. Moreover, this enzyme catalyzed further primer extension reactions after the ImN(O):NaO(N) base pair to afford a faithful replicate, which was confirmed by MALDI-TOF mass spectrometry as well as the kinetics data for extension fidelity next to the ImN(O):NaO(N) base pair. The results presented in this paper revealed that the ImN(O):NaO(N) base pair might be a third base pair beyond the Watson-Crick base pairs.
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Affiliation(s)
- Shintaro Ogata
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
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18
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Minakawa N, Ogata S, Takahashi M, Matsuda A. Selective recognition of unnatural imidazopyridopyrimidine:naphthyridine base pairs consisting of four hydrogen bonds by the Klenow fragment. J Am Chem Soc 2009; 131:1644-5. [PMID: 19146369 DOI: 10.1021/ja807391g] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this work, we investigated how thermally stable ImO(N):NaN(O) and ImN(O):NaO(N) pairs are recognized by the Klenow fragment (KF). As a result, these complementary base pairs, especially the ImN(O):NaO(N) pair, were recognized selectively due to the four hydrogen bonds between the nucleobases and the shape complementarity of the Im:Na pair similar to the purine:pyrimidine base pair.
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Affiliation(s)
- Noriaki Minakawa
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
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19
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Minakawa N, Kawano Y, Murata S, Inoue N, Matsuda A. Oligodeoxynucleotides containing 3-bromo-3-deazaadenine and 7-bromo-7-deazaadenine 2'-deoxynucleosides as chemical probes to investigate DNA-protein interactions. Chembiochem 2008; 9:464-70. [PMID: 18219644 DOI: 10.1002/cbic.200700580] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
We describe the design and proof of concept of a pair of chemical probes for investigating DNA-protein interactions-specifically, the incorporation of 7-bromo-7-deazaadenine and 3-bromo-3-deazaadenine 2'-deoxynucleosides (Br(7)C(7)dA and Br(3)C(3)dA) into oligodeoxynucleotides (ODNs)-and their utility. Whereas the bromo substituent of the Br(7)C(7)dA unit in an ODN duplex acts sterically to inhibit binding with NF-kappaB, which interacts with the duplex in its major groove, the bromo substituent of the Br(3)C(3)dA unit acts sterically to inhibit binding with RNase H, which interacts with the duplex in its minor groove. In addition, the utilization of ODNs containing 7-deazaadenine and 3-deazaadenine 2'-deoxynucleosides (C(7)dA and C(3)dA), together with the pair of chemical probes, afforded valuable information on the requirement for nitrogen atoms located in either the major or minor grooves. Accordingly, we were able to show the utility of ODNs containing Br(7)C(7)dA, Br(3)C(3)dA, C(7)dA, and C(3)dA for the investigation of DNA-protein interactions.
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Affiliation(s)
- Noriaki Minakawa
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
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20
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Havemann SA, Hoshika S, Hutter D, Benner SA. Incorporation of multiple sequential pseudothymidines by DNA polymerases and their impact on DNA duplex structure. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2008; 27:261-78. [PMID: 18260010 DOI: 10.1080/15257770701853679] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Thermal denaturation and circular dichroism studies suggested that multiple (up to 12), sequential pseudothymidines, a representative C-glycoside, do not perturb the structure of a representative DNA duplex. Further, various Family A and B DNA polymerases were found to extend a primer by incorporating four sequential pseudothymidine triphosphates, and then continue the extension to generate full-length product. Detailed studies showed that Taq polymerase incorporated up to five sequential C-glycosides, but not more. These results constrain architectures for sequencing, quantitating, and analyzing DNA analogs that exploit C-glycosides, and define better the challenge of creating a synthetic biology using these with natural polymerases.
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Affiliation(s)
- Stephanie A Havemann
- Department of Microbiology & Cell Science, Space Life Sciences Laboratory, Kennedy Space Center, University of Florida, FL, USA
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21
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Seley-Radtke KL, Zhang Z, Wauchope OR, Zimmermann SC, Ivanov A, Korba B. Hetero-expanded purine nucleosides. Design, synthesis and preliminary biological activity. NUCLEIC ACIDS SYMPOSIUM SERIES (2004) 2008; 52:635-6. [PMID: 18776540 PMCID: PMC2785017 DOI: 10.1093/nass/nrn321] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Several thieno-expanded purine nucleoside analogues were synthesized for use as tools in ongoing investigations into nucleic acid structure and function in our laboratories. The inclusion of the thiophene ring system in the nucleoside endows the purine scaffold with advantages not previously available in other reported expanded purines. The synthesis and preliminary biological studies are reported herein.
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22
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Yang Z, Sismour AM, Sheng P, Puskar NL, Benner SA. Enzymatic incorporation of a third nucleobase pair. Nucleic Acids Res 2007; 35:4238-49. [PMID: 17576683 PMCID: PMC1934989 DOI: 10.1093/nar/gkm395] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
DNA polymerases are identified that copy a non-standard nucleotide pair joined by a hydrogen bonding pattern different from the patterns joining the dA:T and dG:dC pairs. 6-Amino-5-nitro-3-(1′-β-d-2′-deoxyribofuranosyl)-2(1H)-pyridone (dZ) implements the non-standard ‘small’ donor–donor–acceptor (pyDDA) hydrogen bonding pattern. 2-Amino-8-(1′-β-D-2′-deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one (dP) implements the ‘large’ acceptor–acceptor–donor (puAAD) pattern. These nucleobases were designed to present electron density to the minor groove, density hypothesized to help determine specificity for polymerases. Consistent with this hypothesis, both dZTP and dPTP are accepted by many polymerases from both Families A and B. Further, the dZ:dP pair participates in PCR reactions catalyzed by Taq, Vent (exo−) and Deep Vent (exo−) polymerases, with 94.4%, 97.5% and 97.5%, respectively, retention per round. The dZ:dP pair appears to be lost principally via transition to a dC:dG pair. This is consistent with a mechanistic hypothesis that deprotonated dZ (presenting a pyDAA pattern) complements dG (presenting a puADD pattern), while protonated dC (presenting a pyDDA pattern) complements dP (presenting a puAAD pattern). This hypothesis, grounded in the Watson–Crick model for nucleobase pairing, was confirmed by studies of the pH-dependence of mismatching. The dZ:dP pair and these polymerases, should be useful in dynamic architectures for sequencing, molecular-, systems- and synthetic-biology.
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Affiliation(s)
| | | | | | | | - Steven A. Benner
- *To whom correspondence should be addressed. +352-271-7005+352-271-7076
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23
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Beckman J, Kincaid K, Hocek M, Spratt T, Engels J, Cosstick R, Kuchta RD. Human DNA polymerase alpha uses a combination of positive and negative selectivity to polymerize purine dNTPs with high fidelity. Biochemistry 2007; 46:448-60. [PMID: 17209555 PMCID: PMC2515318 DOI: 10.1021/bi061243s] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA polymerases accurately replicate DNA by incorporating mostly correct dNTPs opposite any given template base. We have identified the chemical features of purine dNTPs that human pol alpha uses to discriminate between right and wrong dNTPs. Removing N-3 from guanine and adenine, two high-fidelity bases, significantly lowers fidelity. Analogously, adding the equivalent of N-3 to low-fidelity benzimidazole-derived bases (i.e., bases that pol alpha rapidly incorporates opposite all four natural bases) and to generate 1-deazapurines significantly strengthens the ability of pol alpha to identify the resulting 1-deazapurines as wrong. Adding the equivalent of the purine N-1 to benzimidazole or to 1-deazapurines significantly decreases the rate at which pol alpha polymerizes the resulting bases opposite A, C, and G while simultaneously enhancing polymerization opposite T. Conversely, adding the equivalent of adenine's C-6 exocyclic amine (N-6) to 1- and 3-deazapurines also enhances polymerization opposite T but does not significantly decrease polymerization opposite A, C, and G. Importantly, if the newly inserted bases lack N-1 and N-6, pol alpha does not efficiently polymerize the next correct dNTP, whereas if it lacks N-3, one additional nucleotide is added and then chain termination ensues. These data indicate that pol alpha uses two orthogonal screens to maximize its fidelity. During dNTP polymerization, it uses a combination of negative (N-1 and N-3) and positive (N-1 and N-6) selectivity to differentiate between right and wrong dNTPs, while the shape of the base pair is essentially irrelevant. Then, to determine whether to add further dNTPs onto the just added nucleotide, pol alpha appears to monitor the shape of the base pair at the primer 3'-terminus. The biological implications of these results are discussed.
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Affiliation(s)
- Jeff Beckman
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309-0215
| | - Kristi Kincaid
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309-0215
| | - Michal Hocek
- Centre for New Antivirals and Antineoplastics, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, CZ-16610 Prague 6, Czech Republic
| | - Thomas Spratt
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, 500 University Drive, Hershey PA 17033
| | - Joachim Engels
- Institut für Organische Chemie, Johann Wolfgang Goethe Universität, Marie Curie Strasse 11, D-60439 Frankfurt am Main, Germany
| | - Richard Cosstick
- Department of Chemistry, University of Liverpool, Crown Street, Liverpool L69 3BX
| | - Robert D. Kuchta
- To whom correspondence should be addressed. . Phone: 303-492-7027. FAX: 303-492-5894
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24
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Yang Z, Hutter D, Sheng P, Sismour AM, Benner SA. Artificially expanded genetic information system: a new base pair with an alternative hydrogen bonding pattern. Nucleic Acids Res 2006; 34:6095-101. [PMID: 17074747 PMCID: PMC1635279 DOI: 10.1093/nar/gkl633] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
To support efforts to develop a ‘synthetic biology’ based on an artificially expanded genetic information system (AEGIS), we have developed a route to two components of a non-standard nucleobase pair, the pyrimidine analog 6-amino-5-nitro-3-(1′-β-D-2′-deoxyribofuranosyl)-2(1H)-pyridone (dZ) and its Watson–Crick complement, the purine analog 2-amino-8-(1′-β-D-2′-deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one (dP). These implement the pyDDA:puAAD hydrogen bonding pattern (where ‘py’ indicates a pyrimidine analog and ‘pu’ indicates a purine analog, while A and D indicate the hydrogen bonding patterns of acceptor and donor groups presented to the complementary nucleobases, from the major to the minor groove). Also described is the synthesis of the triphosphates and protected phosphoramidites of these two nucleosides. We also describe the use of the protected phosphoramidites to synthesize DNA oligonucleotides containing these AEGIS components, verify the absence of epimerization of dZ in those oligonucleotides, and report some hybridization properties of the dZ:dP nucleobase pair, which is rather strong, and the ability of each to effectively discriminate against mismatches in short duplex DNA.
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Affiliation(s)
| | | | | | | | - Steven A. Benner
- To whom correspondence should be addressed at Foundation for Applied Molecular Evolution, P.O. Box 13174, Gainesville FL 32604-1174, USA. Tel: +1 352 271 7005; Fax: +1 352 271 7076;
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25
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Kuwahara M, Nagashima JI, Hasegawa M, Tamura T, Kitagata R, Hanawa K, Hososhima SI, Kasamatsu T, Ozaki H, Sawai H. Systematic characterization of 2'-deoxynucleoside- 5'-triphosphate analogs as substrates for DNA polymerases by polymerase chain reaction and kinetic studies on enzymatic production of modified DNA. Nucleic Acids Res 2006; 34:5383-94. [PMID: 17012278 PMCID: PMC1636466 DOI: 10.1093/nar/gkl637] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2006] [Revised: 07/28/2006] [Accepted: 08/14/2006] [Indexed: 11/26/2022] Open
Abstract
We synthesized C5-modified analogs of 2'-deoxyuridine triphosphate and 2'-deoxycytidine triphosphate and investigated them as substrates for PCRs using Taq, Tth, Vent(exo-), KOD Dash and KOD(exo-) polymerases and pUC 18 plasmid DNA as a template. These assays were performed on two different amplifying regions of pUC18 with different T/C contents that are expected to have relatively high barriers for incorporation of either modified dU or dC. On the basis of 260 different assays (26 modified triphosphates x 5 DNA polymerases x 2 amplifying regions), it appears that generation of the full-length PCR product depends not only on the chemical structures of the substitution and the nature of the polymerase but also on whether the substitution is on dU or dC. Furthermore, the template sequence greatly affected generation of the PCR product, depending on the combination of the DNA polymerase and modified triphosphate. By examining primer extension reactions using primers and templates containing C5-modified dUs, we found that a modified dU at the 3' end of the elongation strand greatly affects the catalytic efficiency of DNA polymerases, whereas a modified dU opposite the elongation site on the template strand has less of an influence on the catalytic efficiency.
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Affiliation(s)
- Masayasu Kuwahara
- Department of Applied Chemistry, Faculty of Engineering, Gunma University, Gunma 376-8515, Japan.
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26
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Matsuda S, Henry AA, Romesberg FE. Optimization of unnatural base pair packing for polymerase recognition. J Am Chem Soc 2006; 128:6369-75. [PMID: 16683801 PMCID: PMC2536690 DOI: 10.1021/ja057575m] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
As part of an effort to expand the genetic alphabet, we have been examining the ability of predominately hydrophobic nucleobase analogues to pair in duplex DNA and during polymerase-mediated replication. We previously reported the synthesis and thermal stability of unnatural base pairs formed between nucleotides bearing simple methyl-substituted phenyl ring nucleobase analogues. Several of these pairs are virtually as stable and selective as natural base pairs in the same sequence context. Here, we report the characterization of polymerase-mediated replication of the same unnatural base pairs. We find that every facet of replication, including correct and incorrect base pair synthesis, as well as continued primer extension beyond the unnatural base pair, is sensitive to the specific methyl substitution pattern of the nucleobase analogue. The results demonstrate that neither hydrogen bonding nor large aromatic surface area is required for polymerase recognition, and that interstrand interactions between small aromatic rings may be optimized for replication. Combined with our previous results, these studies suggest that appropriately derivatized phenyl nucleobase analogues represent a promising approach toward developing a third base pair and expanding the genetic alphabet.
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Affiliation(s)
- Shigeo Matsuda
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California, 92037
| | - Allison A. Henry
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California, 92037
| | - Floyd E. Romesberg
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California, 92037
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Nakano SI, Uotani Y, Uenishi K, Fujii M, Sugimoto N. DNA base flipping by a base pair-mimic nucleoside. Nucleic Acids Res 2005; 33:7111-9. [PMID: 16361269 PMCID: PMC1316115 DOI: 10.1093/nar/gki1018] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
On the basis of non-covalent bond interactions in nucleic acids, we synthesized the deoxyadenosine derivatives tethering a phenyl group (X) and a naphthyl group (Z) by an amide linker, which mimic a Watson–Crick base pair. Circular dichroism spectra indicated that the duplexes containing X and Z formed a similar conformation regardless of the opposite nucleotide species (A, G, C, T and an abasic site analogue F), which was not observed for the natural duplexes. The ΔG370 values among the natural duplexes containing the A/A, A/G, A/C, A/T and A/F pairs differed by 5.2 kcal mol−1 while that among the duplexes containing X or Z in place of the adenine differed by only 1.9 or 2.8 kcal mol−1, respectively. Fluorescence quenching experiments confirmed that 2-amino purine opposite X adopted an unstacked conformation. The structural and thermodynamic analyses suggest that the aromatic hydrocarbon group of X and Z intercalates into a double helix, resulting in the opposite nucleotide base flipping into an unstacked position regardless of the nucleotide species. This observation implies that modifications at the aromatic hydrocarbon group and the amide linker may expand the application of the base pair-mimic nucleosides for molecular biology and biotechnology.
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Affiliation(s)
- Shu-ichi Nakano
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University8-9-1 Okamoto, Higashinada-ku, Kobe 658-8501, Japan
| | - Yuuki Uotani
- Department of Chemistry, Faculty of Science and Engineering, Konan University8-9-1 Okamoto, Higashinada-ku, Kobe 658-8501, Japan
| | - Kazuya Uenishi
- Molecular Engineering Institute, Kinki University11-6 Kayanomori, Iizuka, Fukuoka 820-8555, Japan
| | - Masayuki Fujii
- Molecular Engineering Institute, Kinki University11-6 Kayanomori, Iizuka, Fukuoka 820-8555, Japan
- Department of Environmental and Biological Chemistry, Kinki University11-6 Kayanomori, Iizuka, Fukuoka 820-8555, Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University8-9-1 Okamoto, Higashinada-ku, Kobe 658-8501, Japan
- Department of Chemistry, Faculty of Science and Engineering, Konan University8-9-1 Okamoto, Higashinada-ku, Kobe 658-8501, Japan
- To whom correspondence should be addressed. Tel: +81 78 435 2497; Fax: +81 78 435 2539;
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28
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Ahle JD, Barr S, Chin AM, Battersby TR. Sequence determination of nucleic acids containing 5-methylisocytosine and isoguanine: identification and insight into polymerase replication of the non-natural nucleobases. Nucleic Acids Res 2005; 33:3176-84. [PMID: 15933210 PMCID: PMC1142403 DOI: 10.1093/nar/gki628] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Nucleobase analogs 5-methylisocytosine (MeisoC) and isoguanine (isoG) form a non-natural base pair in duplex nucleic acids with base pairing specificity orthogonal to the natural nucleobase pairs. Sequencing reactions were conducted with oligodeoxyribonucleotides (ODNs) containing dMeisoC and disoG using modified pyrosequencing and dye terminator methods. Modified dye terminator sequencing was generally useful for the sequence identification of ODNs containing the non-natural nucleobases. The two sequencing methods were also used to monitor nucleotide incorporation and subsequent extension by Family A polymerases used in the sequencing methods with a six-nucleobase system that includes dMeisoC and disoG. Nucleic acids containing the six-nucleobase system could be replicated well, but not as well as natural nucleic acids, especially in regions of high dMeisoC–disoG content. Challenges in replication with dMeisoC–disoG are consistent with nucleobase tautomerism in the insertion step and disrupted minor groove nucleobase pair–polymerase contacts in subsequent extension.
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Affiliation(s)
| | | | - A. Michael Chin
- Sequetech Corporation935 Sierra Vista Avenue, Mountain View, CA 94043, USA
| | - Thomas R. Battersby
- To whom correspondence should be addressed at PO Box 2466, Berkeley, CA 94702, USA. Tel: +1 510 705 5979; Fax: +1 510 705 5938;
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Abstract
This Account describes work done in these laboratories that has used synthetic, physical organic, and biological chemistry to understand the roles played by the nucleobases, sugars, and phosphates of DNA in the molecular recognition processes central to genetics. The number of nucleobases has been increased from 4 to 12, generating an artificially expanded genetic information system. This system is used today in the clinic to monitor the levels of HIV and hepatitis C viruses in patients, helping to manage patient care. Work with uncharged phosphate replacements suggests that a repeating charge is a universal feature of genetic molecules operating in water and will be found in extraterrestrial life (if it is ever encountered). The use of ribose may reflect prebiotic processes in the presence of borate-containing minerals, which stabilize ribose formed from simple organic precursors. A new field, synthetic biology, is emerging on the basis of these experiments, where chemistry mimics biological processes as complicated as Darwinian evolution.
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Affiliation(s)
- Steven A Benner
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, USA.
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30
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Meyer AS, Blandino M, Spratt TE. Escherichia coli DNA polymerase I (Klenow fragment) uses a hydrogen-bonding fork from Arg668 to the primer terminus and incoming deoxynucleotide triphosphate to catalyze DNA replication. J Biol Chem 2004; 279:33043-6. [PMID: 15210707 DOI: 10.1074/jbc.c400232200] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Interactions between the minor groove of the DNA and DNA polymerases appear to play a major role in the catalysis and fidelity of DNA replication. In particular, Arg668 of Escherichia coli DNA polymerase I (Klenow fragment) makes a critical contact with the N-3-position of guanine at the primer terminus. We investigated the interaction between Arg668 and the ring oxygen of the incoming deoxynucleotide triphosphate (dNTP) using a combination of site-specific mutagenesis of the protein and atomic substitution of the DNA and dNTP. Hydrogen bonds from Arg668 were probed with the site-specific mutant R668A. Hydrogen bonds from the DNA were probed with oligodeoxynucleotides containing either guanine or 3-deazaguanine (3DG) at the primer terminus. Hydrogen bonds from the incoming dNTP were probed with (1 'R,3 'R,4 'R)-1-[3-hydroxy-4-(triphosphorylmethyl)cyclopent-1-yl]uracil (dcUTP), an analog of dUTP in which the ring oxygen of the deoxyribose moiety was replaced by a methylene group. We found that the pre-steady-state parameter kpol was decreased 1,600 to 2,000-fold with each of the single substitutions. When the substitutions were combined, there was no additional decrease (R668A and 3DG), a 5-fold decrease (3DG and dcUTP), and a 50-fold decrease (R668A and dcUTP) in kpol. These results are consistent with a hydrogen-bonding fork from Arg668 to the primer terminus and incoming dNTP. These interactions may play an important role in fidelity as well as catalysis of DNA replication.
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Affiliation(s)
- Aviva S Meyer
- Institute for Cancer Prevention, American Health Foundation Cancer Center, Valhalla, New York 10595, USA
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