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Karig, Gunter; Fuchs, Andreas; Büsing, Arne; Brandstetter, Tilmann W.; Scherer, S.; Bats, Jan W.; Eschenmoser, Albert; Quinkert, Gerhard

doi:10.1002/1522-2675(20000607)83:6<1049::aid-hlca1049>3.0.co;2-1

Cited by 30 publications

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“…Simulated annealing calculations of the structure of the p-RNA duplex derived from pr(CGAATTCG) based on the NMR data of [4] by Schwalbe and co-workers [66] corroborated the conclusions drawn by Jaun and Schlˆnvogt [4]. Complementary information on, and a further illustration of, such a quasi-linear type of oligonucleotide structure comes from a NMR structure analysis carried out by Schwalbe et al [67] of a duplex derived from the partially selfcomplementary AATAT sequence in the series of Quinkert×s d-peptide analogues of p-RNA [68].…”

supporting

confidence: 69%

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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confidence: 69%

Pentopyranosyl Oligonucleotide Systems. 9th Communication

Pitsch

Wendeborn

Krishnamurthy

et al. 2003

Helvetica Chimica Acta

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“…Our results suggest that the topology and quantity of a charge cluster may provide low affinity molecular recognition to microbial surfaces and confer organism specificity and salt insensitivity. The principle of clustering cationic and hydrophobic regions of antimicrobial peptides has inspired the design of novel antimicrobials with ␤-and ␥-peptide backbones (40) as well as dendrimeric peptides with ␦-and ⑀-peptide backbones (41). Studies in the requirements of cationic clusters in the amphipathic design may further the understanding and lead to the development of antimicrobial peptides with high specificity and potency that are useful as therapeutic agents.…”

Section: Table IV Antimicrobial Activity Of Cctp-14 and Their Analoguesmentioning

confidence: 99%

Correlations of Cationic Charges with Salt Sensitivity and Microbial Specificity of Cystine-stabilized β-Strand Antimicrobial Peptides

Tam

Yang

2002

Journal of Biological Chemistry

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The electrostatic interaction of the charge cluster of an amphipathic peptide antibiotic with microbial membranes is a salt-sensitive step that often determines organism specificity. We have examined the correlation between charge clusters and salt insensitivity and microbial specificity in linear, cyclic, and retro-isomeric cystine-stabilized ␤-strand (CS␤) tachyplesin (TP) in a panel of 10 test organisms. Cyclic tachyplesins consisting of 14 and 18 amino acids are constrained by an end-to-end peptide backbone and two or three disulfide bonds to cross-brace the anti-parallel ␤-strand that approximates a "␤-tile" structure. Circular dichroism measurements of ␤-tile TPs showed that they displayed ordered structures. Control peptides containing the same number of basic amino acids as TP but lacking disulfide constraints were highly salt sensitive. Cyclic TP analogues with six cationic charges were more broadly active and salt-insensitive than those with fewer cationic charges. Reducing their proximity or number of cationic charges, particularly those with three or fewer basic amino acids, led to a significant decrease in potency and salt insensitivity, but an increased selectivity to certain Gram-positive bacteria. An end-group effect of the dibasic N-terminal Lys of TP in the open-chain TP and its retroisomer was observed in certain Gram-negative bacteria under high-salt conditions, an effect that was not found in the cyclic analogs. These results suggest that a stable folded structure together with three or more basic amino acids closely packed in a charged region in CS␤ peptides is important for salt insensitivity and organism specificity.

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“…In compound (221), hydroxyl group at position 4 of the starting amino acid is used to insert the base via Mitsunobu reaction. (70) [105,106]. The synthesis is shown in Fig.…”

Section: δ-Amino Acids For Pna Designmentioning

confidence: 99%

γ- and δ-Amino Acids: Synthetic Strategies and Relevant Applications

Trabocchi¹,

Guarna

2005

COC

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Over the years, γand δ-amino acids have gathered much interest in drug discovery, especially in the peptidomimetic area. Much work on γ-amino acids has been focused towards the generation of γ-amino butyric acid (GABA) analogues, and the development of asymmetric approaches starting from unsaturated compounds, while few examples have been reported about carbohydrate-derived scaffolds as γ-amino acids. δ-Amino acids became of great importance as they have been selected as building blocks for backbone generation of peptide nucleic acid (PNA) structures. As further applications of δ-amino acids, carbohydrate research produced interesting examples of new δ-amino acids as building blocks for peptidomimetic design, and several reverse turn mimetics have been reported, too. Moreover, many studies have been concentrated on the conformational analysis of oligomeric sequences in analogy with β-peptides. This report is a description of relevant synthetic approaches to new γ-amino acids through the use of sugar chemistry and asymmetric synthesis, and to synthetic strategies for δ-amino acids, covering the area of carbohydrate chemistry, alkenebased chemistry, and asymmetric synthesis. 10γ -and δ -Amino Acids: Synthetic Strategies

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Cited by 30 publications

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Pentopyranosyl Oligonucleotide Systems. 9th Communication

Pentopyranosyl Oligonucleotide Systems. 9th Communication

Correlations of Cationic Charges with Salt Sensitivity and Microbial Specificity of Cystine-stabilized β-Strand Antimicrobial Peptides

γ- and δ-Amino Acids: Synthetic Strategies and Relevant Applications

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Cited by 30 publications

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Pentopyranosyl Oligonucleotide Systems. 9th Communication

Pentopyranosyl Oligonucleotide Systems. 9th Communication

Correlations of Cationic Charges with Salt Sensitivity and Microbial Specificity of Cystine-stabilized β-Strand Antimicrobial Peptides

&#947;- and &#948;-Amino Acids: Synthetic Strategies and Relevant Applications

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γ- and δ-Amino Acids: Synthetic Strategies and Relevant Applications