trans-5-Aminopipecolyl-aegPNA Chimera:  Design, Synthesis, and Study of Binding Preferences with DNA/RNA in Duplex/Triplex Mode

Lonkar, Pallavi; Kumar, Vaijayanti A.

doi:10.1021/jo0506884

Cited by 8 publications

(2 citation statements)

References 25 publications

(49 reference statements)

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“…The chimeric aminopipecolyl/aegPNA with (2S,4S)stereoisomer decreased the stability of the PNA 2 ÁDNA triplex but increased the stability of the PNAÁDNA duplex and the opposite is true for the (2S,5R)-stereoisomer. 103,104 Although technically the (2S,5R)-aminopipecolyl PNA should be regarded as an (a-g)-linked system, it is more convenient to compare it with the (2S,4R)-aminopipecolyl PNA here.…”

Section: Rsc Chemical Biology Reviewmentioning

confidence: 99%

Perspectives on conformationally constrained peptide nucleic acid (PNA): insights into the structural design, properties and applications

Suparpprom

Vilaivan

2022

RSC Chem. Biol.

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Section: Rsc Chemical Biology Reviewmentioning

confidence: 99%

Perspectives on conformationally constrained peptide nucleic acid (PNA): insights into the structural design, properties and applications

Suparpprom

Vilaivan

2022

RSC Chem. Biol.

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“… Chemical structures of different PNAs indicating C2–C3 carbons of PNA backbone, marked in red (a) Aminoethyl glycyl, aeg PNA [1] (b) Cyclohexyl, ch PNA [17,18] (c) Cyclopentyl, cp PNA [19,20] (d) Diaminopyrrolidine, dap PNA, (e) N‐(Pyrrolidinyl‐2‐methyl)glycine, pmg‐ PNA [21] , (f) pipecolyl ‐PNA [22] and (g) pyrrolidinyl PNA [23] …”

Section: Introductionmentioning

confidence: 99%

Electrostatics Favor PNA : DNA Stability over Stereochemistry in Pyrrolidine‐Based Cationic Dual‐Backbone PNA Analogues

Sharma

Ganesh

2021

Eur J Org Chem

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Modifications to the peptide nucleic acid (PNA) backbone has been well known to alter the thermodynamical parameters of PNA : DNA complexes to broaden their utility for different applications. Electrostatic interactions between a modified PNA having a positively charged backbone and the negatively charged DNA has been shown to enhance thermal stabilities of PNA : DNA complexes at various instances. On the other hand, chiral introduction in PNA backbone leads to stereochemical preference that affects binding properties. However, the interplay between electrostatics and stereochemistry has not been systematically studied so far. Herein, we report the synthesis and biophysical characterization of cationic PNA named dapPNA, first of its kind, having a dual PNA backbone constituting of a pyrrolidine ring having a β‐substitution. One of the aims of this study was to investigate the role of electrostatics over stereochemical preferences. The results show that electrostatic attraction between cationic dapPNA and negatively charged DNA overcomes the unfavorable stereochemical effects and enhances stability of PNA : DNA complexes. Moreover, two different PNA backbones derived from a single PNA monomer expands the repertoire of pyrrolidine based PNA analogues.

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Synthesis of a novel Fmoc-protected nucleoaminoacid for the solid phase assembly of 4-piperidyl glycine/l-arginine-containing nucleopeptides and preliminary RNA interaction studies

et al. 2010

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In this work, we report the synthesis of a novel Fmoc-protected nucleoaminoacid, based on 4-piperidinyl glycine, carrying the DNA nucleobase on the secondary amino group, suitable for the solid-phase synthesis of nucleopeptides. After ESI-MS and NMR characterization this building block was used for the assembly of a thymine-functionalized tetrapeptide, composed of 4-piperidinyl glycine and L-arginine moieties alternated in the backbone. The ability to interact with RNA and the efficiency in interfering with the reverse transcription of eukaryotic mRNA of the novel nucleo-tetrapeptide found in this study are in favour of the employment of chiral nucleopeptides based on alternate 4-piperidinyl glycine/L-arginine backbone in biomedicine.

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trans-5-Aminopipecolyl-aegPNA Chimera: Design, Synthesis, and Study of Binding Preferences with DNA/RNA in Duplex/Triplex Mode

Cited by 8 publications

References 25 publications

Perspectives on conformationally constrained peptide nucleic acid (PNA): insights into the structural design, properties and applications

Perspectives on conformationally constrained peptide nucleic acid (PNA): insights into the structural design, properties and applications

Electrostatics Favor PNA : DNA Stability over Stereochemistry in Pyrrolidine‐Based Cationic Dual‐Backbone PNA Analogues

Synthesis of a novel Fmoc-protected nucleoaminoacid for the solid phase assembly of 4-piperidyl glycine/l-arginine-containing nucleopeptides and preliminary RNA interaction studies

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