ABSTRACT
In order to expand the target sequence used in triplex DNA formation, seven novel nucleotide analogues were synthesized and incorporated into triplex-forming oligonucleotides by post-elongation modification approaches. Among them, , equipped with a suitable restricted conformation of sugar and nucleobase moieties, was found to have the highest sequence-selectivity and affinity towards CG base pairs within double-stranded DNA.
Subject(s)
Base Pairing , DNA/chemistry , Guanidine/analogs & derivatives , Pyrrolidines/chemistry , Base SequenceABSTRACT
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
We succeeded in the synthesis of triplex-forming oligonucleotides (TFOs) that contain a deoxyribonucleotide (Py) bearing a 2-pyridine nucleobase or the 2',4'-BNA congener (Py(B)). By UV melting experiments, it was found that 2-pyridine was a very promising nucleobase for the sequence-selective recognition of a CG base pair within double-stranded DNA (dsDNA) in a parallel motif triplex. Moreover, Py(B) in TFOs showed stronger affinity to a CG base pair than Py with further increase in the selectivity. Using TFO including multiple Py(B) units, triplex formation with dsDNA containing three CG base pairs was observed.
