Selectivity and affinity of triplex-forming oligonucleotides containing 2'-aminoethoxy-5-(3-aminoprop-1-ynyl)uridine for recognizing AT base pairs in duplex DNA

Osborne, Sadie D.; Powers, Vicki E. C.; Rusling, David A.; Lack, Oliver; Fox, Keith R.; Brown, Tom

doi:10.1093/nar/gkh776

Cited by 42 publications

(49 citation statements)

References 38 publications

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“…1 H NMR spectra were recorded at 300 MHz or 400 MHz: δ in ppm relative to residual non-or partially deuterated solvent (CHCl 3 [28,29] To a solution of -ribose (1) (20 g, 133 mmol) in MeOH (400 mL) was added Dowex-50 (H + form, 10-20 % w/w) at 0°C. The mixture was stirred at 4°C overnight.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

2′‐O‐Aminoethyl Oligoribonucleotides Containing Novel Base Analogues: Synthesis and Triple‐Helix Formation At Pyrimidine/Purine Inversion Sites

Buchini¹,

Leumann²

2006

Eur J Org Chem

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The synthesis of a common sugar intermediate for the 2Ј-aminoethyl-ribonucleoside synthesis in 9 steps and an overall yield of 33 % starting from D-ribose is described. This intermediate was successfully used for the synthesis of the 2Ј-aminoethyl-ribonucleosides containing the bases thymine (t), 5-methylcytosine (c), 5-methyl-2-pyrimidinone (x), 2-aminopurine (ap) and guanine (g). These were subsequently transformed into the corresponding cyanoethyl phosphoramidite building blocks for oligonucleotide synthesis. 2Ј-Aminoethyl oligonucleotide 15-mers were prepared with a DNA synthesizer, and an optimized post-synthetic deprotection protocol has been developed which prevents cyanoethylation of the 2Ј-amino side chains during conventional ammonia deprotection. A series of fully modified, triplex forming 2Ј-aminoethyl oligoribonucleotides (2ЈAE-TFOs) were prepared in which x was designed to bind to CG inversion sites and ap as well as g to TA inversion sites on a double-helical DNA target. The affinity of x-CG base-triple formation in different

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Section: Discussionmentioning

confidence: 99%

“…H 2 SO 4 in MeOH according to known protocols [28,29] but was only obtained in poor yields (20-50 %). The use of a resin-bound acid (Dowex-50 H + ) in MeOH at 4°C overnight greatly enhanced the practicality of this reaction and lead to riboside 2 (predominantly the β anomer) in almost quantitative yield.…”

Section: Sugar Building Blockmentioning

confidence: 99%

2′‐O‐Aminoethyl Oligoribonucleotides Containing Novel Base Analogues: Synthesis and Triple‐Helix Formation At Pyrimidine/Purine Inversion Sites

Buchini¹,

Leumann²

2006

Eur J Org Chem

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“…An alternative less selective approach has been to use base analogues or linkers that skip or intercalate at such inversions (36–38). Attempts to increase the strength of binding of TFOs have included the addition of positively charged groups (39–42), increasing the base stacking (43,44) or changing the phosphodiester backbone (2). …”

Section: Introductionmentioning

confidence: 99%

“…We have, therefore, examined the ability of a TFO containing four different modified nucleosides (BAU, Me P, A PP and S; see Figure 1A) to selectively target a mixed sequence at physiological pHs. BAU forms a very stable triplet with AT (41,42); Me P has a p K a that is higher than cytosine and targets GC base pairs at higher pHs (14–16); S has been proposed for recognizing TA inversions (30,45), while A PP recognizes CG (46). …”

Section: Introductionmentioning

confidence: 99%

Four base recognition by triplex-forming oligonucleotides at physiological pH

Rusling

Powers²,

Ranasinghe³

et al. 2005

Nucleic Acids Research

133

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We have achieved recognition of all 4 bp by triple helix formation at physiological pH, using triplex-forming oligonucleotides that contain four different synthetic nucleotides. BAU [2′-aminoethoxy-5-(3-aminoprop-1-ynyl)uridine] recognizes AT base pairs with high affinity, MeP (3-methyl-2 aminopyridine) binds to GC at higher pHs than cytosine, while APP (6-(3-aminopropyl)-7-methyl-3H-pyrrolo[2,3-d]pyrimidin-2(7H)-one) and S [N-(4-(3-acetamidophenyl)thiazol-2-yl-acetamide)] bind to CG and TA base pairs, respectively. Fluorescence melting and DNase I footprinting demonstrate successful triplex formation at a 19mer oligopurine sequence that contains two CG and two TA interruptions. The complexes are pH dependent, but are still stable at pH 7.0. BAU, MeP and APP retain considerable selectivity, and single base pair changes opposite these residues cause a large reduction in affinity. In contrast, S is less selective and tolerates CG pairs as well as TA.

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“…Triplex melting curves are commonly used to assess the stabilising effects of nucleotide substitutions [16,19,23,[30][31][32][33][34][35]. Such modifications can produce complexes in which the triplex and duplex melts overlap, producing a single melting transition.…”

Section: Comparison Of Different Nucleoside Analogues On Intermoleculmentioning

confidence: 99%

The stability of triplex DNA is affected by the stability of the underlying duplex

Rusling

Rachwal

Brown

et al. 2009

Biophysical Chemistry

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International audienceWe have studied the formation of DNA triple helices in different sequence contexts and show that, for the most stable triplexes, their apparent stability is affected by the stability of the underlying duplex. For a 14-mer parallel triplex-forming oligonucleotide (generating C.GC and T.AT triplets) at pH 5.0 the is more than 10°C lower with an intermolecular 14-mer duplex target, than it is with an intramolecular duplex, or one which is flanked by 6 GC base pairs at either end. A similar effect is seen with triplex-forming oligonucleotides that contain stabilising analogues, for which the is higher for an intramolecular than an intermolecular duplex target. These results suggest that the use of simple intermolecular duplex targets may underestimate the triplex stabilisation that is produced by some nucleotide analogue

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Selectivity and affinity of triplex-forming oligonucleotides containing 2'-aminoethoxy-5-(3-aminoprop-1-ynyl)uridine for recognizing AT base pairs in duplex DNA

Cited by 42 publications

References 38 publications

2′‐O‐Aminoethyl Oligoribonucleotides Containing Novel Base Analogues: Synthesis and Triple‐Helix Formation At Pyrimidine/Purine Inversion Sites

2′‐O‐Aminoethyl Oligoribonucleotides Containing Novel Base Analogues: Synthesis and Triple‐Helix Formation At Pyrimidine/Purine Inversion Sites

Four base recognition by triplex-forming oligonucleotides at physiological pH

The stability of triplex DNA is affected by the stability of the underlying duplex

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