NDLI: An Integrated Reaction-Transport Model for DNA Surface Hybridization: Implications for DNA Microarrays

Content Provider	Springer Nature Link
Author	Singh, Raghvendra Nitsche, Johannes Andreadis, Stelios T.
Copyright Year	2008
Abstract	DNA microarrays have the potential to revolutionize medical diagnostics and development of individualized medical treatments. However, accurate quantification of scantily expressed genes and precise measurement of small differences between different treatments is not currently feasible. A major challenge remains the understanding of physicochemical processes and rate-limiting steps of hybridization of complex mixtures of DNA targets on immobilized DNA probes. To this end, we developed a mathematical model to describe the effects of molecular orientation and transport on the kinetics and efficiency of hybridization. First, we calculated the hybridization rate constant based on the distance between the complementary nucleotides of the target and probe DNA. The surface reaction rate was then integrated with translational and rotational transport of target DNA to the surface to calculate the kinetics of hybridization. Our model predicts that hybridization of short DNA targets is diffusion limited but long targets are kinetically limited. In addition, for DNA targets with wide size distribution, it may be difficult to distinguish between specific binding of long targets from nonspecific binding of short ones. Our model provides novel insight into the process of DNA hybridization and suggests operating conditions to improve the sensitivity and accuracy of microarray experiments.
Starting Page	255
Ending Page	269
Page Count	15
File Format	PDF
ISSN	00906964
Journal	Annals of Biomedical Engineering
Volume Number	37
Issue Number	1
e-ISSN	15739686
Language	English
Publisher	Springer US
Publisher Date	2008-10-22
Publisher Place	Boston
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Reaction-diffusion model DNA Hybridization Nucleic acid Rotational diffusion Kinetics Biochemistry Mechanics Biophysics/Biomedical Physics Biomedical Engineering Biomedicine general
Content Type	Text
Resource Type	Article
Subject	Biomedical Engineering

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
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3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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