DNA triple helix stabilisation by covalent attachment of a triplex-specific ligand

Keppler, Melanie D.; McKeen, Catherine; Zegrocka, Oliwia; Strękowski, Lucjan; Brown, Tom; Fox, Keith R.

doi:10.1016/s0167-4781(99)00114-1

Cited by 14 publications

(26 citation statements)

References 29 publications

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“…Oligodeoxynucleotides [(dT) 10 and (dA) 15 ] were synthesized according to the standard H-phosphonate procedure. 21 The decathymidylatePzn ribonucleoside conjugate [(dT) 10 Pzn, Fig.…”

Section: Methodsmentioning

confidence: 99%

“…The necessary ionic strength of the solutions was created by the addition of NaCl. The oligonucleotide and polynucleotide concentrations were determined by UV spectrophotometry using the following extinction coefficients (per mole of nucleotides): ⑀ 257 ϭ 9800 M Ϫ1 cm Ϫ1 for (dA) 15 and ⑀ 266 ϭ 8600 M Ϫ1 cm Ϫ1 for (dT) 10 (at 21-23°C) 22 and ⑀ 260 ϭ 6000 M Ϫ1 cm Ϫ1 for poly(dA)⅐poly(dT) (at 20°C). The oligomer concentration of the (dT) 10 Pzn conjugate was calculated from the longwave absorbance of the dye moiety using ⑀ 384 ϭ 22,000 M Ϫ1 cm…”

Section: Methodsmentioning

confidence: 99%

“…The modification of oligonucleotides by the covalent attachment of intercalating dyes was shown to stabilize their double-and triple-helix formations due to the interaction of intercalative chromophores with nucleic bases. [5][6][7][8][9][10][11][12][13][14][15] A flexible linker, such as a polymethylene chain, which gives the dye molecule freedom in choosing an intercalative site, is usually used for the conjugation. Another approach for oligonucleotide modification by dyes was also developed.…”

Section: Introductionmentioning

confidence: 99%

“…1) was shown to significantly enhance the thermal stability of a poly(rA)⅐(dT) 10 duplex. In the present work we studied the effect of the above modification on the thermodynamic stability of duplex and triplex formations of (dT) 10 with (dA) 15 and a triplex formation with poly(dA)⅐poly(dT). The structures of the relevant complexes with these systems are presented in Figure 1.…”

Section: Introductionmentioning

confidence: 99%

“…The formation by the (dT) 10 Pzn conjugate of the duplex complex with (dA) 15 and the triplex complex with (dA) 15 or poly(dA)⅐poly(dT) was studied in buffered solutions with 0.11 and/or 1M sodium ions at the oligomer strand concentration of 10 M. Because of the Pzn emission sensitivity to the interaction with adenine bases, a fluorescence technique was found to be effective in the detection of melting transitions. The attached Pzn substantially enhanced the thermal stability of complexes formed by (dT) 10 because of the intercalation mechanism, which increased the temperature of half-dissociation of the duplex by 10 -12°C and of the triplexes by ϳ13°C.…”

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confidence: 99%

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Anchorage of oligonucleotide hybridization by tethered phenazine nucleoside analogue

et al. 2003

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UV absorption and fluorescence techniques with a thermal denaturation procedure were used in studies of the anchorage of an oligonucleotide hybridization by a covalently tethered nucleoside analogue of an intercalating imidazophenazine derivative (Pzn). The formation by the (dT)(10)Pzn conjugate of the duplex complex with (dA)(15) and the triplex complex with (dA)(15) or poly(dA).poly(dT) was studied in buffered solutions with 0.11 and/or 1M sodium ions at the oligomer strand concentration of 10 microM. Because of the Pzn emission sensitivity to the interaction with adenine bases, a fluorescence technique was found to be effective in the detection of melting transitions. The attached Pzn substantially enhanced the thermal stability of complexes formed by (dT)(10) because of the intercalation mechanism, which increased the temperature of half-dissociation of the duplex by 10-12 degrees C and of the triplexes by approximately 13 degrees C. With the assumption of a two-state model of transition, the thermodynamic parameters for duplex formations were derived. The investigated variant of conjugation has a certain advantage over the widely used attachment via a flexible linker, consisting of a predetermined location of the Pzn chromophore in target sequences that makes it useful as a fluorescent reporter of the hybridization correctness. Molecular modeling was used to construct the geometries of the intercalation sites that turned out to be in conformity with the behavior of the Pzn fluorescence.

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“…Oligodeoxynucleotides [(dT) 10 and (dA) 15 ] were synthesized according to the standard H-phosphonate procedure. 21 The decathymidylatePzn ribonucleoside conjugate [(dT) 10 Pzn, Fig.…”

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

mentioning

confidence: 99%

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Anchorage of oligonucleotide hybridization by tethered phenazine nucleoside analogue

et al. 2003

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High-capacity and high-intensity DNA microarray spots using oxygen-plasma nanotextured polystyrene slides

et al. 2012

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Commercially available polystyrene (PS) slides were plasma nanotextured (nano-roughened) through treatment in oxygen plasma discharges to create substrates with increased surface area for microarray applications. Conditions of plasma treatment were determined for maximum and uniform oligonucleotide immobilization on these nanotextured PS slides. Oligonucleotides were immobilized onto the surface in the form of biotinylated oligonucleotide/streptavidin conjugates to take advantage of increased protein binding capacity of the substrate. It was found that the amount of oligonucleotides that could be immobilized was increased up to ten times on plasma treated as compared with untreated slides. The sensitivity of detection of labelled hybridized probes was improved by a factor of 20. Optimized nanotextured PS slides were subsequently used to develop a microarray for the detection of three deleterious BRCA1 gene mutations by immobilizing oligonucleotides corresponding to wild and mutant-type sequences. The microarray developed on the nanotextured PS slides provided higher specific hybridization signal and discrimination ratios as compared with flat untreated PS slides.

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Selectivity of a bromoacridine-containing fluorophore for triplex DNA

Sharma

Fraser

2021

Monatsh Chem

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Fluorophore 1,8-naphthilamide was linked to 2-bromoacridine through an ethylenediamine spacer using a succinct synthetic route to give a bromoacridine-linked, bifunctional fluorophore conjugate for the detection of triplex DNA. Acridine is well known to intercalate into duplex DNA whereas introduction of a bulky bromine atom at position C2 redirects specificity for triplex over duplex DNA. In this work, photoelectron transfer assay was used to demonstrate that the synthesised 2-bromoacridine-linked fluorophore conjugate had good selectivity for the representative triplex DNA target sequence d(T*A.T)20 compared with double-stranded d(T.A)20, single-stranded dT20 or d(G/A)19 DNA sequences. Graphic abstract

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DNA triple helix stabilisation by covalent attachment of a triplex-specific ligand

Cited by 14 publications

References 29 publications

Anchorage of oligonucleotide hybridization by tethered phenazine nucleoside analogue

Anchorage of oligonucleotide hybridization by tethered phenazine nucleoside analogue

High-capacity and high-intensity DNA microarray spots using oxygen-plasma nanotextured polystyrene slides

Selectivity of a bromoacridine-containing fluorophore for triplex DNA

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