• The Transactions of the Korean Institute of Electrical Engineers C
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• v.51 no.6
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• pp.265-270
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• 2002

The determination of DNA hybridization reaction can apply the molecular biology research, clinic diagnostics, bioengineering, environment monitoring, food science and application area. So, the improvement of DNA hybridization detection method is very important for the determination of this hybridization reaction. Several molecular biological techniques require accurate predictions of matched versus mismatched hybridization thermodynamics, such as PCR, sequencing by hybridization, gene diagnostics and antisense oligonucleotide probes. In addition, recent developments of oligonucleotide chip arrays as means for biochemical assays and DNA sequencing requires accurate knowledge of hybridization thermodynamics and population ratios at matched and mismatched target sites. In this study, we report the characteristics of the probe and matched, mismatched target oligonucleotide hybridization reaction using thermodynamic method. Thermodynamic of 5 oligonucleotides with central and terminal mismatch sequences were obtained by measured UV-absorbance as a function of temperature. The data show that the nearest-neighbor base-pair model is adequate for predicting thermodynamics of oligonucleotides with average deviations for $\Delta$H$^{0}$ , $\Delta$S$^{0}$ , $\Delta$G$_{37}$ $^{0}$ and T$_{m}$, respectively.>$^{0}$ and T$_{m}$, respectively.

• The Journal of the Convergence on Culture Technology
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• v.5 no.3
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• pp.339-344
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• 2019

Global sequence alignment in search of similarity or homology favors larger size of the sequence because it keeps looking for more similar section between two sequences in the hope that it adds up scores for matched part in the rest of the sequence. If a substantial size of mismatched section exists in the middle of the sequence, it greatly reduces the total alignment score. In this case a whole sequence would be better to be divided into multiple sections. Overall alignment score over the multiple sections of the sequence would increase as compared to global alignment. This method is called multiple local alignment. In this paper, we implement a multiple local alignment algorithm, an extension of Smith-Waterman algorithm and show the experimental results for the algorithm that is able to search for sub-optimal sequence.

• Bulletin of the Korean Chemical Society
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• v.32 no.9
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• pp.3223-3228
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• 2011

To quantify the presence of mercuric ions in aqueous solution, double-stranded DNA (dsDNA) of poly(dT) was employed using a light switch compound, $Ru(phen)_2(dppz)^{2+}$ (1) which is reported to intercalate into dsDNA of a right-handed B-form. Addition of mercuric ions induced the dehybridization of poly(dT)${\cdot}$poly(dA) duplexes to form a hairpin structure of poly(dT) at room temperature and the metal-to-ligand charge transfer emission derived from the intercalation of 1 was reduced due to the dehybridization of dsDNA. As the concentration of $Hg^{2+}$ was increased, the emission of 1 progressively decreased. This label-free emission method had a detection limit of 0.2 nM. Other metal ions, such as $K^+$, $Ag^+$, $Ca^{2+}$, $Mg^{2+}$, $Zn^{2+}$, $Mn^{2+}$, $Co^{2+}$, $Ni^{2+}$, $Cu^{2+}$, $Cd^{2+}$, $Cr^{3+}$, $Fe^{3+}$, had no significant effect on reducing emission. This emission method can differentiate matched and mismatched poly(dT) sequences based on the emission intensity of dsDNA.