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Title: Power of surface-based DNA computation

Abstract

A new model of DNA computation that is based on surface chemistry is studied. Such computations involve the manipulation of DNA strands that are immobilized on a surface, rather than in solution as in the work of Adleman. Surface-based chemistry has been a critical technology in many recent advances in biochemistry and offers several advantages over solution-based chemistry, including simplified handling of samples and elimination of loss of strands, which reduce error in the computation. The main contribution of this paper is in showing that in principle, surface-based DNA chemistry can efficiently support general circuit computation on many inputs in parallel. To do this, an abstract model of computation that allows parallel manipulation of binary inputs is described. It is then shown that this model can be implemented by encoding inputs as DNA strands and repeatedly modifying the strands in parallel on a surface, using the chemical processes of hybridization, exonuclease degradation, polymerase extension, and ligation. Thirdly, it is shown that the model supports efficient circuit simulation in the following sense: exactly those inputs that satisfy a circuit can be isolated and the number of parallel operations needed to do this is proportional to the size of the circuit. Finally,more » results are presented on the power of the model when another resource of DNA computation is limited, namely strand length. 12 refs.« less

Authors:
; ;  [1]
  1. Univ. of Wisconsin, Madison, WI (United States) [and others
Publication Date:
Research Org.:
Association for Computing Machinery, New York, NY (United States); Sloan (Alfred P.) Foundation, New York, NY (United States)
OSTI Identifier:
548997
Report Number(s):
CONF-970137-
TRN: 97:005298-0009
Resource Type:
Conference
Resource Relation:
Conference: RECOMB `97: 1. annual conference on research in computational molecular biology, Santa Fe, NM (United States), 20-22 Jan 1997; Other Information: PBD: 1997; Related Information: Is Part Of RECOMB 97. Proceedings of the first annual international conference on computational molecular biology; PB: 370 p.
Country of Publication:
United States
Language:
English
Subject:
55 BIOLOGY AND MEDICINE, BASIC STUDIES; 99 MATHEMATICS, COMPUTERS, INFORMATION SCIENCE, MANAGEMENT, LAW, MISCELLANEOUS; DNA; BIOCHEMISTRY; DNA HYBRIDIZATION; MOLECULAR STRUCTURE; SOLIDIFICATION; DNA SEQUENCING; ALGORITHMS; ERRORS; COMPUTERIZED SIMULATION; COMPUTER CODES; MATHEMATICAL MODELS; MOLECULAR BIOLOGY; SURFACE PROPERTIES; OLIGONUCLEOTIDES

Citation Formats

Cai, Weiping, Condon, A.E., and Corn, R.M. Power of surface-based DNA computation. United States: N. p., 1997. Web.
Cai, Weiping, Condon, A.E., & Corn, R.M. Power of surface-based DNA computation. United States.
Cai, Weiping, Condon, A.E., and Corn, R.M. 1997. "Power of surface-based DNA computation". United States. doi:.
@article{osti_548997,
title = {Power of surface-based DNA computation},
author = {Cai, Weiping and Condon, A.E. and Corn, R.M.},
abstractNote = {A new model of DNA computation that is based on surface chemistry is studied. Such computations involve the manipulation of DNA strands that are immobilized on a surface, rather than in solution as in the work of Adleman. Surface-based chemistry has been a critical technology in many recent advances in biochemistry and offers several advantages over solution-based chemistry, including simplified handling of samples and elimination of loss of strands, which reduce error in the computation. The main contribution of this paper is in showing that in principle, surface-based DNA chemistry can efficiently support general circuit computation on many inputs in parallel. To do this, an abstract model of computation that allows parallel manipulation of binary inputs is described. It is then shown that this model can be implemented by encoding inputs as DNA strands and repeatedly modifying the strands in parallel on a surface, using the chemical processes of hybridization, exonuclease degradation, polymerase extension, and ligation. Thirdly, it is shown that the model supports efficient circuit simulation in the following sense: exactly those inputs that satisfy a circuit can be isolated and the number of parallel operations needed to do this is proportional to the size of the circuit. Finally, results are presented on the power of the model when another resource of DNA computation is limited, namely strand length. 12 refs.},
doi = {},
journal = {},
number = ,
volume = ,
place = {United States},
year = 1997,
month =
}

Conference:
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