Investigation of kinetics and thermodynamics of DNA hybridization by means of 2-D fluorescence spectroscopy and soft/hard modeling techniques

Analytica Chimica Acta
Sara Ebrahimi, Mohsen Kompany-Zareh

Abstract

Reversible hybridization reaction plays a key role in fundamental biological processes, in many laboratory techniques, and also in DNA based sensing devices. Comprehensive investigation of this process is, therefore, essential for the development of more sophisticated applications. Kinetics and thermodynamics of the hybridization reaction, as a second order process, are systematically investigated with the aid of the soft and hard chemometric methods. Labeling two complementary 21 mer DNA single strands with FAM and Texas red fluorophores, enabled recording of the florescence excitation-emission matrices during the experiments which led to three-way data sets. The presence of fluorescence resonance energy transfer in excitation and emission modes and the closure in concentration mode, made the three-way data arrays rank deficient. To acquire primary chemical information, restricted Tucker3 as a soft method was employed. Herein a model-based method, hard restricted trilinear decomposition, is introduced for in depth analysis of rank deficient three-way data sets. By employing proposed hard method, the nonlinear model parameters as well as the correct profiles could be estimated. In addition, a simple constraint is presented to e...Continue Reading

References

Dec 1, 1988·Proceedings of the National Academy of Sciences of the United States of America·R A CardulloD E Wolf
Dec 31, 1995·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·M GotohM Tosu
Feb 16, 2002·Methods : a Companion to Methods in Enzymology·C T WittwerK S Elenitoba-Johnson
Jan 12, 2005·Angewandte Chemie·Razvan Nutiu, Yingfu Li
Sep 15, 2005·Journal of the American Chemical Society·Abigail K R Lytton-Jean, Chad A Mirkin
Jul 11, 2006·Nucleic Acids Research·Yang GaoRosina M Georgiadis
Apr 14, 2007·Nucleic Acids Research·Chunlai ChenXin Sheng Zhao
Feb 6, 2008·Journal of the American Chemical Society·Na Li, Chih-Ming Ho
Oct 22, 2008·Analytical Biochemistry·Ying-Ja Chen, Xiaohua Huang
Apr 22, 2009·Nucleic Acids Research·Chunlai ChenXin Sheng Zhao
Dec 19, 2009·Proceedings of the National Academy of Sciences of the United States of America·Ingmar SchoenDieter Braun
Jan 28, 2011·Journal of the American Chemical Society·Anthony J GenotAndrew J Turberfield
Mar 9, 2011·Biopolymers·Yong YouRichard Owczarzy
Jul 12, 2012·Analytical Chemistry·Yousef AkhlaghiMohammad Reza Hormozi-Nezhad
Jan 30, 2013·Biochemistry·Brittany RauzanAlice A Deckert
Aug 13, 2013·Nucleic Acids Research·Thomas E OuldridgeArd A Louis
Sep 30, 2014·ACS Nano·Sara EbrahimiAsmund Rinnan

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Citations

Sep 2, 2017·Integrative Biology : Quantitative Biosciences From Nano to Macro·Lang-Hong WangCharles S Brennan
Oct 11, 2020·Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy·Mehri RazaviMaryam Khoshkam

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