{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T09:50:19Z","timestamp":1791971419798,"version":"4.3.4"},"publisher-location":"Berlin, Heidelberg","reference-count":93,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"value":"9783540929093","type":"print"},{"value":"9783540929109","type":"electronic"}],"license":[{"start":{"date-parts":[[2012,1,1]],"date-time":"2012-01-01T00:00:00Z","timestamp":1325376000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2012,1,1]],"date-time":"2012-01-01T00:00:00Z","timestamp":1325376000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012]]},"DOI":"10.1007\/978-3-540-92910-9_38","type":"book-chapter","created":{"date-parts":[[2012,8,25]],"date-time":"2012-08-25T10:54:06Z","timestamp":1345892046000},"page":"1281-1318","source":"Crossref","is-referenced-by-count":0,"title":["DNA Memory"],"prefix":"10.1007","author":[{"given":"Masanori","family":"Arita","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Masami","family":"Hagiya","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Masahiro","family":"Takinoue","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fumiaki","family":"Tanaka","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","reference":[{"key":"38_CR003812","doi-asserted-by":"publisher","first-page":"4811","DOI":"10.1093\/nar\/13.13.4811","volume":"13","author":"F Aboul-ela","year":"1985","unstructured":"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\u20134824","journal-title":"Nucleic Acids Res"},{"key":"38_CR00381","doi-asserted-by":"publisher","first-page":"1021","DOI":"10.1126\/science.7973651","volume":"266","author":"L Adleman","year":"1994","unstructured":"Adleman L (1994) Molecular computation of solutions to combinatorial problems. Science 266:1021\u20131024","journal-title":"Science"},{"key":"38_CR00388","doi-asserted-by":"publisher","first-page":"10581","DOI":"10.1021\/bi962590c","volume":"36","author":"H Allawi","year":"1997","unstructured":"Allawi H, SantaLucia J (1997) Thermodynamics and NMR of internal G.T mismatches in DNA. Biochemistry 36:10581\u201310594","journal-title":"Biochemistry"},{"key":"38_CR003815","doi-asserted-by":"publisher","first-page":"9435","DOI":"10.1021\/bi9803729","volume":"37","author":"H Allawi","year":"1998","unstructured":"Allawi H, SantaLucia J (1998a) Nearest-neighbor thermodynamics of internal A.C mismatches in DNA: sequence dependence and pH effects. Biochemistry 37:9435\u20139444","journal-title":"Biochemistry"},{"key":"38_CR003816","doi-asserted-by":"publisher","first-page":"2694","DOI":"10.1093\/nar\/26.11.2694","volume":"26","author":"H Allawi","year":"1998","unstructured":"Allawi H, SantaLucia J (1998b) Thermodynamics of internal C.T mismatches in DNA. Nucleic Acids Res 26:2694\u20132701","journal-title":"Nucleic Acids Res"},{"key":"38_CR003817","doi-asserted-by":"publisher","first-page":"2170","DOI":"10.1021\/bi9724873","volume":"37","author":"H Allawi","year":"1998","unstructured":"Allawi H, SantaLucia J (1998c) Nearest neighbor thermodynamic parameters for internal G.A mismatches in DNA. Biochemistry 37:2170\u20132179","journal-title":"Biochemistry"},{"key":"38_CR003822","doi-asserted-by":"publisher","first-page":"3416","DOI":"10.1093\/nar\/gkg612","volume":"31","author":"M Andronescu","year":"2003","unstructured":"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\u20133422","journal-title":"Nucleic Acids Res"},{"key":"38_CR003823","doi-asserted-by":"publisher","first-page":"607","DOI":"10.1016\/j.jmb.2003.12.041","volume":"336","author":"M Andronescu","year":"2004","unstructured":"Andronescu M, Fejes AP, Hutter F, Hoos HH, Condon AE (2004) A new algorithm for RNA secondary structure design. J Mol Biol 336:607\u2013624","journal-title":"J Mol Biol"},{"key":"38_CR003840","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1007\/BF03037360","volume":"20","author":"M Arita","year":"2002","unstructured":"Arita M, Kobayashi S (2002) DNA sequence design using templates. New Gen Comput 20:263\u2013277","journal-title":"New Gen Comput"},{"key":"38_CR003888","doi-asserted-by":"publisher","first-page":"1605","DOI":"10.1021\/bp049917i","volume":"20","author":"M Arita","year":"2004","unstructured":"Arita M, Ohashi Y (2004) Secret signatures inside genomic DNA. Biotechnol Prog 20:1605\u20131607","journal-title":"Biotechnol Prog"},{"key":"38_CR003852","unstructured":"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\u2013882"},{"key":"38_CR003866","doi-asserted-by":"publisher","first-page":"275","DOI":"10.1038\/nnano.2007.104","volume":"2","author":"J Bath","year":"2007","unstructured":"Bath J, Turberfield AJ (2007) DNA nanomachines. Nat Nanotechnol 2:275\u2013284","journal-title":"Nat Nanotechnol"},{"key":"38_CR00383","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1126\/science.7725109","volume":"268","author":"EB Baum","year":"1995","unstructured":"Baum EB (1995) Building an associative memory vastly larger than the brain. Science 268:583\u2013585","journal-title":"Science"},{"key":"38_CR003874","doi-asserted-by":"publisher","first-page":"423","DOI":"10.1038\/nature02551","volume":"429","author":"Y Benenson","year":"2004","unstructured":"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\u2013429","journal-title":"Nature"},{"key":"38_CR003820","doi-asserted-by":"publisher","first-page":"1929","DOI":"10.1093\/nar\/28.9.1929","volume":"28","author":"S Bommarito","year":"2000","unstructured":"Bommarito S, Peyret N, SantaLucia J (2000) Thermodynamic parameters for DNA sequences with dangling ends. Nucleic Acids Res 28:1929\u20131934","journal-title":"Nucleic Acids Res"},{"key":"38_CR00386","doi-asserted-by":"publisher","first-page":"843","DOI":"10.1016\/0022-2836(74)90357-X","volume":"86","author":"P Borer","year":"1974","unstructured":"Borer P, Dengler B, Tinoco I, Uhlenbeck O (1974) Stability of ribonucleic acid double-stranded helices. J Mol Biol 86:843\u2013853","journal-title":"J Mol Biol"},{"key":"38_CR003834","doi-asserted-by":"publisher","first-page":"499","DOI":"10.1126\/science.1069528","volume":"296","author":"RS Braich","year":"2002","unstructured":"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\u2013502","journal-title":"Science"},{"key":"38_CR003833","doi-asserted-by":"crossref","unstructured":"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\u201342","DOI":"10.1007\/3-540-44992-2_3"},{"key":"38_CR003838","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1016\/S0304-3975(02)00135-4","volume":"287","author":"A Brenneman","year":"2002","unstructured":"Brenneman A, Condon AE (2002) Strand design for bio-molecular computation. Theor Comput Sci 287:39\u201358","journal-title":"Theor Comput Sci"},{"key":"38_CR003883","doi-asserted-by":"publisher","first-page":"533","DOI":"10.1038\/21092","volume":"399","author":"CT Clelland","year":"1999","unstructured":"Clelland CT, Risca V, Bancroft C (1999) Hiding messages in DNA microdots. Nature 399:533\u2013534","journal-title":"Nature"},{"key":"38_CR003886","doi-asserted-by":"publisher","first-page":"416","DOI":"10.1073\/pnas.43.5.416","volume":"43","author":"FH Crick","year":"1957","unstructured":"Crick FH, Griffith JS, Orgel LE (1957) Codes without commas. Proc Natl Acad Sci USA 43:416\u2013421","journal-title":"Proc Natl Acad Sci USA"},{"key":"38_CR003831","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1016\/S0303-2647(99)00030-1","volume":"52","author":"A Cukras","year":"1999","unstructured":"Cukras A, Faulhammer D, Lipton R, Landweber L (1999) Chess games: a model for RNA based computation. Biosystems 52:35\u201345","journal-title":"Biosystems"},{"key":"38_CR003850","unstructured":"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\u201315"},{"key":"38_CR003851","doi-asserted-by":"crossref","unstructured":"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\u2013258","DOI":"10.1090\/dimacs\/044\/20"},{"key":"38_CR003824","doi-asserted-by":"publisher","first-page":"1392","DOI":"10.1093\/nar\/gkh291","volume":"32","author":"RM Dirks","year":"2004","unstructured":"Dirks RM, Lin M, Winfree E, Pierce NA (2004) Paradigms for computational nucleic acid design. Nucleic Acids Res 32:1392\u20131403","journal-title":"Nucleic Acids Res"},{"key":"38_CR003832","doi-asserted-by":"publisher","first-page":"1385","DOI":"10.1073\/pnas.97.4.1385","volume":"97","author":"D Faulhammer","year":"2000","unstructured":"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\u20131389","journal-title":"Proc Natl Acad Sci USA"},{"key":"38_CR003843","doi-asserted-by":"crossref","unstructured":"Feldkamp U, Saghafi S, Rauhe H (2001) DNASequenceGenerator \u2013 a program for the construction of DNA sequences. Proceedings 7th International workshop on DNA-based computers, LNCS 2340, Tampa, pp 23\u201332","DOI":"10.1007\/3-540-48017-X_3"},{"key":"38_CR003825","doi-asserted-by":"publisher","first-page":"4748","DOI":"10.1093\/nar\/25.23.4748","volume":"25","author":"A Frutos","year":"1997","unstructured":"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\u20134757","journal-title":"Nucleic Acids Res"},{"key":"38_CR003893","doi-asserted-by":"publisher","first-page":"339","DOI":"10.1038\/35002131","volume":"403","author":"TS Gardner","year":"2000","unstructured":"Gardner TS, Cantor CR, Collins JJ (2000) Construction of a genetic toggle switch in Escherichia coli. Nature 403:339\u2013342","journal-title":"Nature"},{"key":"38_CR003826","unstructured":"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\u2013478"},{"key":"38_CR003827","unstructured":"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\u2013690"},{"key":"38_CR003887","doi-asserted-by":"publisher","first-page":"202","DOI":"10.4153\/CJM-1958-023-9","volume":"10","author":"S Golomb","year":"1958","unstructured":"Golomb S, Gordon B, Welch L (1958) Comma-free codes. Can J Math 10:202\u2013209","journal-title":"Can J Math"},{"key":"38_CR003872","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1038\/nnano.2008.3","volume":"3","author":"RP Goodman","year":"2008","unstructured":"Goodman RP, Heilemann M, Doose S, Erben CM, Kapanidis AN, Turberfield AJ (2008) Reconfigurable, braced, three-dimensional DNA nanostructures. Nat Nanotechnol 3:93\u201396","journal-title":"Nat Nanotechnol"},{"key":"38_CR003835","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1090\/dimacs\/048\/05","volume":"48","author":"M Hagiya","year":"1999","unstructured":"Hagiya M, Arita M, Kiga D, Sakamoto K, Yokoyama S (1999) Towards parallel evaluation and learning of boolean \u03bc-formulas with molecules. DIMACS Series Discrete Math Theor Comput Sci 48:57\u201372","journal-title":"DIMACS Series Discrete Math Theor Comput Sci"},{"key":"38_CR003869","doi-asserted-by":"publisher","first-page":"198","DOI":"10.1038\/nature06597","volume":"452","author":"Y He","year":"2008","unstructured":"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\u2013201","journal-title":"Nature"},{"key":"38_CR003862","first-page":"190","volume":"75","author":"T Head","year":"2001","unstructured":"Head T, Gal S (2001) Aqueous computing: writing into fluid memory. Bull EATCS 75:190\u2013198","journal-title":"Bull EATCS"},{"key":"38_CR003889","doi-asserted-by":"publisher","first-page":"176","DOI":"10.1186\/1471-2105-8-176","volume":"8","author":"D Heider","year":"2007","unstructured":"Heider D, Barnekow A (2007) DNA-based watermarks using the DNA-crypt algorithm. BMC Bioinformatics 8:176","journal-title":"BMC Bioinformatics"},{"key":"38_CR003890","doi-asserted-by":"publisher","first-page":"40","DOI":"10.1186\/1471-2199-9-40","volume":"9","author":"D Heider","year":"2008","unstructured":"Heider D, Barnekow A (2008) DNA watermarks: a proof of concept. BMC Mol Biol 9:40","journal-title":"BMC Mol Biol"},{"key":"38_CR003891","doi-asserted-by":"publisher","first-page":"1961","DOI":"10.1093\/bioinformatics\/btn342","volume":"24","author":"D Heider","year":"2008","unstructured":"Heider D, Kessler D, Barnekow A (2008) Watermarking sexually reproducing diploid organisms. Bioinformatics 24:1961\u20131962","journal-title":"Bioinformatics"},{"key":"38_CR003821","doi-asserted-by":"publisher","first-page":"3429","DOI":"10.1093\/nar\/gkg599","volume":"31","author":"I L Hofacker","year":"2003","unstructured":"Hofacker IL (2003) Vienna RNA secondary structure server. Nucleic Acids Res 31:3429\u20133431","journal-title":"Nucleic Acids Res"},{"key":"38_CR003865","doi-asserted-by":"crossref","unstructured":"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\u2013118","DOI":"10.1007\/978-3-540-77962-9_11"},{"key":"38_CR003860","doi-asserted-by":"publisher","first-page":"287","DOI":"10.1007\/s11047-007-9035-y","volume":"7","author":"A Kameda","year":"2008","unstructured":"Kameda A, Yamamoto M, Ohuchi A, Yaegashi S, Hagiya M (2008b) Unravel four hairpins! Nat Comput 7:287\u2013298","journal-title":"Nat Comput"},{"key":"38_CR003882","doi-asserted-by":"publisher","first-page":"916","DOI":"10.1126\/science.1068597","volume":"296","author":"P Kapranov","year":"2002","unstructured":"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\u2013919","journal-title":"Science"},{"key":"38_CR003846","first-page":"1446","volume":"E87-A","author":"S Kashiwamura","year":"2004","unstructured":"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\u20131453","journal-title":"IEICE TRANSACTIONS Fundam Electron Commun Comput Sci"},{"key":"38_CR003856","doi-asserted-by":"crossref","unstructured":"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\u2013179","DOI":"10.1007\/978-3-642-03076-5_14"},{"key":"38_CR003855","doi-asserted-by":"crossref","unstructured":"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\u2013139","DOI":"10.1007\/978-3-540-77962-9_13"},{"key":"38_CR003857","doi-asserted-by":"crossref","unstructured":"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\u2013129","DOI":"10.1007\/978-3-540-77962-9_12"},{"key":"38_CR003841","doi-asserted-by":"crossref","unstructured":"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\u2013214","DOI":"10.1007\/3-540-36440-4_18"},{"key":"38_CR003875","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1016\/j.biosystems.2005.07.005","volume":"83","author":"K Komiya","year":"2006","unstructured":"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\u201325","journal-title":"Biosystems"},{"key":"38_CR003859","doi-asserted-by":"crossref","unstructured":"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\u2013214","DOI":"10.1007\/11493785_18"},{"key":"38_CR003884","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1016\/S0303-2647(00)00083-6","volume":"57","author":"A Leier","year":"2000","unstructured":"Leier A, Richter C, Banzhaf W, Rauhe H (2000) Cryptography with DNA binary strands. Biosystems 57:13\u201322","journal-title":"Biosystems"},{"key":"38_CR003836","doi-asserted-by":"publisher","first-page":"805","DOI":"10.1021\/la0112209","volume":"18","author":"M Li","year":"2002","unstructured":"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\u2013812","journal-title":"Langmuir"},{"key":"38_CR003814","doi-asserted-by":"publisher","first-page":"10056","DOI":"10.1021\/bi00031a030","volume":"34","author":"Y Li","year":"1995","unstructured":"Li Y, Agrawal S (1995) Oligonucleotides containing G.A pairs: effect of flanking sequences on structure and stability. Biochemistry 34:10056\u201310062","journal-title":"Biochemistry"},{"key":"38_CR003813","doi-asserted-by":"publisher","first-page":"7566","DOI":"10.1021\/bi00244a028","volume":"30","author":"Y Li","year":"1991","unstructured":"Li Y, Zon G, Wilson W (1991) Thermodynamics of DNA duplexes with adjacent G.A mismatches. Biochemistry 30:7566\u20137572","journal-title":"Biochemistry"},{"key":"38_CR00382","doi-asserted-by":"publisher","first-page":"542","DOI":"10.1126\/science.7725098","volume":"268","author":"RJ Lipton","year":"1995","unstructured":"Lipton RJ (1995) DNA solution of hard computational problems. Science 268:542\u2013545","journal-title":"Science"},{"key":"38_CR003839","doi-asserted-by":"publisher","first-page":"2014","DOI":"10.1021\/ci025645s","volume":"43","author":"W Liu","year":"2003","unstructured":"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\u20132018","journal-title":"J Chem Inf Comput Sci"},{"key":"38_CR003853","doi-asserted-by":"publisher","first-page":"440","DOI":"10.1093\/bioinformatics\/15.6.440","volume":"15","author":"R Lyngso","year":"1999","unstructured":"Lyngso R, Zuker M, Pedersen C (1999) Fast evaluation of internal loops in RNA secondary structure prediction. Bioinformatics 15:440\u2013445","journal-title":"Bioinformatics"},{"key":"38_CR003837","doi-asserted-by":"publisher","first-page":"201","DOI":"10.1089\/10665270152530818","volume":"8","author":"A Marathe","year":"2001","unstructured":"Marathe A, Condon AE, Corn RM (2001) On combinatorial DNA word design. J Comput Biol 8:201\u2013219","journal-title":"J Comput Biol"},{"key":"38_CR003844","doi-asserted-by":"publisher","first-page":"4630","DOI":"10.1093\/nar\/gkh802","volume":"32","author":"P Pancoska","year":"2004","unstructured":"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\u20134645","journal-title":"Nucleic Acids Res"},{"key":"38_CR003818","doi-asserted-by":"publisher","first-page":"3468","DOI":"10.1021\/bi9825091","volume":"38","author":"N Peyret","year":"1999","unstructured":"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\u20133477","journal-title":"Biochemistry"},{"key":"38_CR003870","doi-asserted-by":"publisher","first-page":"418","DOI":"10.1038\/nnano.2008.164","volume":"3","author":"S Rinker","year":"2008","unstructured":"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\u2013422","journal-title":"Nat Nanotechnol"},{"key":"38_CR003871","doi-asserted-by":"publisher","first-page":"297","DOI":"10.1038\/nature04586","volume":"440","author":"PWK Rothemund","year":"2006","unstructured":"Rothemund PWK (2006) Folding DNA to create nanoscale shapes and patterns. Nature 440:297\u2013302","journal-title":"Nature"},{"key":"38_CR003847","doi-asserted-by":"crossref","unstructured":"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\u2013160","DOI":"10.1007\/3-540-48017-X_14"},{"key":"38_CR00387","doi-asserted-by":"publisher","first-page":"1460","DOI":"10.1073\/pnas.95.4.1460","volume":"95","author":"J SantaLucia","year":"1998","unstructured":"SantaLucia J (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci USA 95:1460\u20131465","journal-title":"Proc Natl Acad Sci USA"},{"key":"38_CR003811","doi-asserted-by":"publisher","first-page":"3555","DOI":"10.1021\/bi951907q","volume":"35","author":"J SantaLucia","year":"1996","unstructured":"SantaLucia J, Allawi H, Seneviratne P (1996) Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry 35:3555\u20133562","journal-title":"Biochemistry"},{"key":"38_CR003876","doi-asserted-by":"publisher","first-page":"1585","DOI":"10.1126\/science.1132493","volume":"314","author":"G Seelig","year":"2006","unstructured":"Seelig G, Soloveichik D, Zhang DY, Winfree E (2006) Enzyme-free nucleic acid logic circuits. Science 314:1585\u20131588","journal-title":"Science"},{"key":"38_CR003842","doi-asserted-by":"publisher","first-page":"573","DOI":"10.1080\/07391102.1990.10507829","volume":"8","author":"N Seeman","year":"1990","unstructured":"Seeman N (1990) De novo design of sequences for nucleic acid structural engineering. J Biomol Struct Dyn 8:573\u2013581","journal-title":"J Biomol Struct Dyn"},{"key":"38_CR003867","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1088\/0034-4885\/68\/1\/R05","volume":"68","author":"NC Seeman","year":"2005","unstructured":"Seeman NC, Lukeman PS (2005) Nucleic acid nanostructures: bottom-up control of geometry on the nanoscale. Rep Prog Phys 68:237\u2013270","journal-title":"Rep Prog Phys"},{"key":"38_CR003829","doi-asserted-by":"publisher","first-page":"364","DOI":"10.1038\/334364a0","volume":"334","author":"D Sen","year":"1988","unstructured":"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\u2013366","journal-title":"Nature"},{"key":"38_CR003830","doi-asserted-by":"publisher","first-page":"410","DOI":"10.1038\/344410a0","volume":"344","author":"D Sen","year":"1990","unstructured":"Sen D, Gilbert W (1990) A sodium-potassium switch in the formation of four-stranded G4-DNA. Nature 344:410\u2013414","journal-title":"Nature"},{"key":"38_CR003819","doi-asserted-by":"publisher","first-page":"3879","DOI":"10.1021\/bi00410a053","volume":"27","author":"M Senior","year":"1988","unstructured":"Senior M, Jones R, Breslauer K (1988) Influence of dangling thymidine residues on the stability and structure of two DNA duplexes. Biochemistry 27:3879\u20133885","journal-title":"Biochemistry"},{"key":"38_CR003879","doi-asserted-by":"publisher","first-page":"905","DOI":"10.1021\/nl049658r","volume":"4","author":"JS Shin","year":"2004","unstructured":"Shin JS, Pierce NA (2004) Rewritable memory by controllable nanopatterning of DNA. Nano Lett 4:905\u2013909","journal-title":"Nano Lett"},{"key":"38_CR003868","doi-asserted-by":"publisher","first-page":"284","DOI":"10.1002\/smll.200400111","volume":"1","author":"FC Simmel","year":"2005","unstructured":"Simmel FC, Dittmer WU (2005) DNA nanodevices. Small 1:284\u2013299","journal-title":"Small"},{"key":"38_CR003863","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1016\/0378-1119(95)00511-4","volume":"164","author":"WP Stemmer","year":"1995","unstructured":"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\u201353","journal-title":"Gene"},{"key":"38_CR003810","doi-asserted-by":"publisher","first-page":"4501","DOI":"10.1093\/nar\/24.22.4501","volume":"24","author":"N Sugimoto","year":"1996","unstructured":"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\u20134505","journal-title":"Nucleic Acids Res"},{"key":"38_CR003880","doi-asserted-by":"publisher","first-page":"1244","DOI":"10.1002\/smll.200600237","volume":"2","author":"M Takinoue","year":"2006","unstructured":"Takinoue M, Suyama A (2006) Hairpin-DNA memory using molecular addressing. Small 2:1244\u20131247","journal-title":"Small"},{"key":"38_CR003881","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1273\/cbij.4.93","volume":"4","author":"M Takinoue","year":"2004","unstructured":"Takinoue M, Suyama A (2004) Molecular reactions for a molecular memory based on hairpin DNA. Chem-Bio Inform J 4:93\u2013100","journal-title":"Chem-Bio Inform J"},{"key":"38_CR003877","doi-asserted-by":"publisher","first-page":"041921","DOI":"10.1103\/PhysRevE.78.041921","volume":"78","author":"M Takinoue","year":"2008","unstructured":"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","journal-title":"Phys Rev E"},{"key":"38_CR00389","doi-asserted-by":"publisher","first-page":"7143","DOI":"10.1021\/bi036188r","volume":"43","author":"F Tanaka","year":"2004","unstructured":"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\u20137150","journal-title":"Biochemistry"},{"key":"38_CR003854","doi-asserted-by":"publisher","first-page":"903","DOI":"10.1093\/nar\/gki235","volume":"33","author":"F Tanaka","year":"2005","unstructured":"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\u2013911","journal-title":"Nucleic Acids Res"},{"key":"38_CR003849","doi-asserted-by":"crossref","unstructured":"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\u2013433","DOI":"10.1007\/3-540-44886-1_31"},{"key":"38_CR003848","doi-asserted-by":"crossref","unstructured":"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\u2013241","DOI":"10.1007\/3-540-36440-4_20"},{"key":"38_CR003858","doi-asserted-by":"crossref","unstructured":"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\u201385","DOI":"10.1007\/978-3-540-24628-2_9"},{"key":"38_CR003873","doi-asserted-by":"publisher","first-page":"490","DOI":"10.1038\/nnano.2007.225","volume":"2","author":"S Venkataraman","year":"2007","unstructured":"Venkataraman S, Dirks RM, Rothemund PWK, Winfree E, Pierce NA (2007) An autonomous polymerization motor powered by DNA hybridization. Nat Nanotechnol 2:490\u2013494","journal-title":"Nat Nanotechnol"},{"key":"38_CR00384","doi-asserted-by":"publisher","first-page":"737","DOI":"10.1038\/171737a0","volume":"171","author":"J Watson","year":"1953","unstructured":"Watson J, Crick F (1953) Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature 171:737\u2013738","journal-title":"Nature"},{"issue":"1","key":"38_CR003885","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1145\/602421.602426","volume":"46","author":"P Wong","year":"2003","unstructured":"Wong P, Wong K-K, Foote H (2003) Organic data memory using the DNA approach. Commun ACM 46(1):95\u201398","journal-title":"Commun ACM"},{"key":"38_CR003892","doi-asserted-by":"publisher","first-page":"501","DOI":"10.1021\/bp060261y","volume":"23","author":"N Yachie","year":"2007","unstructured":"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\u2013505","journal-title":"Biotechnol Prog"},{"key":"38_CR003864","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1007\/s11047-008-9076-x","volume":"7","author":"M Yamamoto","year":"2008","unstructured":"Yamamoto M, Kashiwamura S, Ohuchi A, Furukawa M (2008) Large-scale DNA memory based on the nested PCR. Nat Comput 7:335\u2013346","journal-title":"Nat Comput"},{"key":"38_CR003845","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1090\/dimacs\/054\/02","volume":"54","author":"H Yoshida","year":"2000","unstructured":"Yoshida H, Suyama A (2000) Solution to 3-SAT by breadth first search. DIMACS Ser Discrete Math Theor Comput Sci 54:9\u201322","journal-title":"DIMACS Ser Discrete Math Theor Comput Sci"},{"key":"38_CR003861","doi-asserted-by":"publisher","first-page":"605","DOI":"10.1038\/35020524","volume":"406","author":"B Yurke","year":"2000","unstructured":"Yurke B, Turberfield AJ, Mills AP, Simmel FC, Neumann JL (2000) A DNA-fuelled molecular machine made of DNA. Nature 406:605\u2013608","journal-title":"Nature"},{"key":"38_CR003878","doi-asserted-by":"publisher","first-page":"1121","DOI":"10.1126\/science.1148532","volume":"318","author":"DY Zhang","year":"2007","unstructured":"Zhang DY, Turberfield AJ, Yurke B, Winfree E (2007) Engineering entropy-driven reactions and networks catalyzed by DNA. Science 318:1121\u20131125","journal-title":"Science"},{"key":"38_CR00385","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1093\/nar\/9.1.133","volume":"9","author":"M Zuker","year":"1981","unstructured":"Zuker M, Stiegler P (1981) Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res 9:133\u2013148","journal-title":"Nucleic Acids Res"},{"key":"38_CR003828","doi-asserted-by":"publisher","first-page":"3406","DOI":"10.1093\/nar\/gkg595","volume":"31","author":"M Zuker","year":"2003","unstructured":"Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31:3406\u20133415","journal-title":"Nucleic Acids Res"}],"container-title":["Handbook of Natural Computing"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-540-92910-9_38","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T09:06:37Z","timestamp":1791968797000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-3-540-92910-9_38"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012]]},"ISBN":["9783540929093","9783540929109"],"references-count":93,"URL":"https:\/\/doi.org\/10.1007\/978-3-540-92910-9_38","relation":{},"subject":[],"published":{"date-parts":[[2012]]}}}