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Kruse FM, Teichert JS, Trapp O. Prebiotic Nucleoside Synthesis: The Selectivity of Simplicity. Chemistry 2020; 26:14776-14790. [PMID: 32428355 PMCID: PMC7756251 DOI: 10.1002/chem.202001513] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 05/10/2020] [Indexed: 12/29/2022]
Abstract
Ever since the discovery of nucleic acids 150 years ago,[1] major achievements have been made in understanding and decrypting the fascinating scientific questions of the genetic code.[2] However, the most fundamental question about the origin and the evolution of the genetic code remains a mystery. How did nature manage to build up such intriguingly complex molecules able to encode structure and function from simple building blocks? What conditions were required? How could the precursors survive the unhostile environment of early Earth? Over the past decades, promising synthetic concepts were proposed providing clarity in the field of prebiotic nucleic acid research. In this Minireview, we show the current status and various approaches to answer these fascinating questions.
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Affiliation(s)
- Florian M. Kruse
- Department of ChemistryLudwig-Maximilians-University MunichButenandtstr. 5–13'81377MunichGermany
| | - Jennifer S. Teichert
- Department of ChemistryLudwig-Maximilians-University MunichButenandtstr. 5–13'81377MunichGermany
- Max-Planck-Institute for AstronomyKönigstuhl 1769117HeidelbergGermany
| | - Oliver Trapp
- Department of ChemistryLudwig-Maximilians-University MunichButenandtstr. 5–13'81377MunichGermany
- Max-Planck-Institute for AstronomyKönigstuhl 1769117HeidelbergGermany
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2
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Molecular Dynamics Simulation of Homo-DNA: The Role of Crystal Packing in Duplex Conformation. CRYSTALS 2019. [DOI: 10.3390/cryst9100532] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The (4′→6′)-linked DNA homolog 2′,3′-dideoxy-β-D-glucopyranosyl nucleic acid (dideoxy-glucose nucleic acid or homo-DNA) exhibits stable self-pairing of the Watson–Crick and reverse-Hoogsteen types, but does not cross-pair with DNA. Molecular modeling and NMR solution studies of homo-DNA duplexes pointed to a conformation that was nearly devoid of a twist and a stacking distance in excess of 4.5 Å. By contrast, the crystal structure of the homo-DNA octamer dd(CGAATTCG) revealed a right-handed duplex with average values for helical twist and rise of ca. 15° and 3.8 Å, respectively. Other key features of the structure were strongly inclined base-pair and backbone axes in the duplex with concomitant base-pair slide and cross-strand stacking, and the formation of a dimer across a crystallographic dyad with inter-duplex base swapping. To investigate the conformational flexibility of the homo-DNA duplex and a potential influence of lattice interactions on its geometry, we used molecular dynamics (MD) simulations of the crystallographically observed dimer of duplexes and an isolated duplex in the solution state. The dimer of duplexes showed limited conformational flexibility, and key parameters such as helical rise, twist, and base-pair slide exhibited only minor fluctuations. The single duplex was clearly more flexible by comparison and underwent partial unwinding, albeit without significant lengthening. Thus, base stacking was preserved in the isolated duplex and two adenosines extruded from the stack in the dimer of duplexes were reinserted into the duplex and pair with Ts in a Hoogsteen mode. Our results confirmed that efficient stacking in homo-DNA seen in the crystal structure of a dimer of duplexes was maintained in the separate duplex. Therefore, lattice interactions did not account for the different geometries of the homo-DNA duplex in the crystal and earlier models that resembled inclined ladders with large base-pair separations that precluded efficient stacking.
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3
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Zeng Z, Bernstein ER. Studies of Arabinose- and Mannose-Related Anionic Species and Comparison to Ribose and Fructose. J Phys Chem A 2019; 123:2340-2350. [PMID: 30807168 DOI: 10.1021/acs.jpca.8b11838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Gas phase, isolated monosaccharides arabinose- and mannose-related anionic species generated through the matrix-assisted laser desorption ionization (MALDI) method are investigated via negative ion photoelectron spectroscopy (PES) and density functional theory (DFT) calculations. The vertical detachment energies (VDEs) of the observed anionic species are experimentally determined: the corresponding structures are assigned based on good agreement between experimental and theoretical VDEs. Arabinose- parent anion is found to exist as open chain structures in the gas phase, while mannose- parent anionic species are not observed. Both monosaccharides undergo dissociation through loss of H and loss of H2O. (saccharide-H)- anions evidence coexisting positional and conformational isomers. (saccharide-H2O)- species have only two positional isomers, each with conformational differences. The present results for arabinose and mannose are further compared to those previously reported for ribose and fructose. This comparison is based on the anions observed and identified through the same PES/DFT techniques for the four saccharides (arabinose, mannose, ribose, and fructose). The issue of natural selection of ribose as the sugar backbone constituent of RNA is thereby explored from the point of view of anionic electronic structure and stability of the four species. Saccharide phosphates are also discussed in the present work with regard to addressing the unique natural selection of ribose for the backbone support of RNA and DNA.
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Affiliation(s)
- Zhen Zeng
- Department of Chemistry, NSF ERC for Extreme Ultraviolet Science and Technology , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - Elliot R Bernstein
- Department of Chemistry, NSF ERC for Extreme Ultraviolet Science and Technology , Colorado State University , Fort Collins , Colorado 80523 , United States
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Zeng Z, Bernstein ER. Anionic ribose related species explored through PES experiments, DFT calculations, and through comparison with anionic fructose species. Phys Chem Chem Phys 2017; 19:28950-28962. [DOI: 10.1039/c7cp05830f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Generation of (ribose-H)− is dependent on deposition substrates, while generation of two types of (ribose-H2O)− isomers (open chain) is not.
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Affiliation(s)
- Zhen Zeng
- Department of Chemistry
- NSF ERC for Extreme Ultraviolet Science and Technology
- Colorado State University
- Fort Collins
- USA
| | - Elliot R. Bernstein
- Department of Chemistry
- NSF ERC for Extreme Ultraviolet Science and Technology
- Colorado State University
- Fort Collins
- USA
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Eschenmoser A. Ätiologie potentiell primordialer Biomolekül-Strukturen: Vom Vitamin B12 zu den Nukleinsäuren und der Frage nach der Chemie der Entstehung des Lebens - ein Rückblick. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201103672] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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6
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Eschenmoser A. Etiology of potentially primordial biomolecular structures: from vitamin B12 to the nucleic acids and an inquiry into the chemistry of life's origin: a retrospective. Angew Chem Int Ed Engl 2011; 50:12412-72. [PMID: 22162284 DOI: 10.1002/anie.201103672] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Indexed: 11/10/2022]
Abstract
"We'll never be able to know" is a truism that leads to resignation with respect to any experimental effort to search for the chemistry of life's origin. But such resignation runs radically counter to the challenge imposed upon chemistry as a natural science. Notwithstanding the prognosis according to which the shortest path to understanding the metamorphosis of the chemical into the biological is by way of experimental modeling of "artificial chemical life", the scientific search for the route nature adopted in creating the life we know will arguably never truly end. It is, after all, part of the search for our own origin.
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Affiliation(s)
- Albert Eschenmoser
- Organisch-chemisches Laboratorium der ETH Zürich, Hönggerberg, Wolfgang-Pauli-Str. 10, CHI H309, CH-8093 Zürich, Switzerland
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Ebert MO, Jaun B. Oligonucleotides with sugars other than ribo- and 2'-deoxyribofuranose in the backbone: the solution structures determined by NMR in the context of the 'Etiology of nucleic acids' project of Albert Eschenmoser. Chem Biodivers 2011; 7:2103-28. [PMID: 20860021 DOI: 10.1002/cbdv.201000096] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Marc-Olivier Ebert
- Laboratory of Organic Chemistry, ETH Zürich, Wolfgang-Pauli-Strasse 10, Zürich
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8
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Abstract
Starting from pyranose nucleic acids, several series of modified nucleic acids with a six-membered carbohydrate moiety (mimic) have been synthesized and analyzed over a period of 20 years, and this work is summarized here. The process starts with structural and conformational considerations, followed by synthetic efforts and a structural analysis, and ends up with a biological confirmation of the concept, demonstrating that these modified nucleic acids represent very valuable tools in chemistry and biology.
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Affiliation(s)
- Piet Herdewijn
- Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, Minderbroedersstraat 10, B-3000 Leuven.
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9
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Chiba J, Inouye M. Exotic DNAs Made of Nonnatural Bases and Natural Phosphodiester Bonds. Chem Biodivers 2010; 7:259-82. [DOI: 10.1002/cbdv.200900282] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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10
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Follmann H, Brownson C. Darwin’s warm little pond revisited: from molecules to the origin of life. Naturwissenschaften 2009; 96:1265-92. [PMID: 19760276 DOI: 10.1007/s00114-009-0602-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2009] [Revised: 08/05/2009] [Accepted: 08/10/2009] [Indexed: 11/26/2022]
Affiliation(s)
- Hartmut Follmann
- Institute of Biology, University of Kassel, 34109, Kassel, Germany.
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11
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Ebert MO, Mang C, Krishnamurthy R, Eschenmoser A, Jaun B. The structure of a TNA-TNA complex in solution: NMR study of the octamer duplex derived from alpha-(L)-threofuranosyl-(3'-2')-CGAATTCG. J Am Chem Soc 2008; 130:15105-15. [PMID: 18928287 DOI: 10.1021/ja8041959] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
TNA (alpha-( l)-threofuranosyl-(3'-2') nucleic acid) is a nucleic acid in which the ribofuranose building block of the natural nucleic acid RNA is replaced by the tetrofuranose alpha-( l)-threose. This shortens the repetitive unit of the backbone by one bond as compared to the natural systems. Among the alternative nucleic acid structures studied so far in our laboratories in the etiological context, TNA is the only one that exhibits Watson-Crick pairing not only with itself but also with DNA and, even more strongly, with RNA. Using NMR spectroscopy, we have determined the structure of a duplex consisting entirely of TNA nucleotides. The TNA octamer (3'-2')-CGAATTCG forms a right-handed double helix with antiparallel strands paired according to the Watson-Crick mode. The dominant conformation of the sugar units has the 2'- and 3'-phosphodiester substituents in quasi-diaxial position and corresponds to a 4'-exo puckering. With 5.85 A, the average sequential P i -P i+1 distances of TNA are shorter than for A-type DNA (6.2 A). The helix parameters, in particular the slide and x-displacement, as well as the shallow and wide minor groove, place the TNA duplex in the structural vicinity of A-type DNA and RNA.
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Affiliation(s)
- Marc-Olivier Ebert
- Laboratory of Organic Chemistry, ETH Zurich, Wolfgang-Pauli-Strasse 10, CH-8093 Zürich, Switzerland
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12
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Pallan PS, Lubini P, Bolli M, Egli M. Backbone-base inclination as a fundamental determinant of nucleic acid self- and cross-pairing. Nucleic Acids Res 2007; 35:6611-24. [PMID: 17905816 PMCID: PMC2095819 DOI: 10.1093/nar/gkm612] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The crystal structure of the duplex formed by oligo(2′,3′-dideoxy-β-d-glucopyranosyl)nucleotides (homo-DNA) revealed strongly inclined backbone and base-pair axes [Egli,M., Pallan,P.S., Pattanayek,R., Wilds,C.J., Lubini,P., Minasov,G., Dobler,M., Leumann,C.J. and Eschenmoser,A. (2006) Crystal structure of homo-DNA and nature's choice of pentose over hexose in the genetic system. J. Am. Chem. Soc., 128, 10847–10856]. This inclination is easily perceived because homo-DNA exhibits only a modest helical twist. Conversely, the tight coiling of strands conceals that the backbone-base inclinations for A- (DNA and RNA) and B-form (DNA) duplexes differ considerably. We have defined a parameter ηB that corresponds to the local inclination between sugar-phosphate backbone and base plane in nucleic acid strands. Here, we show its biological significance as a predictive measure for the relative strand polarities (antiparallel, aps, or parallel, ps) in duplexes of DNA, RNA and artificial nucleic acid pairing systems. The potential of formation of ps duplexes between complementary 16-mers with eight A and U(T) residues each was investigated with DNA, RNA, 2′-O-methylated RNA, homo-DNA and p-RNA, the ribopyranosyl isomer of RNA. The thermodynamic stabilities of the corresponding aps duplexes were also measured. As shown previously, DNA is capable of forming both ps and aps duplexes. However, all other tested systems are unable to form stable ps duplexes with reverse Watson–Crick (rWC) base pairs. This observation illustrates the handicap encountered by nucleic acid systems with inclinations ηB that differ significantly from 0° to form a ps rWC paired duplex. Accordingly, RNA with a backbone-base inclination of −30°, pairs strictly in an aps fashion. On the other hand, the more or less perpendicular orientation of backbone and bases in DNA allows it to adopt a ps rWC paired duplex. In addition to providing a rationalization of relative strand polarity with nucleic acids, the backbone-base inclination parameter is also a determinant of cross-pairing. Thus, systems with strongly deviating ηB angles will not pair with each other. Nucleic acid pairing systems with significant backbone-base inclinations can also be expected to display different stabilities depending on which terminus carries unpaired nucleotides. The negative inclination of RNA is consistent with the higher stability of duplexes with 3′- compared to those with 5′-dangling ends.
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Affiliation(s)
- Pradeep S. Pallan
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA, Alta Scuola Pedagogica, CH-6600 Locarno and Actelion Pharmaceuticals Ltd., CH-4123 Allschwil, Switzerland
| | - Paolo Lubini
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA, Alta Scuola Pedagogica, CH-6600 Locarno and Actelion Pharmaceuticals Ltd., CH-4123 Allschwil, Switzerland
| | - Martin Bolli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA, Alta Scuola Pedagogica, CH-6600 Locarno and Actelion Pharmaceuticals Ltd., CH-4123 Allschwil, Switzerland
| | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA, Alta Scuola Pedagogica, CH-6600 Locarno and Actelion Pharmaceuticals Ltd., CH-4123 Allschwil, Switzerland
- *To whom correspondence should be addressed. +1 615 343 8070+1 615 322 7122
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13
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Egli M, Pallan PS, Pattanayek R, Wilds CJ, Lubini P, Minasov G, Dobler M, Leumann CJ, Eschenmoser A. Crystal structure of homo-DNA and nature's choice of pentose over hexose in the genetic system. J Am Chem Soc 2007; 128:10847-56. [PMID: 16910680 DOI: 10.1021/ja062548x] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An experimental rationalization of the structure type encountered in DNA and RNA by systematically investigating the chemical and physical properties of alternative nucleic acids has identified systems with a variety of sugar-phosphate backbones that are capable of Watson-Crick base pairing and in some cases cross-pairing with the natural nucleic acids. The earliest among the model systems tested to date, (4' --> 6')-linked oligo(2',3'-dideoxy-beta-d-glucopyranosyl)nucleotides or homo-DNA, shows stable self-pairing, but the pairing rules for the four natural bases are not the same as those in DNA. However, a complete interpretation and understanding of the properties of the hexapyranosyl (4' --> 6') family of nucleic acids has been impeded until now by the lack of detailed 3D-structural data. We have determined the crystal structure of a homo-DNA octamer. It reveals a weakly twisted right-handed duplex with a strong inclination between the hexose-phosphate backbones and base-pair axes, and highly irregular values for helical rise and twist at individual base steps. The structure allows a rationalization of the inability of allo-, altro-, and glucopyranosyl-based oligonucleotides to form stable pairing systems.
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Affiliation(s)
- Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA.
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14
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Nauwelaerts K, Lescrinier E, Herdewijn P. Structure of the alpha-homo-DNA:RNA duplex and the function of twist and slide to catalogue nucleic acid duplexes. Chemistry 2007; 13:90-8. [PMID: 16991180 DOI: 10.1002/chem.200600363] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
High-resolution NMR studies of an alpha-homo-DNA:RNA duplex reveal the formation of a right-handed parallel-oriented helix. It differs significantly from a standard A- or B-type helix by a small twist value (26.2 degrees ), which leads to a helical pitch of 13.7 base pairs per helical turn, a negative inclination (-1.78 Angstrom) and a large x displacement (5.90 Angstrom). The rise (3.4 Angstrom) is similar to that found in B-DNA. The solution of this new helix structure has stimulated us to develop a mathematical and geometrical model based on slide and twist parameters to describe nucleic acid duplexes. All existing duplexes can be positioned within this landscape, which can be used to understand the helicalization process.
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Affiliation(s)
- Koen Nauwelaerts
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Minderbroedersstraat 10, 3000 Leuven, Belgium
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15
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Abstract
Homo-DNA ((4'-->6')-linked oligo-2',3'-dideoxy-beta-D-glucopyranose nucleic acid) constitutes the earliest synthetic model system whose pairing properties have been studied within an etiology of nucleic acid structure. Its conception as part of a program directed at a rationalization of Nature's selection of pentoses over other candidates as the carbohydrate building block in the genetic material was motivated by the question: why pentose and not hexose? Homo-DNA forms an autonomous pairing system and its duplexes are entropically stabilized relative to DNA duplexes. Moreover, the base pairing priorities in homo-DNA duplexes differ from those in DNA. A deeper understanding of the particular properties of homo-DNA requires knowledge of its structure. Although diffraction data for crystals of a homo-DNA octamer duplex were available to medium resolution in the mid-1990s, it took another decade for the structure to be solved. In this tutorial Review we describe the odyssey from the crystallization to the final structure determination with its many failures and disappointments and the development of selenium chemistry to derivatize nucleic acids for crystallographic phasing. More than fifty years after the discovery of the DNA double helix, the story of homo-DNA also provides a demonstration of the limits of theoretical models and offers a fresh view of fundamental issues in regard to the natural nucleic acids, such as the origins of antiparallel pairing and helicality.
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Affiliation(s)
- Martin Egli
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, TN 37232, USA.
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Schlönvogt I, Pitsch S, Lesueur C, Eschenmoser A, Jaun B, Wolf RM. Pyranosyl-RNA (‘p-RNA’): NMR and Molecular-Dynamics Study of the Duplex Formed by Self-pairing of Ribopyranosyl-(C-G-A-A-T-T-C-G). Helv Chim Acta 2004. [DOI: 10.1002/hlca.19960790820] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Haraguchi K, Delaney MO, Wiederholt CJ, Sambandam A, Hantosi Z, Greenberg MM. Synthesis and characterization of oligodeoxynucleotides containing formamidopyrimidine lesions and nonhydrolyzable analogues. J Am Chem Soc 2002; 124:3263-9. [PMID: 11916409 DOI: 10.1021/ja012135q] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Oligodeoxynucleotides containing formamidopyrimidine lesions and C-nucleoside analogues at defined sites were prepared by solid-phase synthesis and in some cases enzymatic ligation. Formamidopyrimidine lesions were introduced as dinucleotides to prevent rearrangement to their pyranose isomers. Oligodeoxynucleotides containing single diastereomers of C-nucleoside analogues of Fapy.dA were introduced by using the respective phosphoramidites. The formamidopyrimidine lesions reduce the T(M) of dodecamers relative to their unmodified nucleotide counterparts when opposite the nucleotide proper base-pairing partner. However, duplexes containing Fapy.dG-dA mispairs melt significantly higher than those comprised of dG-dA. All duplexes containing Fapy.dA-dX or its C-nucleoside analogue melt lower than the respective complexes containing dA-dX. Studies of the alkaline lability of oligodeoxynucleotides containing formamidopyrimidine lesions indicate that Fapy.dA is readily identified as an alkali-labile lesion with use of piperidine (1.0 M, 90 degrees C, 20 min), but Fapy.dG is less easily identified in this manner.
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Affiliation(s)
- Kazuhiro Haraguchi
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
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19
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Abstract
Mainly driven by the needs of antisense research, a large number of oligonucleotide analogues have been prepared and evaluated over the last 15 years. Besides minor structural modifications of the building blocks of DNA and RNA itself, a considerable effort has been devoted to the de novo design of nucleoside analogues with improved binding properties. A particularly successful concept turned out to be that of conformational restriction. This review focuses on recent advances in this area and tries to summarize scope and limitations of this design principle.
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Affiliation(s)
- Christian J Leumann
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012, Bern, Switzerland.
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20
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Declercq R, Van Aerschot A, Read RJ, Herdewijn P, Van Meervelt L. Crystal structure of double helical hexitol nucleic acids. J Am Chem Soc 2002; 124:928-33. [PMID: 11829600 DOI: 10.1021/ja016570w] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A huge variety of chemically modified oligonucleotide derivatives has been synthesized for possible antisense applications. One such derivative, hexitol nucleic acid (HNA), is a DNA analogue containing the standard nucleoside bases, but with a phosphorylated 1',5'-anhydrohexitol backbone. Hexitol nucleic acids are some of the strongest hybridizing antisense compounds presently known, but HNA duplexes are even more stable. We present here the first high-resolution structure of a double helical nucleic acid with all sugars being hexitols. Although designed to have a restricted conformational flexibility, the hexitol oligomer h(GTGTACAC) is able to crystallize in two different double helical conformations. Both structures display a high x-displacement, normal Watson-Crick base pairing, similar base stacking patterns, and a very deep major groove together with a minor groove with increased hydrophobicity. One of the conformations displays a major groove which is wide enough to accommodate a second HNA double helix resulting in the formation of a double helix of HNA double helices. Both structures show most similarities with the A-type helical structure, the anhydrohexitol chair conformation thereby acting as a good mimic for the furanose C3'-endo conformation observed in RNA. As compared to the quasi-linear structure of homo-DNA, the axial position of the base in HNA allows efficient base stacking and hence double helix formation.
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Affiliation(s)
- Ruben Declercq
- Biomolecular Architecture, Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, B-3001 Leuven (Heverlee), Belgium
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Ilin S, Schlönvogt I, Ebert MO, Jaun B, Schwalbe H. Comparison of the NMR Spectroscopy Solution Structures of Pyranosyl-RNA and Its Nucleo-δ-peptide Analogue. Chembiochem 2002; 3:93-9. [PMID: 17590959 DOI: 10.1002/1439-7633(20020104)3:1<93::aid-cbic93>3.0.co;2-0] [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: 11/09/2022]
Abstract
The design of polymers that could mimic biomolecules in their ability to form assemblies similar to ribo- and deoxyribonucleic acids has become an attractive field of chemical research, and NMR spectroscopy has played a vital role in the determination of the three-dimensional structure of these newly designed nonnatural polymers. The structure of a self-complementary octamer duplex of pyranosyl-RNA (pRNA) has been determined by using NMR spectroscopy experimental data and an Xplor structure calculation protocol. The structure has been compared with the structure of a duplex formed by a designed nucleo-delta-peptide analogue of pRNA. The two duplexes assume one predominant conformation and show a high structural similarity. The conformation type of both structures agrees with those predicted based on qualitative conformational analysis and both structures show a good convergence toward the average torsion angles derived by NMR spectroscopy.
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Affiliation(s)
- Sergey Ilin
- Department of Chemistry and MIT/Harvard Center for Magnetic Resonance, Francis Bitter Magnet Laboratory Massachusetts Institute of Technology 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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Affiliation(s)
- D J Hill
- Department of Chemistry and Materials Science & Engineering, The Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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Schöning K, Scholz P, Guntha S, Wu X, Krishnamurthy R, Eschenmoser A. Chemical etiology of nucleic acid structure: the alpha-threofuranosyl-(3'-->2') oligonucleotide system. Science 2000; 290:1347-51. [PMID: 11082060 DOI: 10.1126/science.290.5495.1347] [Citation(s) in RCA: 411] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
TNAs [(L)-alpha-threofuranosyl oligonucleotides] containing vicinally connected (3'-->2') phosphodiester bridges undergo informational base pairing in antiparallel strand orientation and are capable of cross-pairing with RNA and DNA. Being derived from a sugar containing only four carbons, TNA is structurally the simplest of all potentially natural oligonucleotide-type nucleic acid alternatives studied thus far. This, along with the base-pairing properties of TNA, warrants close scrutiny of the system in the context of the problem of RNA's origin.
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Affiliation(s)
- K Schöning
- The Skaggs Institute for Chemical Biology at The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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Lescrinier E, Esnouf R, Schraml J, Busson R, Heus H, Hilbers C, Herdewijn P. Solution structure of a HNA-RNA hybrid. CHEMISTRY & BIOLOGY 2000; 7:719-31. [PMID: 10980452 DOI: 10.1016/s1074-5521(00)00017-x] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND Synthetic nucleic acid analogues with a conformationally restricted sugar-phosphate backbone are widely used in antisense strategies for biomedical and biochemical applications. The modified backbone protects the oligonucleotides against degradation within the living cell, which allows them to form stable duplexes with sequences in target mRNAs with the aim of arresting their translation. The biologically most active antisense oligonucleotides also trigger cleavage of the target RNA through activation of endogenous RNase H. Systematic studies of synthetic oligonucleotides have also been conducted to delineate the origin of the chirality of DNA and RNA that are both composed of D-nucleosides. RESULTS Hexitol nucleic acids (HNA) are the first example of oligonucleotides with a six-membered carbohydrate moiety that can bind strongly and selectively to complementary RNA oligomers. We present the first high resolution nuclear magnetic resonance structure of a HNA oligomer bound to a complementary RNA strand. The HNA-RNA complex forms an anti-parallel heteroduplex and adopts a helical conformation that belongs to the A-type family. Possibly, due to the rigidity of the rigid chair conformation of the six-membered ring both the HNA and RNA strand in the duplex are well defined. The observed absence of end-fraying effects also indicate a reduced conformational flexibility of the HNA-RNA duplex compared to canonical dsRNA or an RNA-DNA duplex. CONCLUSIONS The P-P distance across the minor groove, which is close to A-form, and the rigid conformation of the HNA-RNA complex, explain its resistance towards degradation by Rnase H. The A-form character of the HNA-RNA duplex and the reduced flexibility of the HNA strand is possibly responsible for the stereoselectivity of HNA templates in non-enzymatic replication of oligonucleotides, supporting the theory that nucleosides with six-membered rings could have existed at some stage in molecular evolution.
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Affiliation(s)
- E Lescrinier
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
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Herdewijn P. Conformationally restricted carbohydrate-modified nucleic acids and antisense technology. BIOCHIMICA ET BIOPHYSICA ACTA 1999; 1489:167-79. [PMID: 10807006 DOI: 10.1016/s0167-4781(99)00152-9] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The study of conformationally restricted carbohydrate modified nucleic acids has given new insights into the concept of the antisense technology. We learned to understand the structural requirements of a modified nucleic acid to function as steric blocker for RNA. Several of the physicochemical and conformational factors influencing duplex stabilization are analyzed with respect to their relative importance for the antisense field.
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Affiliation(s)
- P Herdewijn
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Belgium.
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Abstract
Systematic chemical studies indicate that the capability of Watson-Crick base-pairing is widespread among potentially natural nucleic acid alternatives taken from RNA's close structural neighborhood. A comparison of RNA and such alternatives with regard to chemical properties that are fundamental to the biological function of RNA provides chemical facts that may contain clues to RNA's origin.
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Affiliation(s)
- A Eschenmoser
- The Skaggs Institute for Chemical Biology at The Scripps Research Institute (TSRI), 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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Micura R, Kudick R, Pitsch S, Eschenmoser A. Die gegensätzliche Orientierung der Rückgratneigung in Pyranosyl-RNA und homo-DNA korreliert mit einer entsprechend gegensätzlichen Orientierung von Duplexeigenschaften. Angew Chem Int Ed Engl 1999. [DOI: 10.1002/(sici)1521-3757(19990301)111:5<715::aid-ange715>3.0.co;2-j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Marquez VE, Ezzitouni A, Russ P, Siddiqui MA, Ford, H, Feldman RJ, Mitsuya H, George C, Barchi JJ. HIV-1 Reverse Transcriptase Can Discriminate between Two Conformationally Locked Carbocyclic AZT Triphosphate Analogues. J Am Chem Soc 1998. [DOI: 10.1021/ja973535+] [Citation(s) in RCA: 126] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Epple C, Leumann C. Bicyclo[3.2.1]-DNA, a new DNA analog with a rigid backbone and flexibly linked bases: pairing properties with complementary DNA. CHEMISTRY & BIOLOGY 1998; 5:209-16. [PMID: 9545434 DOI: 10.1016/s1074-5521(98)90634-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND The structural and conformational variety in nucleic acid complexes is largely controlled by the sugar-phosphate backbone. In order to modulate specific features such as strength or selectivity of complex formation by designing nucleotide analogs, a deeper understanding of the relationship between mononucleotide structures and the properties of their oligomers is necessary. One approach involves comparing the properties of DNA analogs displaying well defined modifications in their backbone structure with those of natural DNA and RNA. RESULTS We have designed and synthesized a new DNA analog, 'bicyclo[3.2.1]-DNA', which has a rigid phosphodiester backbone that emulates a B-DNA-type conformation, to which the nucleobases are attached via a flexible open-chain linker. A UV-melting curve analysis shows that bicyclo[3.2.1]-DNA forms stable duplexes with complementary DNA, although generally with lower Tm values than pure DNA duplexes. Duplex formation is strictly constrained to antiparallel complementary sequences, and base-mismatch discrimination is slightly enhanced compared to pure DNA duplexes. In addition, bicyclo[3.2.1]-DNA sequences are resistant to a 3'-exonuclease. CONCLUSIONS The furanose unit present in natural nucleosides is not necessary for a competent and stable phosphodiester-based pairing system, provided that the backbone is conformationally constrained. The information for the preference of antiparallel strand association in B-DNA is not merely a consequence of bases being attached to a specific side of the furanose unit, but is also encoded in the backbone itself. Furthermore, conformational flexibility in the base-pairing region does not lead to a loss of selectivity in base-pair formation.
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Affiliation(s)
- C Epple
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012, Bern, Switzerland
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Groebke K, Hunziker J, Fraser W, Peng L, Diederichsen U, Zimmermann K, Holzner A, Leumann C, Eschenmoser A. Warum Pentose- und nicht Hexose-Nucleins�uren?? Teil V. (Purin-Purin)-Basenpaarung in der homo-DNS-Reihe: Guanin, Isoguanin, 2,6-Diaminopurin und Xanthin. Helv Chim Acta 1998. [DOI: 10.1002/hlca.19980810302] [Citation(s) in RCA: 76] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Bolli M, Micura R, Pitsch S, Eschenmoser A. Pyranosyl-RNA: Further Observations on Replication. Helv Chim Acta 1997. [DOI: 10.1002/hlca.19970800613] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Peng L, Roth HJ. Synthesis and Properties of 2?-Deoxy-1?,2?-seco-D-ribosyl (5? ? 3?)oligonucleotides (= 1?,2?-seco-DNA) containing adenine and thymine. Helv Chim Acta 1997. [DOI: 10.1002/hlca.19970800513] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Kolb VM. Novel and unusual nucleosides as drugs. PROGRESS IN DRUG RESEARCH. FORTSCHRITTE DER ARZNEIMITTELFORSCHUNG. PROGRES DES RECHERCHES PHARMACEUTIQUES 1997; 48:195-232. [PMID: 9204688 DOI: 10.1007/978-3-0348-8861-5_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- V M Kolb
- Department of Chemistry, University of Wisconsin-Parkside, Kenosha 53141-2000, USA
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35
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Simonyi M. The concept of chiral conformers and its significance in molecular pharmacology. ADVANCES IN DRUG RESEARCH 1997. [DOI: 10.1016/s0065-2490(97)80005-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Bolli M, Litten JC, Schütz R, Leumann CJ. Bicyclo-DNA: a Hoogsteen-selective pairing system. CHEMISTRY & BIOLOGY 1996; 3:197-206. [PMID: 8807846 DOI: 10.1016/s1074-5521(96)90263-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
BACKGROUND The natural nucleic acids (DNA and RNA) can adopt a variety of structures besides the antiparallel double helix described by Watson and Crick, depending on base sequence and solvent conditions. Specifically base-paired DNA structures with regular backbone units include left-handed and parallel duplexes and triple and quadruple helical arrangements. Given the base-pairing pattern of the natural bases, preferences for how single strands associate are determined by the structure and flexibility of the sugar-phosphate backbone. We set out to determine the role of the backbone in complex formation by designing DNA analogs with well defined modifications in backbone structure. RESULTS We recently developed a DNA analog (bicyclo-DNA) in which one (gamma) of the six torsion angles (alpha-zeta) describing the DNA-backbone conformation is fixed in an orientation that deviates from that observed in B-DNA duplexes by about + 100 degrees , a shift from the synclinal to the antiperiplanar range. Upon duplex formation between homopurine and homopyrimidine sequences, this analog preferentially selects the Hoogsteen and reversed Hoogsteen mode, forming A-T and G-C+ base pairs. Base-pair formation is highly selective, but degeneracy is observed with respect to strand orientation in the duplex. CONCLUSIONS The flexibility and orientation of the DNA backbone can influence the preferences of the natural bases for base-pairing modes, and can alter the relative stability of duplexes and triplexes.
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Affiliation(s)
- M Bolli
- Institut für Organische Chemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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James KD, Ellington AD. The search for missing links between self-replicating nucleic acids and the RNA world. ORIGINS LIFE EVOL B 1995; 25:515-30. [PMID: 7494634 DOI: 10.1007/bf01582021] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The notion that modern metabolism was derived from a complex 'RNA world' in which most reactions were catalyzed by ribozymes has received wide acceptance. However, the evolutionary links between the first self-replicating systems and ribozymes as complex as, say, the Group I self-splicing intron or the HDV ribozyme, have remained elusive. While prebiotic chemists have succeeded in synthesizing short oligonucleotides, it is not immediately obvious how these could have replicated and evolved to the point where they could assume complex shapes and catalytic functions. Nonetheless, recent experiments from a variety of disciplines suggest a plausible pathway from prebiotic chemistry to complex metabolism, and this review is intended as a hypothetical roadmap for the origin and subsequent evolution of life.
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Affiliation(s)
- K D James
- Department of Chemistry, Indiana University, Bloomington 47405, USA
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Van Schepdael A, Smets K, Vandendriessche F, Van Aerschot A, Herdewijn P, Roets E, Hoogmartens J. Comparative stability study of thymidine and (dideoxy-d-erythro-hexopyranosyl)thymine analogues monitored by capillary electrophoresis. J Chromatogr A 1994. [DOI: 10.1016/0021-9673(94)00764-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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