Hybridization Studies with Chiral Peptide Nucleic Acids

Lowe, Gordoǹ; Vilaivan, Tirayut; Westwell, Martin S.

doi:10.1006/bioo.1997.1078

Cited by 14 publications

(7 citation statements)

References 26 publications

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“…Ribosomal 16S and 23S RNA genes, and the archaeobacterial 7S RNA gene were identi¢ed by homology search using FASTA version 3.0 [22] in the GCG package version 9.0 (Genetics Computer Group) to reference RNA gene sequences of other archaeobacteria collected in databases (Ribosomal Database Project [23], GenBank [24], EMBL database [25] and DDBJ [26]). The tRNA genes were identi¢ed by using the algorithm tRNA scan-SE [27].…”

Section: Identi¢cation Of Rna Genesmentioning

confidence: 99%

A transcription frame‐based analysis of the genomic DNA sequence of a hyper‐thermophilic archaeon for the identification of genes, pseudo‐genes and operon structures

et al. 1998

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An algorithm for identifying transcription units, independently regulated genes and operons, and pseudo-genes that are not expected to be expressed, has been developed by combining a system for predicting transcription and translation signals, and a system for scoring the triplet periodicity in ORF candidates. By using the algorithm, the 1.09 Mb sequence that covers approximately 60% of the genome of Pyrococcus sp. OT3 has been analyzed. The identified ORFs show the expected biological and physical characteristics, while the rejected ORF candidates do not. Frequent use of operon structures for transcription, and gene duplication followed by mutation or termination of the duplicated genes, are discussed.z 1998 Federation of European Biochemical Societies.

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Section: Identi¢cation Of Rna Genesmentioning

confidence: 99%

A transcription frame‐based analysis of the genomic DNA sequence of a hyper‐thermophilic archaeon for the identification of genes, pseudo‐genes and operon structures

et al. 1998

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“…[1][2][3][4][5] A number of related pyrrolidine-containing oligonucleotide mimics, or peptide nucleic acid analogues, have similarly been developed. [6][7][8][9][10][11][12][13][14][15][16] Several of these pyrrolidine-containing mimics also exhibit promising nucleic acid recognition and other physiochemical properties, which might be useful for a wide range of applications including in vivo DNA and RNA targeting, [17][18][19] diagnostics and bioanalysis, 20, 21 or programmed assembly of nanostructures. 22 Despite this, most of the results compiled so far, 1-12,14, 15 with the exception of a few studies, 13,16 are based on the properties of chimeric oligomers containing a mix of PNA and pyrrolidine monomer units or fully modified pyrrolidinyl-homopolymers (e.g.…”

Section: Introductionmentioning

confidence: 99%

Mixed-sequence pyrrolidine-amide oligonucleotide mimics: Boc(Z) synthesis and DNA/RNA binding properties

et al. 2007

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Pyrrolidine-amide oligonucleotide mimics (POMs) exhibit promising properties for potential applications, including in vivo DNA and RNA targeting, diagnostics and bioanalysis. Before POMs can be evaluated in these applications it is first necessary to synthesise and establish the properties of fully modified oligomers, with biologically relevant mixed sequences. Accordingly, Boc-Z-protected thyminyl, adeninyl and cytosinyl POM monomers were prepared and used in the first successful solid phase synthesis of a mixed sequence POM, Lys-TCACAACTT-NH2. UV thermal denaturation studies revealed that the POM oligomer is capable of hybridising with sequence selectivity to both complementary parallel and antiparallel RNA and DNA strands. Whilst the duplex melting temperatures (Tm) were higher than the corresponding duplexes formed with isosequential PNA, DNA and RNA oligomers the rates of association/dissociation of the mixed sequence POM with DNA/RNA targets were noticeably slower.

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“…As a result of these critical stereochemical and conformational features POM is predicted to bind in an antiparallel fashion and differs conceptually from other oligonucleotide systems incorporating pyrrolidine units. [33][34][35][36][37][38][39][40] These systems were designed as conformationally restricted analogues of PNA, unlike POM which we envisage shares little conformational or electrostatic similarity with PNA.…”

Section: Design and Molecular Modellingmentioning

confidence: 99%

Design, synthesis, conformational analysis and nucleic acid hybridisation properties of thymidyl pyrrolidine-amide oligonucleotide mimics (POM)Electronic supplementary information (ESI) available: experimental details (16 Figures, 3 Tables). See http://www.rsc.org/suppdata/ob/b3/b306156f/

et al. 2003

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Pyrrolidine-amide oligonucleotide mimics (POM) 1 were designed to be stereochemically and conformationally similar to natural nucleic acids, but with an oppositely charged, cationic backbone. Molecular modelling reveals that the lowest energy conformation of a thymidyl-POM monomer is similar to the conformation adopted by ribonucleosides. An efficient solution phase synthesis of the thymidyl POM oligomers has been developed, using both N-alkylation and acylation coupling strategies. 1H NMR spectroscopy confirmed that the highly water soluble thymidyl-dimer, T2-POM, preferentially adopts both a configuration about the pyrrolidine N-atom and an overall conformation in D2O that are very similar to a typical C3'-endo nucleotide in RNA. In addition the nucleic acid hybridisation properties of a thymidyl-pentamer, T5-POM, with an N-terminal phthalimide group were evaluated using both UV spectroscopy and surface plasmon resonance (SPR). It was found that T5-POM exhibits very high affinity for complementary ssDNA and RNA, similar to that of a T5-PNA oligomer. SPR experiments also showed that T5-POM binds with high sequence fidelity to ssDNA under near physiological conditions. In addition, it was found possible to attenuate the binding affinity of T5-POM to ssDNA and RNA by varying both the ionic strength and pH. However, the most striking feature exhibited by T5-POM is an unprecedented kinetic binding selectivity for ssRNA over DNA.

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Hybridization Studies with Chiral Peptide Nucleic Acids

Cited by 14 publications

References 26 publications

A transcription frame‐based analysis of the genomic DNA sequence of a hyper‐thermophilic archaeon for the identification of genes, pseudo‐genes and operon structures

A transcription frame‐based analysis of the genomic DNA sequence of a hyper‐thermophilic archaeon for the identification of genes, pseudo‐genes and operon structures

Mixed-sequence pyrrolidine-amide oligonucleotide mimics: Boc(Z) synthesis and DNA/RNA binding properties

Design, synthesis, conformational analysis and nucleic acid hybridisation properties of thymidyl pyrrolidine-amide oligonucleotide mimics (POM)Electronic supplementary information (ESI) available: experimental details (16 Figures, 3 Tables). See http://www.rsc.org/suppdata/ob/b3/b306156f/

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