Abstract
This chapter summarizes the efforts that have been made so far to build a huge memory using DNA molecules. These efforts are targeted at increasing the size of the address space of a molecular memory and making operations on a specified word in the address space more efficient and reliable. The former issue should be solved by careful design of the base sequences of the address portions. The latter issue depends on the architecture of a molecular memory and the available memory operations. Concrete examples of molecular memories described in this chapter are classified into in vitro DNA memory, DNA memory on surfaces, and in vivo DNA memory. This chapter also describes the technology for designing base sequences of DNA molecules.
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Aboul-ela F, Koh D, Tinoco I, Martin F (1985) Base-base mismatches. Thermodynamics of double helix formation for dCA3XA3G + dCT3YT3G (X, Y = A,C,G,T). Nucleic Acids Res 13:4811–4824
Adleman L (1994) Molecular computation of solutions to combinatorial problems. Science 266:1021–1024
Allawi H, SantaLucia J (1997) Thermodynamics and NMR of internal G.T mismatches in DNA. Biochemistry 36:10581–10594
Allawi H, SantaLucia J (1998a) Nearest-neighbor thermodynamics of internal A.C mismatches in DNA: sequence dependence and pH effects. Biochemistry 37:9435–9444
Allawi H, SantaLucia J (1998b) Thermodynamics of internal C.T mismatches in DNA. Nucleic Acids Res 26:2694–2701
Allawi H, SantaLucia J (1998c) Nearest neighbor thermodynamic parameters for internal G.A mismatches in DNA. Biochemistry 37:2170–2179
Andronescu M, Aguirre-Hernandez R, Condon AE, Hoos HH (2003) RNAsoft: a suite of RNA secondary structure prediction and design software tools. Nucleic Acids Res 31:3416–3422
Andronescu M, Fejes AP, Hutter F, Hoos HH, Condon AE (2004) A new algorithm for RNA secondary structure design. J Mol Biol 336:607–624
Arita M, Kobayashi S (2002) DNA sequence design using templates. New Gen Comput 20:263–277
Arita M, Ohashi Y (2004) Secret signatures inside genomic DNA. Biotechnol Prog 20:1605–1607
Arita M, Nishikawa A, Hagiya M, Komiya K, Gouzu H, Sakamoto K (2000) Improving sequence design for DNA computing. In Proceedings of the genetic and evolutionary computation conference (GECCO-2000) Orlando, pp 875–882
Bath J, Turberfield AJ (2007) DNA nanomachines. Nat Nanotechnol 2:275–284
Baum EB (1995) Building an associative memory vastly larger than the brain. Science 268:583–585
Benenson Y, Gil B, Ben-Dor U, Adar R, Shapiro E (2004) An autonomous molecular computer for logical control of gene expression. Nature 429:423–429
Bommarito S, Peyret N, SantaLucia J (2000) Thermodynamic parameters for DNA sequences with dangling ends. Nucleic Acids Res 28:1929–1934
Borer P, Dengler B, Tinoco I, Uhlenbeck O (1974) Stability of ribonucleic acid double-stranded helices. J Mol Biol 86:843–853
Braich RS, Chelyapov N, Johnson C, Rothemund PWK, Adleman L (2002) Solution of a 20-variable 3-SAT problem on a DNA computer. Science 296:499–502
Braich RS, Johnson C, Rothemund PWK, Hwang D, Chelyapov N, Adleman L (2000) Solution of a satisfiability problem on a gel-based DNA computer. Proceedings of the 6th International Workshop on DNA-Based Computers, LNCS 2054: Berlin, pp 27–42
Brenneman A, Condon AE (2002) Strand design for bio-molecular computation. Theor Comput Sci 287:39–58
Clelland CT, Risca V, Bancroft C (1999) Hiding messages in DNA microdots. Nature 399:533–534
Crick FH, Griffith JS, Orgel LE (1957) Codes without commas. Proc Natl Acad Sci USA 43:416–421
Cukras A, Faulhammer D, Lipton R, Landweber L (1999) Chess games: a model for RNA based computation. Biosystems 52:35–45
Deaton R, Murphy RC, Rose JA, Garzon M, Franceschetti DT, Stevens SEJ (1996) Genetic search for reliable encodings for DNA-based computation. In First genetic programming conference, Stanford, pp 9–15
Deaton R, Murphy RC, Garzon M, Franceschetti DR, Stevens SEJ (1998) Good encodings for DNA-based solutions to combinatorial problems. Proceedings of the second annual meeting on DNA based computers, DIMACS: series in discrete mathematics and theoretical computer science, vol 44, Princeton, pp 247–258
Dirks RM, Lin M, Winfree E, Pierce NA (2004) Paradigms for computational nucleic acid design. Nucleic Acids Res 32:1392–1403
Faulhammer D, Cukras A, Lipton R, Landweber L (2000) Molecular computation: RNA solutions to chess problems. Proceedings of the Natl Acad Sci USA 97:1385–1389
Feldkamp U, Saghafi S, Rauhe H (2001) DNASequenceGenerator – a program for the construction of DNA sequences. Proceedings 7th International workshop on DNA-based computers, LNCS 2340, Tampa, pp 23–32
Frutos A, Liu Q, Thiel A, Sanner A, Condon AE, Smith L, Corn RM (1997) Demonstration of a word design strategy for DNA computing on surfaces. Nucleic Acids Res 25:4748–4757
Gardner TS, Cantor CR, Collins JJ (2000) Construction of a genetic toggle switch in Escherichia coli. Nature 403:339–342
Garzon M, Deaton R, Neather P, Franceschetti DR, Murphy RC (1997) A new metric for DNA computing. In Proceedings of the 2nd Genetic Programming Conference, San Mateo, pp 472–478
Garzon M, Deaton R, Nino L, Stevens SEJ, Wittner M (1998) Encoding genomes for DNA computing. In Proceedings of the 3rd Genetic Programming Conference, San Mateo, pp 684–690
Golomb S, Gordon B, Welch L (1958) Comma-free codes. Can J Math 10:202–209
Goodman RP, Heilemann M, Doose S, Erben CM, Kapanidis AN, Turberfield AJ (2008) Reconfigurable, braced, three-dimensional DNA nanostructures. Nat Nanotechnol 3:93–96
Hagiya M, Arita M, Kiga D, Sakamoto K, Yokoyama S (1999) Towards parallel evaluation and learning of boolean μ-formulas with molecules. DIMACS Series Discrete Math Theor Comput Sci 48:57–72
He Y, Ye T, Su M, Zhang C, Ribbe AE, Jiang W, Mao C (2008) Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra. Nature 452:198–201
Head T, Gal S (2001) Aqueous computing: writing into fluid memory. Bull EATCS 75:190–198
Heider D, Barnekow A (2007) DNA-based watermarks using the DNA-crypt algorithm. BMC Bioinformatics 8:176
Heider D, Barnekow A (2008) DNA watermarks: a proof of concept. BMC Mol Biol 9:40
Heider D, Kessler D, Barnekow A (2008) Watermarking sexually reproducing diploid organisms. Bioinformatics 24:1961–1962
Hofacker IL (2003) Vienna RNA secondary structure server. Nucleic Acids Res 31:3429–3431
Kameda A, Kashiwamura S, Yamamoto M, Ohuchi A, Hagiya M (2008a) Combining randomness and a high-capacity DNA memory. 13th International meeting on DNA computing, DNA13, LNCS 4848, Berlin, pp 109–118
Kameda A, Yamamoto M, Ohuchi A, Yaegashi S, Hagiya M (2008b) Unravel four hairpins! Nat Comput 7:287–298
Kapranov P, Cawley SE, Drenkow J, Bekiranov S, Strausberg RL, Fodor SPA, Gingeras TR (2002) Large-scale transcriptional activity in chromosomes 21 and 22. Science 296:916–919
Kashiwamura S, Kameda A, Yamamoto M, Ohuchi A (2004) Two-step search for DNA sequence design. IEICE TRANSACTIONS Fundam Electron Commun Comput Sci E87-A:1446–1453
Kawashimo S, Ng YK, Ono H, Sadakane K, Yamashita M (2009) Speeding up local-search type algorithms for designing DNA sequences under thermodynamical constraints. Proceedings of the 14th International meeting on DNA computing, LNCS 5347, Prague, pp 168–179
Kawashimo S, Ono H, Sadakane K, Yamashita M (2008) Dynamic neighborhood searches for thermodynamically designing DNA sequence. 13th International meeting on DNA computing, DNA13, LNCS 4848, Memphis, pp 130–139
Kitajima T, Takinoue M, Shohda K, Suyama A (2008) Design of code words for DNA computers and nanostructures with consideration of hybridization kinetics. 13th International meeting on DNA computing, DNA13, LNCS 4848, Berlin, pp 119–129
Kobayashi S, Kondo T, Arita M (2003) On template method for DNA sequence design. Proceedings of the 8th International workshop on DNA-based computers, LNCS 2568, Berlin, pp 205–214
Komiya K, Sakamoto K, Kameda A, Yamamoto M, Ohuchi A, Kiga D, Yokoyama S, Hagiya M (2006) DNA polymerase programmed with a hairpin DNA incorporates a multiple-instruction architecture into molecular computing. Biosystems 83:18–25
Kubota M, Hagiya M (2005) Minimum basin algorithm: an effective analysis technique for DNA energy landscapes. Proceedings of the 10th International workshop on DNA computing, LNCS 3384, New York, pp 202–214
Leier A, Richter C, Banzhaf W, Rauhe H (2000) Cryptography with DNA binary strands. Biosystems 57:13–22
Li M, Lee HJ, Condon AE, Corn RM (2002) DNA word design strategy for creating sets of non-interacting oligonucleotides for DNA microarrays. Langmuir 18:805–812
Li Y, Agrawal S (1995) Oligonucleotides containing G.A pairs: effect of flanking sequences on structure and stability. Biochemistry 34:10056–10062
Li Y, Zon G, Wilson W (1991) Thermodynamics of DNA duplexes with adjacent G.A mismatches. Biochemistry 30:7566–7572
Lipton RJ (1995) DNA solution of hard computational problems. Science 268:542–545
Liu W, Wang S, Gao L, Zhang F, Xu J (2003) DNA sequence design based on template strategy. J Chem Inf Comput Sci 43:2014–2018
Lyngso R, Zuker M, Pedersen C (1999) Fast evaluation of internal loops in RNA secondary structure prediction. Bioinformatics 15:440–445
Marathe A, Condon AE, Corn RM (2001) On combinatorial DNA word design. J Comput Biol 8:201–219
Pancoska P, Moravek Z, Moll UM (2004) Rational design of DNA sequences for nanotechnology, microarrays and molecular computers using Eulerian graphs. Nucleic Acids Res 32:4630–4645
Peyret N, Seneviratne P, Allawi H, SantaLucia J (1999) Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A.A, C.C, G.G, and T.T mismatches. Biochemistry 38:3468–3477
Rinker S, Ke Y, Liu Y, Chhabra R, Yan H (2008) Self-assembled DNA nanostructures for distance-dependent multivalent ligand-protein binding. Nat Nanotechnol 3:418–422
Rothemund PWK (2006) Folding DNA to create nanoscale shapes and patterns. Nature 440:297–302
Ruben AJ, Freeland SJ, Landweber LF (2001) PUNCH: An evolutionary algorithm for optimizing bit set selection. Proceedings of the 7th International workshop on DNA-based computers, LNCS 2340, Tampa, pp 150–160
SantaLucia J (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci USA 95:1460–1465
SantaLucia J, Allawi H, Seneviratne P (1996) Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry 35:3555–3562
Seelig G, Soloveichik D, Zhang DY, Winfree E (2006) Enzyme-free nucleic acid logic circuits. Science 314:1585–1588
Seeman N (1990) De novo design of sequences for nucleic acid structural engineering. J Biomol Struct Dyn 8:573–581
Seeman NC, Lukeman PS (2005) Nucleic acid nanostructures: bottom-up control of geometry on the nanoscale. Rep Prog Phys 68:237–270
Sen D, Gilbert W (1988) Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis. Nature 334:364–366
Sen D, Gilbert W (1990) A sodium-potassium switch in the formation of four-stranded G4-DNA. Nature 344:410–414
Senior M, Jones R, Breslauer K (1988) Influence of dangling thymidine residues on the stability and structure of two DNA duplexes. Biochemistry 27:3879–3885
Shin JS, Pierce NA (2004) Rewritable memory by controllable nanopatterning of DNA. Nano Lett 4:905–909
Simmel FC, Dittmer WU (2005) DNA nanodevices. Small 1:284–299
Stemmer WP, Crameri A, Ha KD, Brennan TM, Heyneker HL (1995) Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides. Gene 164:49–53
Sugimoto N, Nakano S, Yoneyama M, Honda K (1996) Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acids Res 24:4501–4505
Takinoue M, Suyama A (2006) Hairpin-DNA memory using molecular addressing. Small 2:1244–1247
Takinoue M, Suyama A (2004) Molecular reactions for a molecular memory based on hairpin DNA. Chem-Bio Inform J 4:93–100
Takinoue M, Kiga D, Shohda K, Suyama A (2008) Experiments and simulation models of a basic computation element of an autonomous molecular computing system. Phys Rev E 78:041921
Tanaka F, Kameda A, Yamamoto M, Ohuchi A (2004) Thermodynamic parameters based on a nearest-neighbor model for DNA sequences with a single-bulge loop. Biochemistry 43:7143–7150
Tanaka F, Kameda A, Yamamoto M, Ohuchi A (2005) Design of nucleic acid sequences for DNA computing based on a thermodynamic approach. Nucleic Acids Res 33:903–911
Tulpan D, Hoos H (2003) Hybrid randomised neighbourhoods improve stochastic local search for DNA code design. In: Advances in artificial intelligence: 16th conference of the Canadian society for computational studies of intelligence, Berlin, vol 2671, pp 418–433
Tulpan D, Hoos H, Condon A (2003) Stochastic local search algorithms for DNA word design. Proceedings of the 8th International workshop on DNA-based computers, LNCS 2568, Berlin, pp 229–241
Uejima H, Hagiya M (2004) Secondary structure design of multi-state DNA machines based on sequential structure transitions. Proceedings of the 9th International workshop on DNA-based computers, LNCS 2943, Berlin, pp 74–85
Venkataraman S, Dirks RM, Rothemund PWK, Winfree E, Pierce NA (2007) An autonomous polymerization motor powered by DNA hybridization. Nat Nanotechnol 2:490–494
Watson J, Crick F (1953) Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature 171:737–738
Wong P, Wong K-K, Foote H (2003) Organic data memory using the DNA approach. Commun ACM 46(1):95–98
Yachie N, Sekiyama K, Sugahara J, Ohashi Y, Tomita M (2007) Alignment-based approach for durable data storage into living organisms. Biotechnol Prog 23:501–505
Yamamoto M, Kashiwamura S, Ohuchi A, Furukawa M (2008) Large-scale DNA memory based on the nested PCR. Nat Comput 7:335–346
Yoshida H, Suyama A (2000) Solution to 3-SAT by breadth first search. DIMACS Ser Discrete Math Theor Comput Sci 54:9–22
Yurke B, Turberfield AJ, Mills AP, Simmel FC, Neumann JL (2000) A DNA-fuelled molecular machine made of DNA. Nature 406:605–608
Zhang DY, Turberfield AJ, Yurke B, Winfree E (2007) Engineering entropy-driven reactions and networks catalyzed by DNA. Science 318:1121–1125
Zuker M, Stiegler P (1981) Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res 9:133–148
Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31:3406–3415
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Arita, M., Hagiya, M., Takinoue, M., Tanaka, F. (2012). DNA Memory. In: Rozenberg, G., Bäck, T., Kok, J.N. (eds) Handbook of Natural Computing. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-92910-9_38
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DOI: https://doi.org/10.1007/978-3-540-92910-9_38
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