Quick, Selective and Reversible Photocrosslinking Reaction between 5-Methylcytosine and 3-Cyanovinylcarbazole in DNA Double Strand
Abstract
:1. Introduction
2. Results and Discussion
2.1. Reactivity and Selectivity of the Photocrosslinking Reaction to mC
2.2. Thermodynamics and Kinetics of the Hybridization between CNVK-ODN and ODN(mC)
2.3. Extinction Coefficient of CNVK in DNA Duplex
3. Experimental Section
3.1. Preparation of ODNs
3.2. Photoirradiation and UPLC Analysis
3.3. Enzymatic Digestion, HPLC and MALDI-TOF-MS Analysis
3.4. Thermodynamic and Kinetic Analysis of the Hybridization
4. Conclusions
Supplementary Information
ijms-14-05765-s001.pdfAcknowledgments
Conflict of Interest
References
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Duplex | T50 (s) | |
---|---|---|
Photocrosslinking | Photosplitting | |
CNVK-ODN/ODN(C) | 19.6 | 25.5 |
CNVK-ODN/ODN(mC) | 0.6 | 17.0 |
CNVK-ODN(A)/ODN(U) | 0.6 | - |
CNVK-ODN(A)/ODN(T) | 0.5 | - |
Duplex | ΔG°37 kcal/mol | ΔH° kcal/mol | ΔS° cal/mol K | TM °C |
---|---|---|---|---|
CNVK-ODN/ODN(C) | −7.7 | −49.8 | −135 | 37.9 ± 0.9 |
CNVK-ODN/ODN(mC) | −7.6 | −41.8 | −110 | 37.4 ± 0.7 |
Duplex | KD (μM) | ka (×103 s−1 M−1) | kd (s−1) |
---|---|---|---|
CNVK-ODN/ODN(C) | 2.4 ± 0.14 | 48 | 0.11 |
CNVK-ODN/ODN(mC) | 2.2 ± 0.05 | 52 | 0.11 |
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Fujimo, K.; Konishi-Hiratsuka, K.; Sakamoto, T. Quick, Selective and Reversible Photocrosslinking Reaction between 5-Methylcytosine and 3-Cyanovinylcarbazole in DNA Double Strand. Int. J. Mol. Sci. 2013, 14, 5765-5774. https://doi.org/10.3390/ijms14035765
Fujimo K, Konishi-Hiratsuka K, Sakamoto T. Quick, Selective and Reversible Photocrosslinking Reaction between 5-Methylcytosine and 3-Cyanovinylcarbazole in DNA Double Strand. International Journal of Molecular Sciences. 2013; 14(3):5765-5774. https://doi.org/10.3390/ijms14035765
Chicago/Turabian StyleFujimo, Kenzo, Kaoru Konishi-Hiratsuka, and Takashi Sakamoto. 2013. "Quick, Selective and Reversible Photocrosslinking Reaction between 5-Methylcytosine and 3-Cyanovinylcarbazole in DNA Double Strand" International Journal of Molecular Sciences 14, no. 3: 5765-5774. https://doi.org/10.3390/ijms14035765