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Hatano A, Matsuzaka R, Shimane G, Wakana H, Suzuki K, Nishioka C, Kojima A, Kidowaki M. Introduction of pseudo-base benzimidazole derivatives into nucleosides via base exchange by a nucleoside metabolic enzyme. Bioorg Med Chem 2023; 91:117411. [PMID: 37451053 DOI: 10.1016/j.bmc.2023.117411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/07/2023] [Accepted: 07/08/2023] [Indexed: 07/18/2023]
Abstract
In alternate organic synthesis, biocatalysis using enzymes provides a more stereoselective and cost-effective approach. Synthesis of unnatural nucleosides by nucleoside base exchange reactions using nucleoside-metabolizing enzymes has previously shown that the 5-position recognition of pyrimidine bases on nucleoside substrates is loose and can be used to introduce functional molecules into pyrimidine nucleosides. Here we explored the incorporation of purine pseudo bases into nucleosides by the base exchange reaction of pyrimidine nucleoside phosphorylase (PyNP), demonstrating that an imidazole five-membered ring is an essential structure for the reaction. In the case of benzimidazole, the base exchange proceeded to give the deoxyribose form in 96 % yield, and the ribose form in 23 % yield. The reaction also proceeded with 1H-imidazo[4,5-b]phenazine, a benzimidazole analogue with an additional ring, although the yield of nucleoside was only 31 %. Docking simulations between 1H and imidazo[4,5-b]phenazine nucleoside and the active site of PyNP (PDB 1BRW) supported our observation that 1H-imidazo[4,5-b]phenazine can be used as a substrate by PyNP. Thus, the enzymatic substitution reaction using PyNP can be used to incorporate many purine pseudo bases and benzimidazole derivatives with various functional groups into nucleoside structures, which have potential utility as diagnostic or therapeutic agents.
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Affiliation(s)
- Akihiko Hatano
- Department of Materials Science and Engineering, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan.
| | - Riki Matsuzaka
- Department of Materials Science and Engineering, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Genki Shimane
- Department of Materials Science and Engineering, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Hiroyuki Wakana
- Department of Materials Science and Engineering, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Kou Suzuki
- Department of Materials Science and Engineering, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Chisato Nishioka
- Department of Materials Science and Engineering, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Aoi Kojima
- Department of Materials Science and Engineering, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Masatoshi Kidowaki
- Department of Applied Chemistry, Shibaura Institute of Technology, 3-7-5, Toyosu, Koto-ku, Tokyo 135-8548, Japan
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Loakes D, Hill F, Brown DM, Ball S, Reeve MA, Robinson PS. 5′-Tailed Octanucleotide Primers for Cycle Sequencing. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328319908044634] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- D. Loakes
- a Medical Research Council, Laboratory of Molecular Biology , Hills Road, Cambridge , CB2 2QH , UK
| | - F. Hill
- a Medical Research Council, Laboratory of Molecular Biology , Hills Road, Cambridge , CB2 2QH , UK
| | - D. M. Brown
- a Medical Research Council, Laboratory of Molecular Biology , Hills Road, Cambridge , CB2 2QH , UK
| | - S. Ball
- b Nycomed Amersham plc, Amersham Laboratories , White Lion Road, Amersham, Buckinghamshire , HP7 9LL , UK
| | - M. A. Reeve
- b Nycomed Amersham plc, Amersham Laboratories , White Lion Road, Amersham, Buckinghamshire , HP7 9LL , UK
| | - P. S. Robinson
- b Nycomed Amersham plc, Amersham Laboratories , White Lion Road, Amersham, Buckinghamshire , HP7 9LL , UK
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Chiaramonte M, Moore CL, Kincaid K, Kuchta RD. Facile polymerization of dNTPs bearing unnatural base analogues by DNA polymerase alpha and Klenow fragment (DNA polymerase I). Biochemistry 2003; 42:10472-81. [PMID: 12950174 DOI: 10.1021/bi034763l] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The high fidelity of DNA replication is largely dependent upon accurate incorporation of dNTPs by DNA polymerases. To study the mechanism underlying nucleotide selection, we synthesized four nucleotide analogues bearing the unnatural bases benzimidazole, 5-nitrobenzimidazole, 6-nitrobenzimidazole, and 5-nitroindole and analyzed their incorporation by three DNA polymerases. We have found that human DNA polymerase alpha (pol alpha) and the Klenow fragment of Escherichia coli DNA polymerase I (KF) incorporate all four nucleotide analogues opposite all four canonical bases up to 4000-fold more efficiently than an incorrect natural dNTP (i.e., rates that approach those of a correct, natural dNTP), even though the shape of any base pair formed between the analogue and the template likely does not resemble a normal base pair. While pol alpha preferentially incorporated the analogues opposite template pyrimidines, KF surprisingly preferred to polymerize them opposite template purines. Although neither pol alpha nor KF readily polymerized a natural dNTP opposite either 5- or 6-nitrobenzimidazole in the template strand, the enzymes did incorporate the analogues to generate novel base pairs. Both pol alpha and KF polymerized the analogues up to 140-fold more efficiently than dATP both across from abasic sites and as 3'-overhangs on blunt-ended templates. Although Maloney murine leukemia virus reverse transcriptase did not measurably incorporate the analogues, this enzyme bound the analogues with K(I)'s only slightly higher than the K(m) for polymerization of the normal dNTP. The implications of these results with respect to how polymerases discriminate between correct and incorrect dNTPs are discussed.
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Affiliation(s)
- Molly Chiaramonte
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, USA
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Vallone PM, Benight AS. Melting studies of short DNA hairpins containing the universal base 5-nitroindole. Nucleic Acids Res 1999; 27:3589-96. [PMID: 10446251 PMCID: PMC148605 DOI: 10.1093/nar/27.17.3589] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Effects of the universal base 5-nitroindole on the thermodynamic stability of DNA hairpins having a 6 bp stem and four base loops were investigated by optical absorbance and differential scanning calorimetry techniques. Melting studies were conducted in buffer containing 115 mM Na(+). Five different modified versions of DNA hairpins containing a 5-nitroindole base or bases substituted at different positions in the stem and loop regions were examined. Thermo-dynamic parameters of the melting transitions estimated from a two-state analysis of optical melting curves and measured directly by calorimetry revealed that the presence of 5-nitroindole bases in the duplex stem or loop regions of short DNA hairpins significantly affects both their enthalpic and entropic melting components in a compensating manner, while the transition free energy varies linearly with the transition temperature. The calorimetrically determined enthalpy and entropy values of the modified hairpins were considerably smaller (43-53%) than the two-state optical parameters, suggesting that solvent effects may be significant in the melting processes of these hairpins. Results of circular dichroism measurements also revealed slight differences between the modified hairpins and the control in both the duplex and melted states, suggesting subtle structural differences between the control and DNA hairpins containing a 5-nitroindole base or bases.
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Affiliation(s)
- P M Vallone
- Department of Chemistry, 845 West Taylor Street, Room 4500, University of Illinois at Chicago, Chicago, IL 60607, USA
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Ball S, Reeve MA, Robinson PS, Hill F, Brown DM, Loakes D. The use of tailed octamer primers for cycle sequencing. Nucleic Acids Res 1998; 26:5225-7. [PMID: 9801324 PMCID: PMC147975 DOI: 10.1093/nar/26.22.5225] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Studies have been carried out on the use of octamer oligonucleotides tailed with different base analogues as primers in cycle sequencing reactions. 5-Nitroindole tails improved the performance as primers of a number of octamers. A tail length of three or four 5-nitroindole residues significantly increased the sequencing signal intensity for almost all primers. The use of incomplete libraries of tailed octamer primers for primer walking is discussed.
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Affiliation(s)
- S Ball
- Nycomed Amersham plc, Amersham Laboratories, White Lion Road, Amersham, Buckinghamshire HP7 9LL, UK
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