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Lowe PT, O'Hagan D. 4'-Fluoro-nucleosides and nucleotides: from nucleocidin to an emerging class of therapeutics. Chem Soc Rev 2023; 52:248-276. [PMID: 36472161 DOI: 10.1039/d2cs00762b] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The history and development of 4'-fluoro-nucleosides is discussed in this review. This is a class of nucleosides which have their origin in the discovery of the rare fluorine containing natural product nucleocidin. Nucleocidin contains a fluorine atom located at the 4'-position of its ribose ring. From its early isolation as an unexpected natural product, to its total synthesis and bioactivity assessment, nucleocidin has played a role in inspiring the exploration of 4'-fluoro-nucleosides as a privileged motif for nucleoside-based therapeutics.
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Affiliation(s)
- Phillip T Lowe
- School of Chemistry and Biomedical Sciences Research Centre, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK.
| | - David O'Hagan
- School of Chemistry and Biomedical Sciences Research Centre, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK.
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2
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Zhou Y, Lu K, Li Q, Fan C, Zhou C. C4'-Fluorinated Oligodeoxynucleotides: Synthesis, Stability, Structural Studies. Chemistry 2021; 27:14738-14746. [PMID: 34432342 DOI: 10.1002/chem.202102561] [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: 07/14/2021] [Indexed: 11/06/2022]
Abstract
Fluoro-substitution on the ribose moiety (e. g., 2'-F-deoxyribonucleotide) represents a popular way to modulate the ribose conformation and, hence, the structure and function of nucleic acids. In the present study, we synthesized 4'-F-deoxythymidine (4'-F T) and introduced it to oligodeoxyribonucleotides (ODNs). Though scission of the glycosylic bond of 4'-F T followed by strand cleavage occurred to some extent under alkaline conditions, the 4'-F T-modified ODNs were rather stable in neutral buffers. NMR studies showed that like 2'-F-deoxyribonucleoside, 4'-F T exists predominantly in the North conformation not only in the nucleoside form but also in the context of ODN strands. Circular dichroism spectroscopy, thermal denaturing and RNase H1 footprinting studies of 4'-F T-modified ODN/cDNA and ODN/cRNA duplexes indicated that the North conformation tendency of 4'-F T is maintained in the duplexes, leading to a local structural perturbation. Collectively, 4'-F-deoxyribonucleotide structurally resembles the 2'-F-deoxyribonucleotide but imparts less structural perturbation to the duplex than the latter.
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Affiliation(s)
- Yifei Zhou
- State Key Laboratory of Elemento-Organic Chemistry, and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Kuan Lu
- State Key Laboratory of Elemento-Organic Chemistry, and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Qiang Li
- State Key Laboratory of Elemento-Organic Chemistry, and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Chaochao Fan
- State Key Laboratory of Elemento-Organic Chemistry, and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Chuanzheng Zhou
- State Key Laboratory of Elemento-Organic Chemistry, and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin, 300071, China
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3
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Espinasse A, Lembke HK, Cao AA, Carlson EE. Modified nucleoside triphosphates in bacterial research for in vitro and live-cell applications. RSC Chem Biol 2020; 1:333-351. [PMID: 33928252 PMCID: PMC8081287 DOI: 10.1039/d0cb00078g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/21/2020] [Indexed: 12/12/2022] Open
Abstract
Modified nucleoside triphosphates (NTPs) are invaluable tools to probe bacterial enzymatic mechanisms, develop novel genetic material, and engineer drugs and proteins with new functionalities. Although the impact of nucleobase alterations has predominantly been studied due to their importance for protein recognition, sugar and phosphate modifications have also been investigated. However, NTPs are cell impermeable due to their negatively charged phosphate tail, a major hurdle to achieving live bacterial studies. Herein, we review the recent advances made to investigate and evolve bacteria and their processes with the use of modified NTPs by exploring alterations in one of the three moieties: the nucleobase, the sugar and the phosphate tail. We also present the innovative methods that have been devised to internalize NTPs into bacteria for in vivo applications.
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Affiliation(s)
- Adeline Espinasse
- Department of Chemistry, University of Minnesota207 Pleasant Street SEMinneapolisMinnesota 55455USA
| | - Hannah K. Lembke
- Department of Chemistry, University of Minnesota207 Pleasant Street SEMinneapolisMinnesota 55455USA
| | - Angela A. Cao
- Department of Chemistry, University of Minnesota207 Pleasant Street SEMinneapolisMinnesota 55455USA
| | - Erin E. Carlson
- Department of Chemistry, University of Minnesota207 Pleasant Street SEMinneapolisMinnesota 55455USA
- Department of Medicinal Chemistry, University of Minnesota208 Harvard Street SEMinneapolisMinnesota 55454USA
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota321 Church St SEMinneapolisMinnesota 55454USA
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4
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Zhou Y, Zang C, Wang H, Li J, Cui Z, Li Q, Guo F, Yan Z, Wen X, Xi Z, Zhou C. 4'-C-Trifluoromethyl modified oligodeoxynucleotides: synthesis, biochemical studies, and cellular uptake properties. Org Biomol Chem 2020; 17:5550-5560. [PMID: 31112186 DOI: 10.1039/c9ob00765b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Herein, we report the synthesis of 4'-C-trifluoromethyl (4'-CF3) thymidine (T4'-CF3) and its incorporation into oligodeoxynucleotides (ODNs) through solid-supported DNA synthesis. The 4'-CF3 modification leads to a marginal effect on the deoxyribose conformation and a local helical structure perturbation for ODN/RNA duplexes. This type of modification slightly decreases the thermal stability of ODN/RNA duplexes (-1 °C/modification) and leads to improved nuclease resistance. Like the well-known phosphorothioate (PS) modification, heavy 4'-CF3 modifications enable direct cellular uptake of the modified ODNs without any delivery reagents. This work highlights that 4'-CF3 modified ODNs are promising candidates for antisense-based therapeutics, which will, in turn, inspire us to develop more potent modifications for antisense ODNs and siRNAs.
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Affiliation(s)
- Yifei Zhou
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China.
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5
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Morihiro K, Hoshino H, Hasegawa O, Kasahara Y, Nakajima K, Kuwahara M, Tsunoda SI, Obika S. Polymerase incorporation of a 2'-deoxynucleoside-5'-triphosphate bearing a 4-hydroxy-2-mercaptobenzimidazole nucleobase analogue. Bioorg Med Chem Lett 2015; 25:2888-91. [PMID: 26048797 DOI: 10.1016/j.bmcl.2015.05.075] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Revised: 05/21/2015] [Accepted: 05/23/2015] [Indexed: 01/06/2023]
Abstract
Here, we describe the enzymatic construction of a new larger base pair formed between adenine (A) and a 4-hydroxy-2-mercaptobenzimidazole (SB) nucleobase analogue. We investigated the enzymatic incorporation of 2'-deoxynucleoside-5'-triphosphate bearing a SB nucleobase analogue (dSBTP) into oligonucleotides (ONs) by DNA polymerases. dSBTP could be effectively incorporated at the site opposite a dA in a DNA template by several B family DNA polymerases. These findings provide new insights into various aspects of biotechnology, including the design of non-natural base pairs.
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Affiliation(s)
- Kunihiko Morihiro
- National Institute of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan; Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Hidekazu Hoshino
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Osamu Hasegawa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yuuya Kasahara
- National Institute of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan; Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kohsuke Nakajima
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-Cho, Kiryu, Gunma 376-8515, Japan
| | - Masayasu Kuwahara
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-Cho, Kiryu, Gunma 376-8515, Japan
| | - Shin-ichi Tsunoda
- National Institute of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Satoshi Obika
- National Institute of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan; Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
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6
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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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7
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Loakes D, Holliger P. Polymerase engineering: towards the encoded synthesis of unnatural biopolymers. Chem Commun (Camb) 2009:4619-31. [PMID: 19641798 DOI: 10.1039/b903307f] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
DNA is not only a repository of genetic information for life, it is also a unique polymer with remarkable properties: it associates according to well-defined rules, it can be assembled into diverse nanostructures of defined geometry, it can be evolved to bind ligands and catalyse chemical reactions and it can serve as a supramolecular scaffold to arrange chemical groups in space. However, its chemical makeup is rather uniform and the physicochemical properties of the four canonical bases only span a narrow range. Much wider chemical diversity is accessible through solid-phase synthesis but oligomers are limited to <100 nucleotides and variations in chemistry can usually not be replicated and thus are not amenable to evolution. Recent advances in nucleic acid chemistry and polymerase engineering promise to bring the synthesis, replication and ultimately evolution of nucleic acid polymers with greatly expanded chemical diversity within our reach.
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Affiliation(s)
- David Loakes
- Medical Research Council, Laboratory of Molecular Biology, Hills Road, Cambridge, Cambridgeshire, UKCB2 0QH
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8
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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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9
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Cramer J, Rangam G, Marx A, Restle T. Varied active-site constraints in the klenow fragment of E. coli DNA polymerase I and the lesion-bypass Dbh DNA polymerase. Chembiochem 2008; 9:1243-50. [PMID: 18399510 DOI: 10.1002/cbic.200700634] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We report on comparative pre-steady-state kinetic analyses of exonuclease-deficient Escherichia coli DNA polymerase I (Klenow fragment, KF-) and the archaeal Y-family DinB homologue (Dbh) of Sulfolobus solfataricus. We used size-augmented sugar-modified thymidine-5'-triphosphate (T(R)TP) analogues to test the effects of steric constraints in the active sites of the polymerases. These nucleotides serve as models for study of DNA polymerases exhibiting both relatively high and low intrinsic selectivity. Substitution of a hydrogen atom at the 4'-position in the nucleotide analogue by a methyl group reduces the maximum rate of nucleotide incorporation by about 40-fold for KF- and about twelve fold for Dbh. Increasing the size to an ethyl group leads to a further twofold reduction in the rates of incorporation for both enzymes. Interestingly, the affinity of KF- for the modified nucleotides is only marginally affected, which would indicate no discrimination during the binding step. Dbh even has a higher affinity for the modified analogues than it does for the natural substrate. Misincorporation of either TTP or T(Me)TP opposite a G template causes a drastic decline in incorporation rates for both enzymes. At the same time, the binding affinities of KF- for these nucleotides drop by about 16- and fourfold, respectively, whereas Dbh shows only a twofold reduction. Available structural data for ternary complexes of relevant DNA polymerases indicate that both enzymes make close contacts with the sugar moiety of the dNTP. Thus, the varied proficiencies of the two enzymes in processing the size-augmented probes indicate varied flexibility of the enzymes' active sites and support the notion of active site tightness being a criterion for DNA polymerase selectivity.
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Affiliation(s)
- Janina Cramer
- Max-Planck-Institut für molekulare Physiologie, Abteilung Physikalische Biochemie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
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10
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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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11
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Di Pasquale F, Fischer D, Grohmann D, Restle T, Geyer A, Marx A. Opposed steric constraints in human DNA polymerase beta and E. coli DNA polymerase I. J Am Chem Soc 2008; 130:10748-57. [PMID: 18627154 DOI: 10.1021/ja8028284] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA polymerase selectivity is crucial for the survival of any living species, yet varies significantly among different DNA polymerases. Errors within DNA polymerase-catalyzed DNA synthesis result from the insertion of noncanonical nucleotides and extension of misaligned DNA substrates. The substrate binding characteristics among DNA polymerases are believed to vary in properties such as shape and tightness of the binding pocket, which might account for the observed differences in fidelity. Here, we employed 4'-alkylated nucleotides and primer strands bearing 4'-alkylated nucleotides at the 3'-terminal position as steric probes to investigate differential active site properties of human DNA polymerase beta (Pol beta) and the 3'-->5'-exonuclease-deficient Klenow fragment of E. coli DNA polymerase I (KF(exo-)). Transient kinetic measurements indicate that both enzymes vary significantly in active site tightness at both positions. While small 4'-methyl and -ethyl modifications of the nucleoside triphosphate perturb Pol beta catalysis, extension of modified primer strands is only marginally affected. Just the opposite was observed for KF(exo-). Here, incorporation of the modified nucleotides is only slightly reduced, whereas size augmentation of the 3'-terminal nucleotide in the primer reduces the catalytic efficiency by more than 7000- and 260,000-fold, respectively. NMR studies support the notion that the observed effects derive from enzyme substrate interactions rather than inherent properties of the modified substrates. These findings are consistent with the observed differential capability of the investigated DNA polymerases in fidelity such as processing misaligned DNA substrates. The results presented provide direct evidence for the involvement of varied steric effects among different DNA polymerases on their fidelity.
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Affiliation(s)
- Francesca Di Pasquale
- Fachbereich Chemie, Universität Konstanz, Universitätsstrasse 10, D-78457 Konstanz, Germany
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12
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Kranaster R, Marx A. Increased single-nucleotide discrimination in allele-specific polymerase chain reactions through primer probes bearing nucleobase and 2'-deoxyribose modifications. Chemistry 2007; 13:6115-22. [PMID: 17458912 DOI: 10.1002/chem.200601627] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The diagnosis of genetic dissimilarities between individuals is becoming increasingly important due to the discovery that these variations are related to complex phenotypes like the predisposition to certain diseases or compatibility with drugs. The most common among these sequence variations are single-nucleotide polymorphisms (SNPs). The availability of reliable and efficient methods for the interrogation of the respective genotypes is the basis for any progress along these lines. Many methods for the detection of nucleotide variations in genes exist, in which amplification of the target gene is required before analysis can take place. The allele-specific polymerase chain reaction (asPCR) combines target amplification and analysis in a single step. The principle of asPCR is based on the formation of matched or mismatched primer-target complexes. The most important parameter in asPCR is the discrimination of these matched or mismatched pairs. In recent publications we have shown that the reliability of SNP detection through asPCR is increased by employing chemically modified primer probes. In particular, primer probes that bear a polar 4'-C-methoxymethylene residue at the 3' end have superior properties in discriminating single-nucleotide variations by PCR. Here we describe the synthesis of several primer probes that bear nucleobase modifications in addition to the 4'-C-methoxymethylenated 2'-deoxyriboses. We studied the effects of these alterations on single-nucleotide discrimination in allele-specific PCR promoted by a DNA polymerase and completed these results with single-nucleotide-incorporation kinetic studies. Moreover, we investigated thermal denaturing of the primer-probe-template complexes and recorded circular dichroism (CD) spectra for inspecting the thermodynamic and photophysical duplex behaviour of the introduced modifications. In short, we found that primer probes bearing a 4'-C-methoxymethylene residue at the 2'-deoxyribose moiety in combination with a thiolated thymidine moiety have synergistic effects and display significantly increased discrimination properties in asPCR.
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Affiliation(s)
- Ramon Kranaster
- Fachbereich Chemie, Universität Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
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13
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Strerath M, Gloeckner C, Liu D, Schnur A, Marx A. Directed DNA polymerase evolution: effects of mutations in motif C on the mismatch-extension selectivity of thermus aquaticus DNA polymerase. Chembiochem 2007; 8:395-401. [PMID: 17279590 DOI: 10.1002/cbic.200600337] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The selectivity of DNA polymerases for processing the canonical nucleotide and DNA substrate in favor of the noncanonical ones is the key to the integrity of the genome of every living species and to many biotechnological applications. The inborn ability of most DNA polymerases to abort efficient extension of mismatched DNA substrates adds to the overall DNA polymerase selectivity. DNA polymerases have been grouped into families according to their sequence. Within family A DNA polymerases, six motifs that come into contact with the substrates and form the active site have been discovered to be evolutionary highly conserved. Here we present results obtained from amino acid randomization within one motif, motif C, of thermostable Thermus aquaticus DNA polymerase. We have identified several distinct mutation patterns that increase the selectivity of mismatch extension. These results might lead to direct applications such as allele-specific PCR, as demonstrated by real-time PCR experiments and add to our understanding of DNA polymerase selectivity.
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Affiliation(s)
- Michael Strerath
- Fachbereich Chemie, Universität Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
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14
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Liebmann M, Di Pasquale F, Marx A. A new photoactive building block for investigation of DNA backbone interactions: photoaffinity labeling of human DNA polymerase beta. Chembiochem 2007; 7:1965-9. [PMID: 17106908 DOI: 10.1002/cbic.200600333] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The cross-linking of target proteins or nucleic acids to light-activatable ligands is an important tool for elucidating molecular interactions. Through the use of photoaffinity-labeling reagents, several new insights into nucleic acid interactions have been obtained, for example in DNA replication and repair. In most known photoprobes, the applied light-sensitive functionalities are placed directly at the nucleobase or are attached via linkers to either the nucleobase or the phosphate backbone. Here we describe the first photoprobe that bears a light-sensitive aryl(trifluoromethyl)diazirine at the sugar moiety of a DNA oligonucleotide. We devised a route for the synthesis of the modified nucleoside and its incorporation into an oligonucleotide. The photoactive species was proven to be stable under the conditions employed in routine automated DNA synthesis. The modified oligonucleotide was shown by subsequent photolabeling studies of human DNA polymerase beta to form a covalent complex to the enzyme upon irradiation with near-UV light.
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Affiliation(s)
- Meike Liebmann
- Fachbereich Chemie, Universität Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
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15
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Rudinger NZ, Kranaster R, Marx A. Hydrophobic Amino Acid and Single-Atom Substitutions Increase DNA Polymerase Selectivity. ACTA ACUST UNITED AC 2007; 14:185-94. [PMID: 17317572 DOI: 10.1016/j.chembiol.2006.11.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2006] [Revised: 11/28/2006] [Accepted: 11/30/2006] [Indexed: 11/27/2022]
Abstract
DNA polymerase fidelity is of immense biological importance due to the fundamental requirement for accurate DNA synthesis in both replicative and repair processes. Subtle hydrogen-bonding networks between DNA polymerases and their primer/template substrates are believed to have impact on DNA polymerase selectivity. We show that deleting defined interactions of that kind by rationally designed hydrophobic substitution mutations can result in a more selective enzyme. Furthermore, a single-atom replacement within the DNA substrate through chemical modification, which leads to an altered acceptor potential and steric demand of the DNA substrate, further increased the selectivity of the developed systems. Accordingly, this study about the impact of hydrophobic alterations on DNA polymerase selectivity--enzyme and substrate wise--further highlights the relevance of shape complementary and polar interactions on DNA polymerase selectivity.
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Affiliation(s)
- Nicolas Z Rudinger
- Department of Chemistry, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
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16
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Jäger S, Rasched G, Kornreich-Leshem H, Engeser M, Thum O, Famulok M. A versatile toolbox for variable DNA functionalization at high density. J Am Chem Soc 2006; 127:15071-82. [PMID: 16248646 DOI: 10.1021/ja051725b] [Citation(s) in RCA: 256] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To broaden the applicability of chemically modified DNAs in nano- and biotechnology, material science, sensor development, and molecular recognition, strategies are required for introducing a large variety of different modifications into the same nucleic acid sequence at once. Here, we investigate the scope and limits for obtaining functionalized dsDNA by primer extension and PCR, using a broad variety of chemically modified deoxynucleotide triphosphates (dNTPs), DNA polymerases, and templates. All natural nucleobases in each strand were substituted with up to four different base-modified analogues. We studied the sequence dependence of enzymatic amplification to yield high-density functionalized DNA (fDNA) from modified dNTPs, and of fDNA templates, and found that GC-rich sequences are amplified with decreased efficiency as compared to AT-rich ones. There is also a strong dependence on the polymerase used. While family A polymerases generally performed poorly on "demanding" templates containing consecutive stretches of a particular base, family B polymerases were better suited for this purpose, in particular Pwo and Vent (exo-) DNA polymerase. A systematic analysis of fDNAs modified at increasing densities by CD spectroscopy revealed that single modified bases do not alter the overall B-type DNA structure, regardless of their chemical nature. A density of three modified bases induces conformational changes in the double helix, reflected by an inversion of the CD spectra. Our study provides a basis for establishing a generally applicable toolbox of enzymes, templates, and monomers for generating high-density functionalized DNAs for a broad range of applications.
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Affiliation(s)
- Stefan Jäger
- Kekuké-Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Strasse 1, D-53121 Bonn, Germany
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Summerer D, Marx A. 4'C-ethynyl-thymidine acts as a chain terminator during DNA-synthesis catalyzed by HIV-1 reverse transcriptase. Bioorg Med Chem Lett 2005; 15:869-71. [PMID: 15686877 DOI: 10.1016/j.bmcl.2004.12.072] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2004] [Revised: 12/16/2004] [Accepted: 12/23/2004] [Indexed: 10/25/2022]
Abstract
Recently, 4'C-ethynyl nucleoside analogues have been identified as highly potent agents against HIV-1, including several multidrug-resistant strains. In contrast to most known nucleoside inhibitors 4'C-ethynyl nucleoside analogues possess a 3'-hydroxyl function. Here we show that the 5'O-triphosphate of 4'C-ethynyl thymidine gets readily incorporated into a nascent DNA strand by HIV-1 reverse transcriptase and significantly inhibits further post-incorporation chain extension by the enzyme.
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Affiliation(s)
- Daniel Summerer
- Fachbereich Chemie, Universität Konstanz, Universitätsstrasse 10, D-78457 Konstanz, Germany
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Kim TW, Kool ET. A series of nonpolar thymidine analogues of increasing size: DNA base pairing and stacking properties. J Org Chem 2005; 70:2048-53. [PMID: 15760186 DOI: 10.1021/jo048061t] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[reaction: see text] We describe the properties in DNA of a set of five nonpolar nucleoside mimics in which shape is similar but size is increased gradually. The compounds vary in the size of their exocyclic substituents, which range from hydrogen to iodine, and are designed to test the steric effects of nucleosides, nucleotides, and DNA in biological systems in a systematic way. We describe the conversion of toluene, 2,4-difluorotoluene, 2,4-dichlorotoluene, 2,4-dibromotoluene, and 2,4-diiodotoluene deoxyribosides into suitably protected phosphoramidite derivatives and their incorporation into synthetic DNAs. Studies of their behavior in the context of hexamer and dodecamer duplexes were carried out, with comparison to natural thymine. Thermal melting data with compounds in 5' dangling positions showed that all five compounds stack more strongly than thymine, and all the dihalo-substituted cases stack more strongly than the unsubstituted toluene case. Stacking correlated with surface area and hydrophobicity, both of which increase across the series. In base-pairing studies, all five compounds showed destabilized pairing opposite natural bases (relative to thymine-adenine pairing), as expected. Notably, pairing among the nonpolar base analogues was considerably more stable, and some of the pairs involving the largest analogues showed stability equal to that of a natural thymine-adenine pair. The results establish the base pairing properties of a potentially useful new series of biochemical probes for DNA-protein interactions and also identify a set of new, stable hydrophobic base pairs for designed genetic pairing systems.
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Affiliation(s)
- Tae Woo Kim
- Department of Chemistry, Stanford University, Stanford California 94305-5080, USA
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Eriksson J, Gharizadeh B, Nourizad N, Nyrén P. 7-Deaza-2'-deoxyadenosine-5'-triphosphate as an alternative nucleotide for the pyrosequencing technology. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2005; 23:1583-94. [PMID: 15620097 DOI: 10.1081/ncn-200031402] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
A new adenosine nucleotide analog suitable for the Pyrosequencing method is presented. The new analog, 7-deaza-2'-deoxyadenosine-5'-triphosphate (c7dATP), has virtually the same low substrate specificity for luciferase as the currently used analog, 2'-deoxyadenosine-5'-O-(1-thiotriphosphate) (dATPalphaS). The inhibitory effect dATPalphaS displays on the nucleotide degrading activity of apyrase was reduced significantly by substituting the c7dATP for the dATPalphaS. Both analogs show high stability after long time storage at + 8 degrees C. Furthermore, with the new nucleotide a read length of up to 100 bases was obtained for several templates from fungi, bacteria and viruses.
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Affiliation(s)
- Jonas Eriksson
- Department of Biotechnology, SCFAB (Stockholm Centre for Physics, Astronomy, and Biotechnology), KTH (Royal Institute of Technology), Stockholm, Sweden
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Strerath M, Gaster J, Summerer D, Marx A. Increased single-nucleotide discrimination of PCR by primer probes bearing hydrophobic 4'C modifications. Chembiochem 2004; 5:333-9. [PMID: 14997525 DOI: 10.1002/cbic.200300757] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We report on significantly increased selectivity of real-time PCR through employment of primer probes that bear hydrophobic 4'C modifications at the 3'-terminal nucleotide. The primer probes were designed to bind the target sequences in such a way that the 3'-terminal nucleotide defines whether a matched or a single mismatched basepair is present depending on the respective target sequence. Several commercially available thermostable DNA polymerases belonging to different DNA polymerase families were tested for their efficacy in discriminating between PCR amplification of matched substrates and duplexes that contain a single mismatch. It turned out that, depending on the 4'C modification and the employed DNA polymerase, significantly increased differentiation between single matches and mismatches could be observed with real-time PCR. The degrees of the observed effects varied with the employed 4'C modification and the sequence context studied. The system is robust enough to work faithfully under several buffer conditions. Our approach should be useful for the direct diagnosis of single nucleotide variations within genes, like single nucleotide polymorphisms or mutations, by PCR without the need for further time- and cost-intensive post-PCR analysis.
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Affiliation(s)
- Michael Strerath
- Kekulé-Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
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Tews B, Wilhelm J, Summerer D, Strerath M, Marx A, Friedhoff P, Pingoud A, Hahn M. Application of the C4'-alkylated deoxyribose primer system (CAPS) in allele-specific real-time PCR for increased selectivity in discrimination of single nucleotide sequence variants. Biol Chem 2004; 384:1533-41. [PMID: 14669997 DOI: 10.1515/bc.2003.170] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
This study describes a quantitative real-time PCR-based approach for discrimination of single nucleotide sequence variants, called CAPS (C4' alkylated primer system). To increase the discrimination potential of DNA polymerases against competing sequence variants of single nucleotides, 3'-terminally modified primers were designed carrying a methyl residue bound to the C4' of the thymidylate deoxyribose. In a model sequence system positional dependencies of modified thymidylate (at -1, -2, -3) were tested for their influence on discrimination. Highest discrimination factors were obtained with the modification at the ultimate 3'-position. In a comparison between Taq and Pwo DNA polymerases, substantial better results were obtained by Taq DNA polymerase. In contrast to conventional PCR methods for discrimination of sequence variants, achieving a maximum discrimination potential of about 20, CAPS is capable of obtaining sequence-specific amplifications of a desired target among discriminated templates with a dynamic range of 1:100. Therefore, CAPS is a method able to quantitatively discriminate two sequence variants only differing in a single base (e.g., SNP alleles or point mutations). The range of applications of this easy to perform, fast and reliable technique reaches from medical diagnostics, transplantation medicine, molecular and cell biology to human genetics. Targeting of SNPs assures a universal exertion of this method, since these markers are gender-independent, highly abundant and ubiquitous.
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Affiliation(s)
- Björn Tews
- Institut für Biochemie, FB 08, Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany
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Verma S, Jäger S, Thum O, Famulok M. Functional tuning of nucleic acids by chemical modifications: tailored oligonucleotides as drugs, devices, and diagnostics. CHEM REC 2003; 3:51-60. [PMID: 12552531 DOI: 10.1002/tcr.10047] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Chemical modifications of nucleic acids present vast opportunities for extending the functions and properties of these biomolecules. In general, efforts invested in this direction pertain to the introduction of reactive functional groups for further derivatizations of oligonucleotides with numerous reporter groups and for equipping nucleic acids with catalytic chemical moieties. This review deals with representative chemical modifications in the nucleobases, sugars, and the phosphate ester backbone and their application from novel catalytic RNA selection to nucleic acid-based biosensors.
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Affiliation(s)
- Sandeep Verma
- Kekulé-Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Str. 1, D-53121 Bonn, Germany
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Strerath M, Marx A. Tuning PCR specificity by chemically modified primer probes. Angew Chem Int Ed Engl 2002; 41:4766-9. [PMID: 12481353 DOI: 10.1002/anie.200290043] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Michael Strerath
- Kekulé-Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
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Strerath M, Marx A. Erhöhung der PCR-Genauigkeit durch chemisch modifizierte Primersonden. Angew Chem Int Ed Engl 2002. [DOI: 10.1002/ange.200290042] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Detmer I, Summerer D, Marx A. DNA minor groove hydration probed with 4'-alkylated thymidines. Chem Commun (Camb) 2002:2314-5. [PMID: 12430418 DOI: 10.1039/b207582m] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Employing modified oligonucleotides that are 4'-alkylated site-specifically we investigated the involvement of DNA minor groove hydration on DNA duplex stability and helix conformation.
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Affiliation(s)
- Ilka Detmer
- Kekulé-Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
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