ABSTRACT
Phosphoramidites containing 2-propynyloxy or 1-butyn-4-yl as nucleobase precursors were synthesized and introduced into oligonucleotides using an automated DNA synthesizer. Copper-catalyzed alkyne-azide 1,3-dipolar cycloaddition of the oligonucleotides with various azides gave the corresponding triazolylated oligonucleotides, triplex-forming ability of these synthetic oligonucleotides with double-stranded DNA targets was evaluated by UV melting experiments. It was found that nucleobases containing 2-(1-m-carbonylaminophenyl-1,2,3-triazol-4-yl)ethyl units likely interacted with A of a TA base pair in a parallel triplex DNA.
Subject(s)
DNA/chemistry , Nucleosides/chemistry , Oligonucleotides/chemistry , Triazoles/chemistry , Base Pairing , Catalysis , Copper/chemistry , Cycloaddition Reaction , Nucleosides/chemical synthesis , Oligonucleotides/chemical synthesis , Phase Transition , Transition Temperature , Ultraviolet RaysABSTRACT
In order to expand target sequences in triplex DNA formation, the development of a nucleobase that recognizes a CG base pair in dsDNA was attempted. A 4-[(3R,4R)-dihydroxypyrrolidino]pyrimidin-2-one nucleobase was found to recognize a CG base pair with high sequence-selectivity.
Subject(s)
Base Pairing , DNA/chemistry , Pyrimidinones/chemistry , Base Sequence , DNA/genetics , Nucleic Acid Denaturation , Oligodeoxyribonucleotides/chemical synthesis , Oligodeoxyribonucleotides/chemistry , Oligodeoxyribonucleotides/genetics , Substrate Specificity , Transition TemperatureABSTRACT
Using the copper(I)-catalyzed alkyne-azide 1,3-dipolar cycloaddition, a post-elongation modification of 1-ethynyl substituted nucleobases has been employed to construct 18 variations of oligonucleotides from a common oligonucleotide precursor. The triplex-forming ability of each oligonucleotide with dsDNA was evaluated by the UV melting experiment. It was found that triazole nucleobases generally tend to exhibit binding affinities in the following order: CG>TA>AT, GC base pairs. Among the triazole nucleobases examined, a 1-(4-ureidophenyl)triazole provided the best result with regard to affinity and selectivity for the CG base pair.
Subject(s)
DNA/chemistry , Oligonucleotides/chemistry , Oligonucleotides/chemical synthesis , Phenylurea Compounds/chemical synthesis , Triazoles/chemical synthesis , Azides/chemistry , Base Pairing , Drug Design , Heterocyclic Compounds , Phenylurea Compounds/chemistry , Triazoles/chemistryABSTRACT
A novel method for (18)F-radiolabeling of oligodeoxynucleotides (ODNs) by a Cu-catalyzed Huisgen reaction has been developed by using the lowest possible amount of the precursor biomolecule for the realization of stoichiometry-oriented PET (positron emission tomography) chemistry. Under the optimized cyclization conditions of p- or m-azido([(18)F]fluoromethyl)benzene and alkyne-substituted ODN (20nmol) at 40°C for 15min in the presence of CuSO(4), TBTA [tris((1-benzyl-1H-1,2,3-triazol-4-yl)methyl)amine], and sodium ascorbate (2:1:2), the synthesis of (18)F-labeled ODNs with sufficiently high radioactivities of 2.1-2.5GBq and specific radioactivities of 1800-2400GBq/µmol have been accomplished for use in animal and human PET studies.
Subject(s)
Benzene Derivatives/chemistry , Copper/chemistry , Fluorine Radioisotopes/chemistry , Oligodeoxyribonucleotides/chemistry , Animals , Catalysis , Chromatography, High Pressure Liquid , Humans , Male , Positron-Emission Tomography , Rats , Rats, Sprague-Dawley , Spectrometry, Mass, Matrix-Assisted Laser Desorption-IonizationABSTRACT
Oligonucleotides including C-nucleotides having 1-substitued 1H-1,2,3-triazoles as artificial nucleobases were conveniently synthesized by the post-elongation modification method using the copper(I)-catalyzed alkyne-azide 1,3-dipolar cycloaddition (CuAAC) reaction. The base-pairing properties of the triazole nucleobase analogs in forming duplexes with oligonucleotides were investigated by the T(m) experiments.
