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Solutions of SAT Problems Solved by a SPR-Based DNA Processor

[+] Author Affiliations
Tsung-Yao Chang, Chii-Wann Lin

National Taiwan University, Taipei, Taiwan

Paper No. MNHT2008-52036, pp. 1179-1184; 6 pages
doi:10.1115/MNHT2008-52036
From:
  • ASME 2008 First International Conference on Micro/Nanoscale Heat Transfer
  • ASME 2008 First International Conference on Micro/Nanoscale Heat Transfer, Parts A and B
  • Tainan, Taiwan, June 6–9, 2008
  • Conference Sponsors: Nanotechnology Institute
  • ISBN: 0-7918-4292-4 | eISBN: 0-7918-3813-7
  • Copyright © 2007 by ASME

abstract

DNA computation has shown its potential not only on mathematics, but on various practical areas such as diagnosis, single nucleotide polymorphism (SNP) detection, smart amplification, encryption and drug delivery etc. However, most previous researches about DNA computation possess a couple of weaknesses, including time-wasting, effort-wasting, lack of reusability and no miniaturization. In order to address this issue and improve weaknesses mentioned above, we built up a surface plasmon resonance (SPR) system for the detection on the DNA array chip to solve a 3-clause satisfiability (SAT) problem with 3 variables x, y and z. Every variable is defined as a 15-nt single strand DNA (ssDNA) which is immobilized on one spot of the gold surface. We further define SPR reflective intensity changes 0, 0.2 and 2 A.U. caused by changes of molecular weight on surface as Boolean signals False, True and None, respectively. Moreover, False signal represents a positive hybridization reaction via the hydrogen bond that binds the complementary ssDNA conjugating to IgG (150 kDa) by the crosslinker Sulfo-SMPB which can links thiol group labeled on ssDNA and amine group existed on IgG; True signal represents the hybridization reaction that binds the complementary ssDNA-IgG-Antigen which can result in a much larger intensity change. For a SAT problem F = (XT ∪ YF )∩(XF ∪ ZT )∩(YT ∪ ZT ), there are 8 possible answers. Therefore, we established a 3-spot array as a set which is immobilized sequence x, y and z. After one calculation, we read out the solution of this set and then regenerate it by injecting 0.05 N sodium hydroxide solution. In this work, we used 200 ng/ml Xc -Human IgG, Yc -Rabbit IgG and Zc -Goat IgG as reaction agents for hybridization which represent False signal. Furthermore, 100 ng/ml Anti-Human IgG, Rabbit IgG and Goat IgG were taken as True signal agents. A full reaction can be completed within 30 minutes at room temperature. The buffer in the study is 1 x phosphate buffered solution (PBS) with 100 mM sodium chloride. The proposed platform has improved drawbacks that occurred in previous researches about DNA computer. Besides, it is provided with abilities a processor should have which are recalculable and realtime measurement so that provides us a novel approach for addressable and reusable diagnosis.

Copyright © 2007 by ASME
Topics: DNA

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