Conjugation of a 3-(1H-phenanthro[9,10-d]imidazol-2-yl)-1H-indole intercalator to a triplex oligonucleotide and to a three-way junction

A new intercalating nucleic acid monomer M comprising a 4-(1-indole)-butane-1,2-diol moiety was synthesized via a classical alkylation reaction of indole-3-carboxaldehyde followed by a condensation reaction with phenanthrene-9,10-dione in the presence of ammonium acetate to form a phenanthroimidazol...

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Bibliographic Details
Published in:Bioorganic & medicinal chemistry 2012-01, Vol.20 (1), p.207-214
Main Authors: Fatthalla, Maha I., Elkholy, Yehya M., Abbas, Nermeen S., Mandour, Adel H., Jørgensen, Per T., Bomholt, Niels, Pedersen, Erik B.
Format: Article
Language:English
Subjects:
alkylation
ammonium acetate
Biological and medical sciences
branching
condensation
DNA
DNA - chemistry
Fluorescence
hybridization
Imidazoles - chemistry
Indole
Indoles - chemistry
Intercalating Agents - chemical synthesis
Intercalating Agents - chemistry
Medical sciences
Models, Molecular
Molecular modeling
Nucleic Acid Denaturation
Nucleic Acid Hybridization
oligonucleotides
Oligonucleotides - chemistry
Pharmacology. Drug treatments
RNA
Thermal stability
Three-way junction
Triplex Forming Oligonucleotide
Ultraviolet Rays
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Summary:A new intercalating nucleic acid monomer M comprising a 4-(1-indole)-butane-1,2-diol moiety was synthesized via a classical alkylation reaction of indole-3-carboxaldehyde followed by a condensation reaction with phenanthrene-9,10-dione in the presence of ammonium acetate to form a phenanthroimidazole moiety linked to the indole ring. Insertion of the new intercalator as a bulge into a Triplex Forming Oligonucleotide resulted in good thermal stability of the corresponding Hoogsteen-type triplexes. Molecular modeling supports the possible intercalating ability of M. Hybridisation properties of DNA/DNA and RNA/DNA three-way junctions (TWJ) with M in the branching point were also evaluated by their thermal stability at pH 7. DNA/DNA TWJ showed increase in thermal stability compared to wild type oligonucleotides whereas this was not the case for RNA/DNA TWJ.
ISSN:0968-0896
1464-3391
DOI:10.1016/j.bmc.2011.11.013