A New Strategy of Discrimination of a Point Mutation by Tandem of Short Oligonucleotides

Abstract

A new strategy based on the use of cooperative tandems of short oligonucleotide derivatives (TSOD) has been proposed to discriminate a "right" DNA target from a target containing a single nucleotide discrepancy. Modification of a DNA target by oligodeoxyribonucleotide reagents was used to characterize their interaction in the perfect and mismatched complexes. It is possible to detect any nucleotide changes in the binding sites of the target with the short oligonucleotide reagent. In the presence of flanking di-3',5'-N-(2-hydroxyethyl)phenazinium derivatives of short oligonucleotides (effectors) the tetranucleotide alkylating reagent modifies DNA target efficiently and site-specifically only in the perfect complex and practically does not modify it in the mismatched complex. It has been shown that TSOD is much more sensitive tool for the detection of a point mutation in DNA as compared to a longer oligonucleotides.

OWL2: a molecular beacon-based nanostructure for highly selective detection of single-nucleotide variations in folded nucleic acids

“…Previous studies have shown that the stability of multistranded DNA complexes are affected by the distance between adjacent DNA strands hybridized to a complementary nucleic acid. [38][39][40] Therefore, we introduced a single nucleotide gap between the P-strand and T4-arm. The introduced gap did not significantly affect the S/B or DF of the optimal sensor containing P 9 8 (Fig.…”

Analytical consideration of the selectivity of oligonucleotide hybridization

“…Selectivity is also affected by the difference in kinetics of complex formation for complementary and mismatched duplexes [13][14][15][16]. Additionally, changing the probe length [17] or using tandem short probes [18][19][20][21] has been shown to influence selectivity. Another strategy involves the use of nanoparticles bearing immobilized oligonucleotide probes [22][23][24].…”

Tandem Oligonucleotide Synthesis on Solid-Phase Supports for the Production of Multiple Oligonucleotides

“…Additionally, other applications that utilize multiple oligonucleotides are being developed. For example, cooperative base stacking between immediately adjacent hybridization probes has been used to enhance discrimination of single-base mismatches or assist in oligonucleotide capture. − Helper oligonucleotides increase probe signals in fluorescent in-situ hybridization assays (FISH) by opening inaccessible rRNA regions and bridge oligonucleotides are required for chain reaction cloning (CRC) . Multiplexed primer sets for simultaneous forward and reverse DNA sequencing, , positional sequencing by hybridization, multiple PCR, PCR−SSCP, − and RAPD − analysis are also used.…”