Triplex formation involving 2',4'-BNA with 2-pyridone base analogue: efficient and selective recognition of C:G interruption.
We examined the thermodynamic properties of 2',4'-bridged nucleic acid containing 2-pyridone as a nucleobase (PB) to recognize a C interruption in the homopurine strand of the target duplex for pyrimidine motif triplex formation at neutral pH. The triplex formation involving triplex-forming oligonucleotide with PB is highly sequence-selective to specifically recognize C:G target base pair rather than the other G:C, T:A, or A:T base pairs. PB.C:G triad gives significantly larger binding constant than T.C:G triad, which has been known to be the most stable combination in natural base.C:G triad. Our results certainly support the idea that PB could be a key nucleoside to recognize a C interruption in the homopurine strand of the target duplex with high binding affinity and selectivity, and reduce the restriction of target sequences for triplex formation.
Torigoe
H
H
Institute of Physical and Chemical Research (RIKEN), 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan.
Hari
Y
Y
Obika
S
S
Imanishi
T
T
D020029:Base Pairing; D001483:Base Sequence; D003596:Cytosine / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D006147:Guanine / Q000737:chemistry; D011728:Pyridones / Q000737:chemistry*; D011742:Pyrimidine Nucleotides / Q000737:chemistry; D013816:Thermodynamics
D011728:Pyridones; D011742:Pyrimidine Nucleotides; C051802:triplex DNA; D006147:Guanine; C017679:2-hydroxypyridine; D003596:Cytosine; D004247:DNA