Pentopyranosyl Oligonucleotide Systems, Communication No. 10, Theα-L-Lyxopyranosyl-(4′→2′)-oligonucleotide System

Reck, Folkert; Wippo, Harald; Kudick, René; Krishnamurthy, Ramanarayanan; Eschenmoser, Albert

doi:10.1002/1522-2675(20010613)84:6<1778::aid-hlca1778>3.0.co;2-3

Cited by 14 publications

(11 citation statements)

References 27 publications

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“…‡ The Scripps Research Institute. base-pairing(e.g.,thehexopyranosyl-(6′-4′)-oligonucleotides 9-12 ), whereasothers(e.g.,thefamilyofpentopyranosyl-(4′-2′)-oligonucleotides) 13, [16][17][18] were found to undergo efficient and selective Watson-Crick pairing even more strongly than the natural isomers. These studies also revealed the Watson-Crick basepairing mode's capacity to mediate more than one "basepairing language" in the sense that, whereas none of the members of the family of diastereomeric pentopyranosyl-(4′-2′)-systems undergoes intersystem cross-pairing with the natural nucleic acids, they are perfectly fit for intrasystem base-pairing as well as intersystem cross-pairing within the family.…”

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The Structure of a TNA−TNA Complex in Solution: NMR Study of the Octamer Duplex Derived from α-(l)-Threofuranosyl-(3′-2′)-CGAATTCG

et al. 2008

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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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Section: Introductionmentioning

confidence: 99%

The Structure of a TNA−TNA Complex in Solution: NMR Study of the Octamer Duplex Derived from α-(l)-Threofuranosyl-(3′-2′)-CGAATTCG

et al. 2008

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“…While such unambiguous agreement between 'theory' and experiment is of course welcomed, it is to encounter clearcut disagreement with specific details of a 'theory's' predictions that reveals to us the limits of that 'theory' and, therefore, should to be welcomed, too. We encountered such disagreement when we studied the entire family of the four possible diastereomeric pentopyranosyl-oligonucleotide systems (containing equatorial nucleobases) [29], namely, (besides the beta-D-ribo-system) the beta-D-xylo- [30], the alpha-L-lyxo- [31], and the alpha-L-arabino- [32] member (Fig. 13).…”

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Searching for Nucleic Acid Alternatives

Eschenmoser¹

2005

Chimia

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"Back of the envelope" methods have their place in experimental chemical research; they are effective mediators in the generation of research ideas, for instance, the design of molecular structures. Their qualitative character is part of their strength, rather than a drawback for the role they have to play. Qualitative conformational analysis of oligonucleotide and other oligomer systems on the level of idealized conformations is one such method; it has played a helpful role in our work on the chemical etiology of nucleic acid structure. This article, while giving a short overview of that work, shows how.

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“…see [1 ± 8]. The label −Chemistry of Pyranosyl-RNA× previously used for the series of papers on p-RNA [1 ± 8] has been changed (see [9]) into −Pentopyranosyl Oligonucleotide Systems× as a consequence of the extension of our work on p-RNA to a whole family of diastereoisomeric pentopyranosyl oligonucleotides. In [9], the present paper had been assigned No.…”

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“…Scheme 1 summarizes the synthesis of the seven b-d-ribopyranosyl nucleosides 3a ± 3g, all of them ± with the exception of the U and T derivatives ± in a protected form suited for the construction of oligonucleotide sequences. In all cases, the nucleosidation methodology of Vorbr¸ggenÀHilbertÀJohnson [50], previously successfully applied in the homo-DNA series [28], could be adopted without any difficulties by using an a/b-mixture of d-tetrabenzoyl-ribopyranose [51] as starting material 9 ). As usual (see, e.g., [28]), nucleosidation in the G series presented more problems and demanded extended exploratory experimentation.…”

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“…Their base-pairing strength is uniformly greater than that of corresponding RNA and DNA oligonucleotide sequences (Tables 5 and 6). This behavior is not specific to the ribopyranosyl oligonucleotide system, the entire family of pentopyranosyl-(4' 3 2')-oligonucleotide systems shows WatsonÀCrick base pairing that is stronger than that of RNA and DNA [17] [9] [11] [12]. Superiority in base-pairing strength has been interpreted as being connected to a higher degree of conformational pre-organization of single strands toward their duplex conformations, as compared to the single strands of the ribofuranosyl-(5' 3 3')-oligonucleotide system.…”

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Pentopyranosyl Oligonucleotide Systems. 9th Communication

Pitsch

Wendeborn

Krishnamurthy

et al. 2003

Helvetica Chimica Acta

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Dulio Arigoni zu seinem 75. Geburtstag gewidmet, in Erinnerung an gute alte Zeiten Pyranosyl-RNA (−p-RNA× ) is an oligonucleotide system isomeric to natural RNA and composed of the very same building blocks as RNA. Its generational, chemical, and informational properties are deemed to be those of an alternative nucleic acid system that could have been a candidate in Nature×s evolutionary choice of the molecular basis of genetic function. We consider the study of the chemistry of p-RNA as etiologically relevant in the sense that knowledge of its structural, chemical, and informational properties on the chemical level offers both a perspective and reference points for the recognition of specific structural assets of the RNA structure that made it the (supposedly) superior system among possible alternatives and, therefore, the system that became part of biology as we know it today. The paper describes the chemical synthesis of b-d-(and l)ribopyranosyl-(4' 3 2')-oligonucleotide sequences, presents a resume of their structural and chemical properties, and cautiously discusses what we may and may not have learned from the pyranosyl isomer of RNA with respect to the conundrum of RNA×s origin. see [1 ± 8]. The label −Chemistry of Pyranosyl-RNA× previously used for the series of papers on p-RNA [1 ± 8] has been changed (see [9]) into −Pentopyranosyl Oligonucleotide Systems× as a consequence of the extension of our work on p-RNA to a whole family of diastereoisomeric pentopyranosyl oligonucleotides. In [9], the present paper had been assigned No. 9 in this series. The follow-up papers No. 10 [9], 11 [10], 12 [11], and 13 [12] in the series have already appeared. The present paper also is communication No. 30 in the series −Chemistry of a-Aminonitriles×. 4271 hexopyranosyl systems. Such hindrance is expected to occur between an equatorial 2'-OH group of a pyranosyl unit and the neighboring (downstream-positioned) nucleobase; it is clearly to be inferred from model considerations based on homo-DNA×s two types of pairing conformations (À g/ À g and t/ À g), which were derived by qualitative conformational analysis [29] 5 ) ( Fig. 2), and were found to co-exist in a homo-DNA duplex by an NMR structure analysis by Otting et al [26]. The results of experimental studies on 2'-deoxy-and 3'-deoxyallopyranosyl model systems [24] [46] [47] (Table 1) corroborated this interpretation.It was this insight into the consequences of the steric bulk of fully hydroxylated (6' 3 4')-hexopyranosyl building blocks that led us to ask whether base pairing might be Helvetica Chimica Acta ± Vol. 86 (2003) 4275 8 ) See Scheme 1 in [1]. It seems worth pointing out that an analogously built hexopyranosyl-(4' 3 2')oligonucleotide system, e.g., the b-allopyranosyl member depicted below, by the same reasoning, would not be expected to be a base-pairing system. The (repetitive) pairing conformation would suffer serious steric hindrance (see arrow) and, therefore, not become populated in competition with less strained (nonrepetitive) conformations. 9 ) ...

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Pentopyranosyl Oligonucleotide Systems, Communication No. 10, Theα-L-Lyxopyranosyl-(4′→2′)-oligonucleotide System

Cited by 14 publications

References 27 publications

The Structure of a TNA−TNA Complex in Solution: NMR Study of the Octamer Duplex Derived from α-(l)-Threofuranosyl-(3′-2′)-CGAATTCG

The Structure of a TNA−TNA Complex in Solution: NMR Study of the Octamer Duplex Derived from α-(l)-Threofuranosyl-(3′-2′)-CGAATTCG

Searching for Nucleic Acid Alternatives

Pentopyranosyl Oligonucleotide Systems. 9th Communication

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