Abstract
In the universal DNA chip method, target RNAs are mapped onto a set of DNA tags. Parallel hybridization of these tags with an indexed, complementary antitag array then provides an estimate of the relative RNA concentrations in the original solution. Although both error estimation and error reduction are important to process application, a physical model of hybridization fidelity for the TAT system has yet to be proposed. In this work, an equilibrium chemistry model of TAT hybridation is used to estimate the error probability per hybridized tag (ε). The temperature dependence of ε is then discussed in detail, and compared with the predictions of the stringency picture. In combination with a modified statistical zipper model of duplex formation, implemented by the Mjolnir software package, ε is applied to investigate the error behavior of small to moderate sized TAT sets. In the first simulation, the fidelities of (1) 105 random encodings, (2) a recently reported Hamming encoding, and (3) an ε-based, evolved encoding of a 32-strand, length-16 TAT system are estimated, and discussed in detail. In the second simulation, the scaling behavior of the mean error rate of random TAT encodings is investigated. Results are used to discuss the ability of a random strategy to generate high fidelity TAT sets, as a function of set size and encoding length.
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References
D. Lockhart and E. Winzeler, “Genomics, gene expression, and DNA arrays,” Nature 405, 827–836, 2000.
A. Suyama, et al., “Gene Expression Analysis by DNA Computing,” In S. Miyano, et al., editors, Currents in Computational Molecular Biology, (Univeral Academy Press, Tokyo, 2000), 12.
A. BenDor, et al., “Universal DNA Tag Systems: A Combinatorial Scheme,” J. Comput. Biol. 7, 503 (2000).
R. Deaton, et al., “Reliability and Efficiency of a DNA-Based Computation,” Phys. Rev. Lett. 80, 417 (1998).
Q. Liu, et al., “Progress toward demonstration of a surface based DNA computation: a one word approach to solve a model satisfiability problem,” Biosystems 52, 25 (1999).
Q. Liu, et al., “DNA Computing on Surfaces,” Nature 403, 175 (2000).
H. Yoshida and A. Suyama, “Solution to 3-SAT by Breadth-First Search,” in DNA Based Computers V, E. Winfree and D. Gifford eds., (American Mathematical Society, 2000), 9.
P. von Hippel and O. Berg, “On the specificity of DNA-protein interaction,” Proc. Natl. Acad. Sci. USA 83, 1608 (1986).
B. Eaton, et al., “Let’s get specific: the relationship between specificity and affinity,” Chemistry and Biology 2, 635 (1995).
J. Rose, et al. 1999, “A Statistical Mechanical Treatment of Error in the Annealing Biostep of DNA Computation,” in W. Banzhaf, et al., eds., Proceedings of the Genetic and Evolutionary Computation Conference, Volume 2, (Morgan Kauffman, San Francisco, 1999), 1829.
J. Rose and R. Deaton, “The Fidelity of Annealing-Ligation: A Theoretical Analysis,” in DNA Based Computers, A. Condon and G. Rozenberg, eds., (Springer, Berlin, 2001), 231.
M. Zuker, “The Use of Dynamic Programming Algorithms in RNA Secondary Structure Prediction,” in Mathematical Methods for DNA Sequences, M. Waterman, ed., (CRC Press, Boca Raton, 1989), 159.
A. Suyama, “RNA secondary structure and its relation to biological functions”, in Proceedings of the 10th Taniguchi International Symposium, A. Wada ed., (Taniguchi Foundation, Kyoto, 1984), 162.
M. Zuker, D. Mathews, and D. Turner, “Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide,” in RNA Biochemistry and Biotechnology, J. Barciszewski and B. Clark, eds., (NATO ASI Series, Klewer Academic Publishers, 1999).
J. SantaLucia, Jr., “A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics,” Biochemistry 35, 3555 (1998).
R. Wartell and A. Benight, “Thermal Denaturation of DNA Molecules: A Comparison of Theory and Experiment,” PHYSICS REPORTS (Review Section of Physics Letters) 126, 67 (1985).
G. Steger, “Thermal denaturation of double-stranded nucleic acids: prediction of temperatures critical for gradient gel electrophoresis and polymerase chain reaction,” Nuc. Acids Res. 22, 2760 (1994).
R. Blake et al., “Statistical Mechanical Simulation of Polymeric DNA melting with MELTSIM,” Bioinformatics 15, 370 (1999).
A. Hartemink and D. Gifford, “Thermodynamic Simulation of Deoxyribonucleotide Hybridization for DNA Computation,” DNA Based Computers III, edited by H. Rubin and D. Wood, (American Mathematical Society, Providence, RI, 1999), 25.
A. Hartemink, D. Gifford, and J. Khodor, “Automated Constraint-Based Nucleotide Sequence Selection for DNA Computation,” Biosystems 52, 227 (1999).
A. Benight, R. Wartell, and D. Howell, “Theory Agrees with Experimental Thermal Denaturation of Short DNA Restriction Fragments,” Nature 289, 15 (1981).
D. Lando and A. Fridman, “Role of Small Loops in DNA Melting,” Biopolymers 58, 374 (2001).
N. Peyret, et al., “Nearest-Neighbor Thermodynamics and NMR of DNA Sequences with Internal A:A, C:C, G:G, and T:T Mismatches,” Biochemistry 38, 3468 (1999).
S-H Ke and R. Wartell, “The thermal stability of DNA fragments with tandem mismatches at a d(CXYG)/d(CY’X’G) site,” Nucleic Acids Research 24, 707 (1996).
J. Zhu and R. Wartell, “Influence of neighboring base pairs on the stability of single base bulges and base pairs in a DNA fragment,” Biochemistry 38, 15986 (1999).
M. Senior, et al., “Influence of Dangling Thymidine Residues on the Stability and Structure of Two DNA Duplexes,” Biochemistry 27, 3879 (1988).
A. Fotin, et al., “Parallel thermodynamic analysis of duplexes on oligodeoxyri-bonucleotide chips,” Nuc. Acids Res. 26, 1515 (1998).
G. E. P. Box and N. R. Draper, Empirical Model-Building and Response Surfaces, (Wiley, New York, 1987).
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Rose, J.A., Deaton, R.J., Hagiya, M., Suyama, A. (2002). The Fidelity of the Tag-Antitag System. In: Jonoska, N., Seeman, N.C. (eds) DNA Computing. DNA 2001. Lecture Notes in Computer Science, vol 2340. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-48017-X_13
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DOI: https://doi.org/10.1007/3-540-48017-X_13
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