Chemical etiology of nucleic acid structure

Science

Volumn 284, Issue 5423, 1999, Pages 2118-

  Eschenmoser, Albert ^a,b  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b ETH ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; NUCLEIC ACID; OLIGONUCLEOTIDE; PURINE; PYRIMIDINE; RNA;

BASE PAIRING; CHEMICAL ANALYSIS; ISOMERISM; MOLECULAR DYNAMICS; MOLECULAR MODEL; NUCLEIC ACID STRUCTURE; PRIORITY JOURNAL; REVIEW; RNA ANALYSIS; RNA SEQUENCE; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS;

BASE PAIRING; DNA; EVOLUTION, CHEMICAL; ISOMERISM; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; OLIGONUCLEOTIDES; RNA; STRUCTURE-ACTIVITY RELATIONSHIP; TEMPLATES, GENETIC;

EID: 0344326234     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.284.5423.2118     Document Type: Review

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104. On the other hand, substantial progress has recently been made with regard to the formation of (3′→5′)/ (2′→5′)-ribofuranosyl oligonucleotide mixtures by mineral-assisted oligocondensation of activated 5′ mononucleotides [J. P. Ferris and G. Ertem, J. Am. Chem. Soc. 115, 12270 (1993); J. P. Ferris, A. R. Hill Jr., R. Liu, L. E. Orgel, Nature 381, 59 (1996); (53)].
105. On the other hand, substantial progress has recently been made with regard to the formation of (3′→5′)/ (2′→5′)-ribofuranosyl oligonucleotide mixtures by mineral-assisted oligocondensation of activated 5′ mononucleotides [J. P. Ferris and G. Ertem, J. Am. Chem. Soc. 115, 12270 (1993); J. P. Ferris, A. R. Hill Jr., R. Liu, L. E. Orgel, Nature 381, 59 (1996); (53)].
106. Of possible relevance in this context are the preference for ribose formation in kinetically controlled aldolization reactions [D. Müller et al., Helv. Chim. Acta 73, 1410 (1990); G. Zubay, Origins Life Evol. Biosphere 28, 13 (1998)] and the fixation of the furanose form of ribose by preferential functionalization of the sterically least hindered primary hydroxyl group [B. Bennua-Skalmowski, K. Krolikiewicz, H. Vorbrüggen, Tetrahedron Lett. 36, 7845 (1995); J. Wengel and C. Scheuer-Larsen, Bioorg. Med. Chem. Lett. 7, 1999 (1997)] or by annelation of the ribofuranose ring by cis-fused five-membered ring α-diol derivatives, for example, cyclophosphates (C. Spinner, S. Pitsch, R. Krishnamurthy, A. Eschenmoser, unpublished work).
107. Of possible relevance in this context are the preference for ribose formation in kinetically controlled aldolization reactions [D. Müller et al., Helv. Chim. Acta 73, 1410 (1990); G. Zubay, Origins Life Evol. Biosphere 28, 13 (1998)] and the fixation of the furanose form of ribose by preferential functionalization of the sterically least hindered primary hydroxyl group [B. Bennua-Skalmowski, K. Krolikiewicz, H. Vorbrüggen, Tetrahedron Lett. 36, 7845 (1995); J. Wengel and C. Scheuer-Larsen, Bioorg. Med. Chem. Lett. 7, 1999 (1997)] or by annelation of the ribofuranose ring by cis-fused five-membered ring α-diol derivatives, for example, cyclophosphates (C. Spinner, S. Pitsch, R. Krishnamurthy, A. Eschenmoser, unpublished work).
108. Of possible relevance in this context are the preference for ribose formation in kinetically controlled aldolization reactions [D. Müller et al., Helv. Chim. Acta 73, 1410 (1990); G. Zubay, Origins Life Evol. Biosphere 28, 13 (1998)] and the fixation of the furanose form of ribose by preferential functionalization of the sterically least hindered primary hydroxyl group [B. Bennua-Skalmowski, K. Krolikiewicz, H. Vorbrüggen, Tetrahedron Lett. 36, 7845 (1995); J. Wengel and C. Scheuer-Larsen, Bioorg. Med. Chem. Lett. 7, 1999 (1997)] or by annelation of the ribofuranose ring by cis-fused five-membered ring α-diol derivatives, for example, cyclophosphates (C. Spinner, S. Pitsch, R. Krishnamurthy, A. Eschenmoser, unpublished work).
109. Of possible relevance in this context are the preference for ribose formation in kinetically controlled aldolization reactions [D. Müller et al., Helv. Chim. Acta 73, 1410 (1990); G. Zubay, Origins Life Evol. Biosphere 28, 13 (1998)] and the fixation of the furanose form of ribose by preferential functionalization of the sterically least hindered primary hydroxyl group [B. Bennua-Skalmowski, K. Krolikiewicz, H. Vorbrüggen, Tetrahedron Lett. 36, 7845 (1995); J. Wengel and C. Scheuer-Larsen, Bioorg. Med. Chem. Lett. 7, 1999 (1997)] or by annelation of the ribofuranose ring by cis-fused five-membered ring α-diol derivatives, for example, cyclophosphates (C. Spinner, S. Pitsch, R. Krishnamurthy, A. Eschenmoser, unpublished work).
110. Of possible relevance in this context are the preference for ribose formation in kinetically controlled aldolization reactions [D. Müller et al., Helv. Chim. Acta 73, 1410 (1990); G. Zubay, Origins Life Evol. Biosphere 28, 13 (1998)] and the fixation of the furanose form of ribose by preferential functionalization of the sterically least hindered primary hydroxyl group [B. Bennua-Skalmowski, K. Krolikiewicz, H. Vorbrüggen, Tetrahedron Lett. 36, 7845 (1995); J. Wengel and C. Scheuer-Larsen, Bioorg. Med. Chem. Lett. 7, 1999 (1997)] or by annelation of the ribofuranose ring by cis-fused five-membered ring α-diol derivatives, for example, cyclophosphates (C. Spinner, S. Pitsch, R. Krishnamurthy, A. Eschenmoser, unpublished work).
111. Although the numerous nucleic acid analogs synthesized recently in antisense oligonucleotide chemistry [for reviews, see J. Hunziker and C. Leumann, in Modern Synthetic Methods, B. Ernst and C. Leumann, Eds. (Verlag Helvetica Chimica Acta, Basel, Switzerland, 1995), voL 7, p. 331; B. Hyrup and P. E. Nielsen, Bioorg. Med. Chem. Lett. 4, 5 (1996); (29)] are an additional illustration of the remarkably broad spread of the nucleobase-pairing potential among organic oligomer structures, the backbones of most of these systems do not correspond to the criteria adopted here for potentially natural nucleic acid alternatives. In a broader etiological context, however, pairing systems such as Nielsen's "polyamide nucleic acid" [P. E. Nielsen, M. Egholm, R. H. Berg, O. Buchardt, Science 254, 1497 (1991); M. Koppitz, P. E. Nielsen, L. E. Orgel, J. Am. Chem. Soc. 120, 4563 (1998)] or amino acid-based systems of the type described by, for example, U. Diederichsen [Angew. Chem. Int. Ed. Engl. 35, 445 (1996)] or M. Fujii et al. [Chem. Commun. 1998, 717 (1998)] may have to become part of the range of structure types that must be screened with respect to their accessibility under natural conditions.
112. Although the numerous nucleic acid analogs synthesized recently in antisense oligonucleotide chemistry [for reviews, see J. Hunziker and C. Leumann, in Modern Synthetic Methods, B. Ernst and C. Leumann, Eds. (Verlag Helvetica Chimica Acta, Basel, Switzerland, 1995), voL 7, p. 331; B. Hyrup and P. E. Nielsen, Bioorg. Med. Chem. Lett. 4, 5 (1996); (29)] are an additional illustration of the remarkably broad spread of the nucleobase-pairing potential among organic oligomer structures, the backbones of most of these systems do not correspond to the criteria adopted here for potentially natural nucleic acid alternatives. In a broader etiological context, however, pairing systems such as Nielsen's "polyamide nucleic acid" [P. E. Nielsen, M. Egholm, R. H. Berg, O. Buchardt, Science 254, 1497 (1991); M. Koppitz, P. E. Nielsen, L. E. Orgel, J. Am. Chem. Soc. 120, 4563 (1998)] or amino acid-based systems of the type described by, for example, U. Diederichsen [Angew. Chem. Int. Ed. Engl. 35, 445 (1996)] or M. Fujii et al. [Chem. Commun. 1998, 717 (1998)] may have to become part of the range of structure types that must be screened with respect to their accessibility under natural conditions.
113. Although the numerous nucleic acid analogs synthesized recently in antisense oligonucleotide chemistry [for reviews, see J. Hunziker and C. Leumann, in Modern Synthetic Methods, B. Ernst and C. Leumann, Eds. (Verlag Helvetica Chimica Acta, Basel, Switzerland, 1995), voL 7, p. 331; B. Hyrup and P. E. Nielsen, Bioorg. Med. Chem. Lett. 4, 5 (1996); (29)] are an additional illustration of the remarkably broad spread of the nucleobase-pairing potential among organic oligomer structures, the backbones of most of these systems do not correspond to the criteria adopted here for potentially natural nucleic acid alternatives. In a broader etiological context, however, pairing systems such as Nielsen's "polyamide nucleic acid" [P. E. Nielsen, M. Egholm, R. H. Berg, O. Buchardt, Science 254, 1497 (1991); M. Koppitz, P. E. Nielsen, L. E. Orgel, J. Am. Chem. Soc. 120, 4563 (1998)] or amino acid-based systems of the type described by, for example, U. Diederichsen [Angew. Chem. Int. Ed. Engl. 35, 445 (1996)] or M. Fujii et al. [Chem. Commun. 1998, 717 (1998)] may have to become part of the range of structure types that must be screened with respect to their accessibility under natural conditions.
114. Although the numerous nucleic acid analogs synthesized recently in antisense oligonucleotide chemistry [for reviews, see J. Hunziker and C. Leumann, in Modern Synthetic Methods, B. Ernst and C. Leumann, Eds. (Verlag Helvetica Chimica Acta, Basel, Switzerland, 1995), voL 7, p. 331; B. Hyrup and P. E. Nielsen, Bioorg. Med. Chem. Lett. 4, 5 (1996); (29)] are an additional illustration of the remarkably broad spread of the nucleobase-pairing potential among organic oligomer structures, the backbones of most of these systems do not correspond to the criteria adopted here for potentially natural nucleic acid alternatives. In a broader etiological context, however, pairing systems such as Nielsen's "polyamide nucleic acid" [P. E. Nielsen, M. Egholm, R. H. Berg, O. Buchardt, Science 254, 1497 (1991); M. Koppitz, P. E. Nielsen, L. E. Orgel, J. Am. Chem. Soc. 120, 4563 (1998)] or amino acid-based systems of the type described by, for example, U. Diederichsen [Angew. Chem. Int. Ed. Engl. 35, 445 (1996)] or M. Fujii et al. [Chem. Commun. 1998, 717 (1998)] may have to become part of the range of structure types that must be screened with respect to their accessibility under natural conditions.
115. Although the numerous nucleic acid analogs synthesized recently in antisense oligonucleotide chemistry [for reviews, see J. Hunziker and C. Leumann, in Modern Synthetic Methods, B. Ernst and C. Leumann, Eds. (Verlag Helvetica Chimica Acta, Basel, Switzerland, 1995), voL 7, p. 331; B. Hyrup and P. E. Nielsen, Bioorg. Med. Chem. Lett. 4, 5 (1996); (29)] are an additional illustration of the remarkably broad spread of the nucleobase-pairing potential among organic oligomer structures, the backbones of most of these systems do not correspond to the criteria adopted here for potentially natural nucleic acid alternatives. In a broader etiological context, however, pairing systems such as Nielsen's "polyamide nucleic acid" [P. E. Nielsen, M. Egholm, R. H. Berg, O. Buchardt, Science 254, 1497 (1991); M. Koppitz, P. E. Nielsen, L. E. Orgel, J. Am. Chem. Soc. 120, 4563 (1998)] or amino acid-based systems of the type described by, for example, U. Diederichsen [Angew. Chem. Int. Ed. Engl. 35, 445 (1996)] or M. Fujii et al. [Chem. Commun. 1998, 717 (1998)] may have to become part of the range of structure types that must be screened with respect to their accessibility under natural conditions.
116. Although the numerous nucleic acid analogs synthesized recently in antisense oligonucleotide chemistry [for reviews, see J. Hunziker and C. Leumann, in Modern Synthetic Methods, B. Ernst and C. Leumann, Eds. (Verlag Helvetica Chimica Acta, Basel, Switzerland, 1995), voL 7, p. 331; B. Hyrup and P. E. Nielsen, Bioorg. Med. Chem. Lett. 4, 5 (1996); (29)] are an additional illustration of the remarkably broad spread of the nucleobase-pairing potential among organic oligomer structures, the backbones of most of these systems do not correspond to the criteria adopted here for potentially natural nucleic acid alternatives. In a broader etiological context, however, pairing systems such as Nielsen's "polyamide nucleic acid" [P. E. Nielsen, M. Egholm, R. H. Berg, O. Buchardt, Science 254, 1497 (1991); M. Koppitz, P. E. Nielsen, L. E. Orgel, J. Am. Chem. Soc. 120, 4563 (1998)] or amino acid-based systems of the type described by, for example, U. Diederichsen [Angew. Chem. Int. Ed. Engl. 35, 445 (1996)] or M. Fujii et al. [Chem. Commun. 1998, 717 (1998)] may have to become part of the range of structure types that must be screened with respect to their accessibility under natural conditions.
117. The author is deeply indebted to R. Lerner (TSRI, La Jolla) and to R. Hütter (ETH, Zürich) for their support. I thank my present or former collaborators O. Jungmann, H. Wippo, M. Stanek, H. Huynh, R. Kudick, F. Reck, G. Ceulemans, and M. Bolli at TSRI; K.-U. Schöming, P. Scholz, T. Vivlemore, S. Pitsch, and R. Micura at ETH for providing unpublished results mentioned in this article; and R. M. Wolf (Novartis Pharma AG, Basel, Switzerland) for producing Fig. 4. The other figures were drawn by R. Krishnamurthy, to whom I express my appreciation for his assistance in operating the La Jolla branch of my research group. I thank S. Weinberg (University of Texas, Austin) for the source of the Einstein quote; I also thank colleagues who helped with the translation. Finally, I am grateful to C. Wintner (Haverford College, Haverford, PA), who critically read the manuscript, made valuable suggestions, and improved the English.