HyBeaconTM probes: a new tool for DNA sequence detection and allele discrimination

French, David J.; Archard, C.L.; Brown, Tom; McDowell, David G.

doi:10.1006/mcpr.2001.0384

Cited by 91 publications

(41 citation statements)

References 39 publications

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“…Match/mismatch discrimination was highest at elevated temperatures and reached factors of tenfold, which compare well with the discriminative power of dual-labeled hybridization probes. Less pronounced abilities in distinguishing a target sequence from its single-base mutant at temperatures below the T M value of mismatched probe-target complexes have been reported for HyBeacons [74] and 1,10-phenanthroline-modified bases. [50] Recently, fluorescent nucleotides comprised of benzoand naphtho-annulated nucleobases and pyrene-modified pyrimidine bases have been described that sometimes show even higher match/mismatch selectivities (2-20-fold).…”

Section: Fluorescence Propertiesmentioning

confidence: 94%

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

221

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: Fluorescence Propertiesmentioning

confidence: 94%

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

221

172

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“…[2][3][4][5][6][7][8][9] Environmentally sensitive fluorophores can report on binding events such as hybridization and are, thus, principally suited for homogeneous DNA detection. [10][11][12][13][14] Recently, our group and the group of Wagenknecht have introduced intercalator dyes, thiazole orange (TO) [15] and phenanthridinium, [16] respectively, as artificial bases that fluoresce upon hybridization. One of the interesting opportunities provided by such base replacements is to link or even force fluorophores into a specific site of the nucleic acid duplex which under normal circumstances would compete with many other binding sites or even be devoid of binding of fluorophores.…”

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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“…Probes comprise specific linear oligonucleotides that possess a fluorescent dye label attached to an internal nucleotide and a 3V phosphate to prevent PCR extension [1][2][3]. Probes are included in PCR assays and emit greater amounts of fluorescence when hybridised to complementary target sequences than when single-stranded.…”

Section: Hybeacon Probesmentioning

confidence: 99%

“…Increasing the reaction temperature above the melting temperature (Tm) of the HyBeacon causes probe/target duplexes to dissociate and the amount of fluorescence emission to decrease. Sequences differing by as little as a single nucleotide may be detected and differentiated on the basis of melt peak Tm [1,2]. Fifty cycles of amplification and melt analysis may be completed in as little as 16 min using rapid real-time PCR instruments such as the LightCycler.…”

Section: Hybeacon Probesmentioning

confidence: 99%

HyBeacons®: A novel DNA probe chemistry for rapid genetic analysis

French¹,

McDowell²,

Thomson³

et al. 2006

International Congress Series

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HyBeaconTM probes: a new tool for DNA sequence detection and allele discrimination

Cited by 91 publications

References 39 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

HyBeacons®: A novel DNA probe chemistry for rapid genetic analysis

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