Predicting the UV Spectrum of Oligodeoxynucleotide by 2D-Matlab

Abstract:

A 2D-Matlab model was developed to predict the UV absorbance spectra and thus concentration of oligodeoxynucleotide samples. This model will be valuable for researchers designing experiments involving oligodeoxynucleotides. Initial data was acquired from UV absorbance spectra of oligodeoxynucleotides 23, 24 and 34 bases long. The model, which would predict the concentration of DNA from the R₂₆₀ value, is shown to predict absorbance spectra and the extinction coefficient of DNA as shown when compared across a range of concentrations.

• Periodical: Applied Mechanics and Materials (Volume 866)
• Pages: 37-40
• DOI: https://doi.org/10.4028/www.scientific.net/AMM.866.37
• Online since: June 2017
• Authors: Naphat Albutt*, Suejit Pechprasarn
• Keywords: DNA Prediction, Oligodeoxynucleotide, Uv Spectrum

References

[1] C.R. Cantor, M.M. Warshaw, H. Shapiro, Oligonucleotide interaction. III. Circular dichroism studies of the conformation of deoxyoligonucleotides, Biopolymers. 9 (1970) 1059-1077.

DOI: 10.1002/bip.1970.360090909

[2] G. Felsenfeld, S.Z. Hirschman, A neighbor-interaction analysis of the hypochromism and spectra of DNA, J. Mol. Biol. 13 (1965) 407-427.

DOI: 10.1016/s0022-2836(65)80106-1

[3] C. Qiao, S. Bi, Y. Sun, D. Song, H. Zhang, W. Zhou, Study of interactions of anthraquinones with DNA using ethidium bromide as a fluorescence probe, Spectrochimica Acta Part A. 70 (2008) 136-143.

DOI: 10.1016/j.saa.2007.07.038

[4] R. Langer, Perspective: Drug delivery-drugs on target, Science 293 (2001) 58-59.

[5] E.H. Weyand, Y. Wu, S. Patel, B.B. Taylor, D.M. Mauro, Urinary excretion and DNA binding of coal tar components in B6C3F1 mice following ingestion, Chem. Res. Toxicol. 4 (1991) 466-473.

DOI: 10.1021/tx00022a011

[6] M.P. Singh, T. Joseph, S. Kumar, Y. Bathini, J.W. Lown, Synthesis and sequence-specific DNA binding of a topoisomerase inhibitory analog of Hoechst 33258 designed for altered base and sequence recognition, Chem Res Toxicol. 5 (1992) 597-607.

DOI: 10.1021/tx00029a003

[7] S.O. Kelle, G. Orellana, J.K. Barton, Luminescence quenching by DNA-bound viologens: effect of reactant identity on efficiency and dynamics of electron transfer in DNA, J. Photochem Photobiol B, 58 (2000) 72-79.

DOI: 10.1016/s1011-1344(00)00106-8

[8] D.L. Stout, F.F. Becker, Fluorometric quantitation of single-stranded DNA: A method applicable to the technique of alkaline elution, Anal. Biochem. 127 (1982) 302-307.

DOI: 10.1016/0003-2697(82)90177-4

[9] G. Kallansrud, B. Ward, A comparison of measured and calculated single- and double- stranded oligodeoxynucleotide extinction coefficients, Anal. Biochem. 236 (1996) 134-138.

DOI: 10.1006/abio.1996.0141

[10] G.A. Daxhelet, M.M. Coene, P.P. Hoet, C.G. Cocito, Spectrofluorometry of dyes with DNAs of different base composition and conformation, Anal. Biochem. 179 (1989) 401-403.

DOI: 10.1016/0003-2697(89)90152-8

[11] J. -B. Le Pecq, Use of ethidium bromide for separation and nucleic acids of various conformational forms and measurement of their associated enzymes. In methods of biochemical analysis, John Wiley & Sons, New York, 20 (1971) 41-86.

DOI: 10.1002/9780470110393.ch2

[12] R.B. Wallace, C.G. Miyada, Oligonuclotide probes for the screening of recombinant DNA libraries. In methods of enzymology, Academic Press, San Diego, 152 (1987) 432-442.

DOI: 10.1016/0076-6879(87)52050-x