메뉴 건너뛰기




Volumn 5, Issue 1, 2009, Pages 1-10

DNA code word design for DNA computing with real-time polymerase chain reaction

Author keywords

DNA computing; Generate and test; Real time polymerase chain reaction; TaqMan probes

Indexed keywords


EID: 64249162929     PISSN: 15493636     EISSN: None     Source Type: Journal    
DOI: 10.3844/jcs.2009.1.10     Document Type: Article
Times cited : (4)

References (26)
  • 1
    • 0022965004 scopus 로고
    • Specific enzymatic amplification of DNA in vitro: The polymerase chain reaction
    • Mullis, K., 1986. Specific enzymatic amplification of DNA in vitro: The polymerase chain reaction. Cold spring Harb. Symp. Quant. Biol. , 51: 263-273. http://www.ncbi.nlm.nih.gov/pubmed/3472723
    • (1986) Cold spring Harb. Symp. Quant. Biol , vol.51 , pp. 263-273
    • Mullis, K.1
  • 2
    • 0041976029 scopus 로고    scopus 로고
    • The use of real-time reverse transcriptase PCR for the quantification of cytokine gene expression
    • Overbergh, L., 2003. The use of real-time reverse transcriptase PCR for the quantification of cytokine gene expression. J. Biomolecular Tech., 14: 33-43. http://www.pubmedcentral.nih.gov/ articlerender.fcgi?artid=2279895
    • (2003) J. Biomolecular Tech , vol.14 , pp. 33-43
    • Overbergh, L.1
  • 3
    • 0037134017 scopus 로고    scopus 로고
    • A technique whose time has come
    • DOI: 10.1126/science.296.5567.557
    • Walker, N.J., 2002. A technique whose time has come. Science, 296: 557-559. DOI: 10.1126/science.296.5567.557
    • (2002) Science , vol.296 , pp. 557-559
    • Walker, N.J.1
  • 4
    • 8744317168 scopus 로고    scopus 로고
    • Use of real-time PCR for determining copy number and zygosity in transgenic plants
    • Bubner, B. and I.T. Baldwin, 2004. Use of real-time PCR for determining copy number and zygosity in transgenic plants. Plant Cell Reports, 23: 263-271. http://www.ncbi.nlm.nih.gov/pubmed/15368076
    • (2004) Plant Cell Reports , vol.23 , pp. 263-271
    • Bubner, B.1    Baldwin, I.T.2
  • 5
    • 0029957181 scopus 로고    scopus 로고
    • real-time quantitative PCR
    • DOI: 10.1101/gr.6.10.986
    • Heid, C.A., 1996. real-time quantitative PCR. Genome Res., 6: 986-994. DOI: 10.1101/gr.6.10.986
    • (1996) Genome Res , vol.6 , pp. 986-994
    • Heid, C.A.1
  • 6
    • 0025861818 scopus 로고
    • Detection of specific polymerase chain reaction product by utilizing the 5′←3′ exonuclease activity of termus aquaticus dna polymerase
    • Washington, DC, pp
    • Holland, P.M., 1991. Detection of specific polymerase chain reaction product by utilizing the 5′←3′ exonuclease activity of termus aquaticus dna polymerase. Proceedings of the National Academy of Sciences of the United States of America, Washington, DC., pp: 7276-7280. http://cat.inist.fr/?aModele=afficheN&cpsidt=4975395.
    • (1991) Proceedings of the National Academy of Sciences of the United States of America , pp. 7276-7280
    • Holland, P.M.1
  • 7
    • 0025804117 scopus 로고
    • Synthesis from DNA of a molecule with the connectivity of a cube
    • DOI: 10.1038/350631a0
    • Chen, J. and N.C. Seeman, 1991. Synthesis from DNA of a molecule with the connectivity of a cube. Nature, 350: 631-633. DOI: 10.1038/350631a0
    • (1991) Nature , vol.350 , pp. 631-633
    • Chen, J.1    Seeman, N.C.2
  • 8
    • 64249166542 scopus 로고    scopus 로고
    • Deaton, R., R.C. Murphy, M. Garzon, D.T. Franceschetti and Jr. S.E. Stevens, 1996. Good encodings for DNA-based solutions to combinatorial problems. Proceedings of the 2nd Annual Meeting on DNA Based Computers, June 10-12, American Mathematical Society, Princeton University, pp: 159-171. http://www.csce.uark.edu/~rdeaton/dna/papers/mcggood.pdf
    • Deaton, R., R.C. Murphy, M. Garzon, D.T. Franceschetti and Jr. S.E. Stevens, 1996. Good encodings for DNA-based solutions to combinatorial problems. Proceedings of the 2nd Annual Meeting on DNA Based Computers, June 10-12, American Mathematical Society, Princeton University, pp: 159-171. http://www.csce.uark.edu/~rdeaton/dna/papers/mcggood.pdf
  • 9
    • 0033677332 scopus 로고    scopus 로고
    • Universal DNA tag systems: A combinatorial design scheme
    • DOI: 10.1089/106652700750050916
    • Ben-Dor, A., R. Karp, B. Schwikowski and Z. Yakhini, 2000. Universal DNA tag systems: A combinatorial design scheme. J. Comput. Biol., 7: 503-519. DOI: 10.1089/106652700750050916
    • (2000) J. Comput. Biol , vol.7 , pp. 503-519
    • Ben-Dor, A.1    Karp, R.2    Schwikowski, B.3    Yakhini, Z.4
  • 10
    • 0035190608 scopus 로고    scopus 로고
    • Selection of optimal DNA oligos for gene expression arrays
    • Li, F. and G.D. Stormo, 2001, Selection of optimal DNA oligos for gene expression arrays. Bioinformatics, 17: 1067-1076. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/17/11/1067
    • (2001) Bioinformatics , vol.17 , pp. 1067-1076
    • Li, F.1    Stormo, G.D.2
  • 11
    • 62649136103 scopus 로고    scopus 로고
    • A DNA sequence design for molecular computation of HPP with output visualization based on Real-Time PCR. IEEE Congress on Evolutionary Compution, Sept. 25-28
    • Singapore, pp:, DOI: 10.1109/CEC.2007.4424694
    • Ibrahim, Z., T.B. Kurniawan and M. Khalid, 2007. A DNA sequence design for molecular computation of HPP with output visualization based on Real-Time PCR. IEEE Congress on Evolutionary Compution, Sept. 25-28, IEEE Xplore, Singapore, pp: 1823-1828. DOI: 10.1109/CEC.2007.4424694
    • (2007) IEEE Xplore , pp. 1823-1828
    • Ibrahim, Z.1    Kurniawan, T.B.2    Khalid, M.3
  • 13
    • 0037683090 scopus 로고    scopus 로고
    • DNA library design for molecular computation
    • DOI: 10.1089/ 106652703321825973
    • Pechovsky, R. and J. Ackerman, 2003. DNA library design for molecular computation. J. Comput. Bio., 10: 215-229. DOI: 10.1089/ 106652703321825973
    • (2003) J. Comput. Bio , vol.10 , pp. 215-229
    • Pechovsky, R.1    Ackerman, J.2
  • 14
    • 13944261250 scopus 로고    scopus 로고
    • Design of nucleic acid sequences for DNA computing based on a thermodynamic approach
    • DOI: 10.1093/nar/gki235
    • Tanaka, F., A. Kameda, M. Yamamoto and A. Ohuchi, 2005. Design of nucleic acid sequences for DNA computing based on a thermodynamic approach. Nucleic Acids Res., 33: 903-911. DOI: 10.1093/nar/gki235
    • (2005) Nucleic Acids Res , vol.33 , pp. 903-911
    • Tanaka, F.1    Kameda, A.2    Yamamoto, M.3    Ohuchi, A.4
  • 15
    • 40649083423 scopus 로고    scopus 로고
    • A New Readout Approach in DNA computing based on real-time PCR with TaqMan probes
    • DOI: 10.1007/ 11925903_27
    • Ibrahim, Z., Y. Tsuboi, J.A. Rose, O. Ono and M. Khalid, 2006. A New Readout Approach in DNA computing based on real-time PCR with TaqMan probes. Lecture Notes Comput. Sci., 4287: 350-359. DOI: 10.1007/ 11925903_27
    • (2006) Lecture Notes Comput. Sci , vol.4287 , pp. 350-359
    • Ibrahim, Z.1    Tsuboi, Y.2    Rose, J.A.3    Ono, O.4    Khalid, M.5
  • 16
    • 0028114541 scopus 로고
    • Molecular computation of solutions to combinatorial problems
    • Adleman, L., 1994. Molecular computation of solutions to combinatorial problems. Science, 266: 1021-1024 http://www.ncbi.nlm.nih.gov/pubmed/ 7973651
    • (1994) Science , vol.266 , pp. 1021-1024
    • Adleman, L.1
  • 17
    • 64249127794 scopus 로고    scopus 로고
    • Tevfik, M., 2002. Real Time PCR. http://dorakmt.tripod.com/genetics/ realtime.html.
    • (2002) Real Time PCR
    • Tevfik, M.1
  • 19
    • 17744396167 scopus 로고    scopus 로고
    • Multiobjective evolutionary optimization of DNA sequences for reliable DNA computing
    • DOI: 10.1109/TEVC.2005.844166
    • Shin, S.Y., I.H. Lee, D. Kim and B.T. Zhang, 2005. Multiobjective evolutionary optimization of DNA sequences for reliable DNA computing. IEEE Trans. Evolut. Comput., 9: 143-158. DOI: 10.1109/TEVC.2005.844166
    • (2005) IEEE Trans. Evolut. Comput , vol.9 , pp. 143-158
    • Shin, S.Y.1    Lee, I.H.2    Kim, D.3    Zhang, B.T.4
  • 20
    • 0018787038 scopus 로고
    • Hybridization of synthetic oligodeoxyribonucleotides to phi chi 174 DNA: The effect of single base pair mismatch
    • Wallace R.B., J. Shaffer, R.F. Murphy, J. Bonner, T. Hirose and K. Itakura, 1979. Hybridization of synthetic oligodeoxyribonucleotides to phi chi 174 DNA: The effect of single base pair mismatch. Nucleic Acids Res, 6: 3543-3558. http://nar.oxfordjournals.org/cgi/content/abstract/6/ 11/3543
    • (1979) Nucleic Acids Res , vol.6 , pp. 3543-3558
    • Wallace, R.B.1    Shaffer, J.2    Murphy, R.F.3    Bonner, J.4    Hirose, T.5    Itakura, K.6
  • 21
    • 0025944267 scopus 로고    scopus 로고
    • Wetmur, J.G., 1991, DNA probes: Applications of the principles of nucleic acid hybridization. Critical Rev. Biochem. Molecular Bio., 26: 227-259. DOI: 10.3109/10409239109114069
    • Wetmur, J.G., 1991, DNA probes: Applications of the principles of nucleic acid hybridization. Critical Rev. Biochem. Molecular Bio., 26: 227-259. DOI: 10.3109/10409239109114069
  • 22
    • 0001550068 scopus 로고
    • Predicting DNA duplex stability from the base sequence
    • Breslauer, K.J., R. Frank, H. Blocker and L.A. Marky, 1986. Predicting DNA duplex stability from the base sequence. Proc. Natl. Acad. Sci. USA., 83: 3746-3750. http://www.pnas.org/content/83/11/3746.full.pdf
    • (1986) Proc. Natl. Acad. Sci. USA , vol.83 , pp. 3746-3750
    • Breslauer, K.J.1    Frank, R.2    Blocker, H.3    Marky, L.A.4
  • 23
    • 0029968822 scopus 로고    scopus 로고
    • Improved nearest-neighbor parameters for predicting DNA duplex stability
    • DOI: 10.1021/bi951907q
    • Lucia Jr, J.S. H.T. Allawi and P.A. Seneviratne, 1996. Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry, 35: 3555-3562. DOI: 10.1021/bi951907q
    • (1996) Biochemistry , vol.35 , pp. 3555-3562
    • Lucia Jr, J.S.H.T.A.1    Seneviratne, P.A.2
  • 24
    • 0032539693 scopus 로고    scopus 로고
    • A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics
    • Academy of Science, Feb. 17-17, USA, pp
    • Lucia, Jr. JS. 1998. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proceeding of National Academy of Science, Feb. 17-17, USA., pp: 1460-1465. http://www.pnas.org/content/95/4/1460.abstract
    • (1998) Proceeding of National , pp. 1460-1465
    • Lucia Jr., J.S.1
  • 25
    • 0029859713 scopus 로고    scopus 로고
    • Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes
    • Sugimoto, N., S. Nakano, M. Yoneyama, K. Honda, 1996. Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acid Res., 24: 4501-4505. http://nar.oxfordjournals.org/cgi/content/abstract/24/22/4501
    • (1996) Nucleic Acid Res , vol.24 , pp. 4501-4505
    • Sugimoto, N.1    Nakano, S.2    Yoneyama, M.3    Honda, K.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.