A Novel Peptide Nucleic Acid Monomer for Recognition of Thymine in Triple-Helix Structures

Eldrup, Anne B.; Dahl, Otto; Nielsen, Peter E.

doi:10.1021/ja9717424

Cited by 77 publications

(68 citation statements)

References 20 publications

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“…[51] The relative ease of introducing base analogues into PNA, a DNA mimic that binds complementary DNA with increased affinity and selectivity, has been exploited in many studies aiming for enhancements of hybridization properties. [52][53][54][55][56][57][58] Aromatics, [59] heteroaromatics, [60,61] and fluoroaromatics [62] have been incorporated in order to confer universal base pairing, albeit at the cost of compromising duplex stability by DT M = 9-29 8C (DT M = change in the duplex melting temperature). Fluorescent base analogues such as 2-aminopurine, [63] psoralen, [64] flavin, [65,66] and 3,5-diaza-4-oxo-phenothiazine [67] have been placed in the interior of PNA-DNA duplexes.…”

Section: Design Principlesmentioning

confidence: 99%

Forced Intercalation Probes (FIT Probes): Thiazole Orange as a Fluorescent Base in Peptide Nucleic Acids for Homogeneous Single‐Nucleotide‐Polymorphism Detection

Köhler¹,

Jarikote²,

Seitz³

2005

ChemBioChem

216

172

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Fluorescent base analogues in DNA are versatile probes of nucleic acid-nucleic acid and nucleic acid-protein interactions. New peptide nucleic acid (PNA) based probes are described in which the intercalator dye thiazole orange (TO) serves as a base surrogate. The investigation of six TO derivatives revealed that the linker length and the conjugation site decided whether a base surrogate conveys sequence-selective DNA binding and whether fluorescence is increased or decreased upon single-mismatched hybridization. One TO derivative conferred universal PNA-DNA base pairing while maintaining duplex stability and hybridization selectivity. TO fluorescence increased up to 26-fold upon hybridization. In contrast to most other probes, in which fluorescence is invariant once hybridization had occurred, the emission of TO-containing PNA probes is attenuated when forced to intercalate next to a mismatched base pair. The specificity of DNA detection is therefore not limited by the selectivity of probe-target binding and a DNA target can be distinguished from its single-base mutant under nonstringent hybridization conditions. This property should be of advantage for real-time quantitative PCR and nucleic acid detection within living cells.

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Section: Design Principlesmentioning

confidence: 99%

Forced Intercalation Probes (FIT Probes): Thiazole Orange as a Fluorescent Base in Peptide Nucleic Acids for Homogeneous Single‐Nucleotide‐Polymorphism Detection

Köhler¹,

Jarikote²,

Seitz³

2005

ChemBioChem

216

172

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show abstract

“…(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005) analogues into PNA, a DNA mimic that binds complementary DNA with increased affinity and selectivity, [18,19] has been exploited in many studies aimed at enhancements of hybridization properties, [20][21][22][23][24][25][26][27][28] and site-selective incorporation of fluorescent or photoactive base analogues. [29][30][31][32][33][34][35] In these works, single base modifications were introduced into PNA by coupling pre-fabricated monomer building blocks in a linear solid-phase synthesis.…”

Section: Introductionmentioning

confidence: 99%

Divergent and Linear Solid‐Phase Synthesis of PNA Containing Thiazole Orange as Artificial Base

et al. 2005

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Fluorescent nucleobase surrogates provide nucleic acids with interesting properties. We have recently introduced thiazole orange as base surrogate into PNA and found that the so-called FIT (Forced Intercalation of Thiazole orange) PNA probes signal hybridization by enhancements of fluorescence. Common approaches of modifying nucleobases or introducing nucleobase surrogates draw upon the usage of monomer building blocks that have been synthesized in solution phase. The need to prefabricate a base-modified building block can hold up progress if several base modifications or base surrogates are to be evaluated. Herein, a method for divergent solid-phase synthesis is presented that serves the

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“…This result is similar to those reported previously and suggests that in further work analogues with intercalative potential should be avoided. Finally, a pyridazine derivative on an acyclic linker has been shown to form triplets with T:A pairs (101). This analogue showed reasonable base pair discrimination, but was analyzed in the context of a peptide nucleic acid, and has not been examined in an oligonucleotide.…”

Section: Prospects For the Expansion Of The Triplex-binding Codementioning

confidence: 99%

The potential for gene repair via triple helix formation

Seidman¹,

Glazer²

2003

J. Clin. Invest.

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Triplex-forming oligonucleotides (TFOs) can bind to polypurine/polypyrimidine regions in DNA in a sequence-specific manner. The specificity of this binding raises the possibility of using triplex formation for directed genome modification, with the ultimate goal of repairing genetic defects in human cells. Several studies have demonstrated that treatment of mammalian cells with TFOs can provoke DNA repair and recombination, in a manner that can be exploited to introduce desired sequence changes. This review will summarize recent advances in this field while also highlighting major obstacles that remain to be overcome before the application of triplex technology to therapeutic gene repair can be achieved

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A Novel Peptide Nucleic Acid Monomer for Recognition of Thymine in Triple-Helix Structures

Cited by 77 publications

References 20 publications

Forced Intercalation Probes (FIT Probes): Thiazole Orange as a Fluorescent Base in Peptide Nucleic Acids for Homogeneous Single‐Nucleotide‐Polymorphism Detection

Forced Intercalation Probes (FIT Probes): Thiazole Orange as a Fluorescent Base in Peptide Nucleic Acids for Homogeneous Single‐Nucleotide‐Polymorphism Detection

Divergent and Linear Solid‐Phase Synthesis of PNA Containing Thiazole Orange as Artificial Base

The potential for gene repair via triple helix formation

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