Constructing Bio-molecular Databases on a DNA-based Computer

Codd [Codd 1970] wrote the first paper in which the model of a relational database was proposed. Adleman [Adleman 1994] wrote the first paper in which DNA strands in a test tube were used to solve an instance of the Hamiltonian path problem. From [Adleman 1994], it is obviously indicated that for storing information in molecules of DNA allows for an information density of approximately 1 bit per cubic nm (nanometer) and a dramatic improvement over existing storage media such as video tape which store information at a density of approximately 1 bit per 1012 cubic nanometers. This paper demonstrates that biological operations can be applied to construct bio-molecular databases where data records in relational tables are encoded as DNA strands. In order to achieve the goal, DNA algorithms are proposed to perform eight operations of relational algebra (calculus) on bio-molecular relational databases, which include Cartesian product, union, set difference, selection, projection, intersection, join and division. Furthermore, this work presents clear evidence of the ability of molecular computing to perform data retrieval operations on bio-molecular relational databases.

[1]  Michael Shan-Hui Ho.  Fast parallel molecular solutions for DNA-based supercomputing: the subset-product problem. , 2005, Bio Systems.

[2]  Minyi Guo,et al.  Fast parallel molecular solution to the dominating-set problem on massively parallel bio-computing , 2004, Parallel Comput..

[3]  M. Guo,et al.  Solving the set cover problem and the problem of exact cover by 3-sets in the Adleman-Lipton model. , 2003, Bio Systems.

[4]  Marc-Thorsten Hütt,et al.  Informational structure of two closely related eukaryotic genomes. , 2006, Physical review. E, Statistical, nonlinear, and soft matter physics.

[5]  L M Adleman,et al.  Molecular computation of solutions to combinatorial problems. , 1994, Science.

[6]  Gheorghe Paun,et al.  DNA Computing: New Computing Paradigms , 1998 .

[7]  Minyi Guo,et al.  Molecular solutions for the subset-sum problem on DNA-based supercomputing. , 2004, Bio Systems.

[8]  Minyi Guo,et al.  Towards solution of the set-splitting problem on gel-based DNA computing , 2004, Future Gener. Comput. Syst..

[9]  Abbas Nowzari-Dalini,et al.  DNA Simulation of Nand Boolean Circuits , 2004 .

[10]  H ReifJohn,et al.  Autonomous programmable biomolecular devices using self-assembled DNA nanostructures , 2007 .

[11]  Chung-Wei Yeh,et al.  Molecular solutions to the binary integer programming problem based on DNA computation. , 2006, Bio Systems.

[12]  Clifford R. Johnson,et al.  Solution of a 20-Variable 3-SAT Problem on a DNA Computer , 2002, Science.

[13]  F. Simmel,et al.  Single-pair FRET characterization of DNA tweezers. , 2006, Nano letters.

[14]  Jennifer Widom,et al.  A First Course in Database Systems , 1997 .

[15]  Weng-Long Chang.  Fast Parallel DNA-Based Algorithms for Molecular Computation: The Set-Partition Problem , 2007, IEEE Transactions on NanoBioscience.

[16]  Grzegorz Rozenberg,et al.  Cycles and communicating classes in membrane systems and molecular dynamics , 2007, Theor. Comput. Sci..

[17]  Minyi Guo,et al.  Is optimal solution of every NP-complete or NP-hard problem determined from its characteristic for DNA-based computing. , 2005, Bio Systems.

[18]  Erik Winfree,et al.  Thermodynamic Analysis of Interacting Nucleic Acid Strands , 2007, SIAM Rev..

[19]  J. Macdonald,et al.  Medium scale integration of molecular logic gates in an automaton. , 2006, Nano letters.

[20]  Gang Wu,et al.  Multiplying with DNA , 2006, Natural Computing.

[21]  Axel Ekani-Nkodo,et al.  Joining and scission in the self-assembly of nanotubes from DNA tiles. , 2004, Physical review letters.

[22]  Erik Winfree,et al.  On applying molecular computation to the data encryption standard , 1999, DNA Based Computers.

[23]  Minyi Guo,et al.  Fast parallel molecular algorithms for DNA-based computation: factoring integers , 2004, Proceedings. Fourth IEEE Symposium on Bioinformatics and Bioengineering.

[24]  Lila Kari,et al.  Bond-Free Languages: Formalizations, Maximality and Construction Methods , 2004, DNA.

[25]  Leonard M. Adleman,et al.  Solution of a Satisfiability Problem on a Gel-Based DNA Computer , 2000, DNA Computing.

[26]  F. E..  A Relational Model of Data Large Shared Data Banks , 2000 .

[27]  Dongmei Xiao,et al.  Solving maximum cut problems in the Adleman-Lipton model. , 2005, Bio Systems.

[28]  Lila Kari,et al.  Bond-Free Languages: Formalizations, Maximality and Construction Methods , 2004, DNA.

[29]  R J Lipton,et al.  DNA solution of hard computational problems. , 1995, Science.

[30]  Richard J. Lipton,et al.  Breaking DES using a molecular computer , 1995, DNA Based Computers.

[31]  John H. Reif,et al.  Autonomous programmable biomolecular devices using self-assembled DNA nanostructures , 2007, CACM.

[32]  Minyi Guo,et al.  Fast Parallel Solution for Set-Packing and Clique Problems by DNA-Based Computing , 2004, IEICE Trans. Inf. Syst..

[33]  F Guarnieri,et al.  Maya Blue Paint: An Ancient Nanostructured Material , 1996, Science.

[34]  Thomas Bäck,et al.  DNA computing of solutions to knapsack problems , 2007, Biosyst..