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Volumn 9, Issue 4, 2014, Pages

Methods for the preparation of large quantities of complex single-stranded oligonucleotide libraries

Author keywords

[No Author keywords available]

Indexed keywords

OLIGONUCLEOTIDE; COMPLEMENTARY DNA; RNA; SINGLE STRANDED DNA; STREPTAVIDIN;

EID: 84899623691     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0094752     Document Type: Article
Times cited : (43)

References (45)
  • 2
    • 11144247743 scopus 로고    scopus 로고
    • Accurate multiplex gene synthesis from programmable DNA microchips
    • Tian J, Gong H, Sheng N, Zhou X, Gulari E, et al. (2004) Accurate multiplex gene synthesis from programmable DNA microchips. Nature 432: 1050.
    • (2004) Nature , vol.432 , pp. 1050
    • Tian, J.1    Gong, H.2    Sheng, N.3    Zhou, X.4    Gulari, E.5
  • 6
    • 27244436950 scopus 로고    scopus 로고
    • Multiplex amplification enabled by selective circularization of large sets of genomic DNA fragments
    • Dahl F, Gullberg M, Stenberg J, Landegren U, Nilsson M (2005) Multiplex amplification enabled by selective circularization of large sets of genomic DNA fragments. Nucleic Acids Res 33: e71.
    • (2005) Nucleic Acids Res , vol.33
    • Dahl, F.1    Gullberg, M.2    Stenberg, J.3    Landegren, U.4    Nilsson, M.5
  • 8
    • 59849113821 scopus 로고    scopus 로고
    • Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing
    • Gnirke A, Melnikov A, Maguire J, Rogov P, LeProust EM, et al. (2009) Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotech 27: 182.
    • (2009) Nat Biotech , vol.27 , pp. 182
    • Gnirke, A.1    Melnikov, A.2    Maguire, J.3    Rogov, P.4    Leproust, E.M.5
  • 9
    • 80755142727 scopus 로고    scopus 로고
    • Efficient targeted resequencing of human germline and cancer genomes by oligonucleotide-selective sequencing
    • Myllykangas S, Buenrostro JD, Natsoulis G, Bell JM, Ji HP (2011) Efficient targeted resequencing of human germline and cancer genomes by oligonucleotide-selective sequencing. Nat Biotechnol 29: 1024-1027.
    • (2011) Nat Biotechnol , vol.29 , pp. 1024-1027
    • Myllykangas, S.1    Buenrostro, J.D.2    Natsoulis, G.3    Bell, J.M.4    Ji, H.P.5
  • 10
  • 11
    • 20844438492 scopus 로고    scopus 로고
    • Production of complex nucleic acid libraries using highly parallel in situ oligonucleotide synthesis
    • Cleary MA, Kilian K, Wang Y, Bradshaw J, Cavet G, et al. (2004) Production of complex nucleic acid libraries using highly parallel in situ oligonucleotide synthesis. Nat Methods 1: 241-248.
    • (2004) Nat Methods , vol.1 , pp. 241-248
    • Cleary, M.A.1    Kilian, K.2    Wang, Y.3    Bradshaw, J.4    Cavet, G.5
  • 12
    • 27744489219 scopus 로고    scopus 로고
    • Highthroughput site-directed mutagenesis using oligonucleotides synthesized on DNA chips
    • Saboulard D, Dugas V, Jaber M, Broutin J, Souteyrand E, et al. (2005) Highthroughput site-directed mutagenesis using oligonucleotides synthesized on DNA chips. Biotechniques 39: 363-368.
    • (2005) Biotechniques , vol.39 , pp. 363-368
    • Saboulard, D.1    Dugas, V.2    Jaber, M.3    Broutin, J.4    Souteyrand, E.5
  • 13
    • 84875101243 scopus 로고    scopus 로고
    • From design to screening: A new antimicrobial peptide discovery pipeline
    • Guralp SA, Murgha YE, Rouillard JM, Gulari E (2013) From design to screening: a new antimicrobial peptide discovery pipeline. PLoS One 8: e59305.
    • (2013) PLoS One , vol.8
    • Guralp, S.A.1    Murgha, Y.E.2    Rouillard, J.M.3    Gulari, E.4
  • 14
    • 84899626124 scopus 로고    scopus 로고
    • United States: President and Fellows of Havard College (Cambridge, MA, US)
    • Wu C-tB, MA, US), Church, George M. (Brookline, MA, US), Williams, Benjamin Richard (Seattle, WA, US) (2010) Oligonucleotide Paints. United States: President and Fellows of Havard College (Cambridge, MA, US).
    • (2010) Oligonucleotide Paints
    • Wu, C.B.1    Church, G.M.2    Williams, B.R.3
  • 15
    • 0015499976 scopus 로고
    • Gene 6 exonuclease of bacteriophage T7. II. Mechanism of the reaction
    • Kerr C, Sadowski PD (1972) Gene 6 exonuclease of bacteriophage T7. II. Mechanism of the reaction. J Biol Chem 247: 311-318.
    • (1972) J Biol Chem , vol.247 , pp. 311-318
    • Kerr, C.1    Sadowski, P.D.2
  • 16
    • 0019142844 scopus 로고
    • Cloning of the exonuclease III gene of Escherichia coli
    • DOI 10.1016/0378-1119(80)90059-1
    • Rogers SG, Weiss B (1980) Cloning of the exonuclease III gene of Escherichia coli. Gene 11: 187-195. (Pubitemid 11215342)
    • (1980) Gene , vol.11 , Issue.3-4 , pp. 187-195
    • Rogers, S.G.1    Weiss, B.2
  • 17
    • 0028249864 scopus 로고
    • Ordered deletions using exonuclease III
    • Clark D, Henikoff S (1994) Ordered deletions using exonuclease III. Methods Mol Biol 31: 47-55.
    • (1994) Methods Mol Biol , vol.31 , pp. 47-55
    • Clark, D.1    Henikoff, S.2
  • 18
    • 0028210782 scopus 로고
    • The use of phosphorothioate primers and exonuclease hydrolysis for the preparation of single-stranded PCR products and their detection by solid-phase hybridization
    • Nikiforov TT, Rendle RB, Kotewicz ML, Rogers YH (1994) The use of phosphorothioate primers and exonuclease hydrolysis for the preparation of single-stranded PCR products and their detection by solid-phase hybridization. PCR Methods Appl 3: 285-291.
    • (1994) PCR Methods Appl , vol.3 , pp. 285-291
    • Nikiforov, T.T.1    Rendle, R.B.2    Kotewicz, M.L.3    Rogers, Y.H.4
  • 19
    • 0027721986 scopus 로고
    • Rapid production of single-stranded sequencing template from amplified DNA using magnetic beads
    • Bowman BH, Palumbi SR (1993) Rapid production of single-stranded sequencing template from amplified DNA using magnetic beads. Methods Enzymol 224: 399-406.
    • (1993) Methods Enzymol , vol.224 , pp. 399-406
    • Bowman, B.H.1    Palumbi, S.R.2
  • 20
    • 0037443869 scopus 로고    scopus 로고
    • The enzymatic basis of processivity in λ exonuclease
    • DOI 10.1093/nar/gkg266
    • Subramanian K, Rutvisuttinunt W, Scott W, Myers RS (2003) The enzymatic basis of processivity in lambda exonuclease. Nucleic Acids Res 31: 1585-1596. (Pubitemid 36336560)
    • (2003) Nucleic Acids Research , vol.31 , Issue.6 , pp. 1585-1596
    • Subramanian, K.1    Rutvisuttinunt, W.2    Scott, W.3    Myers, R.S.4
  • 22
    • 17044386980 scopus 로고    scopus 로고
    • Design and application of an oligonucleotide microarray for the investigation of compost microbial communities
    • Franke-Whittle IH, Klammer SH, Insam H (2005) Design and application of an oligonucleotide microarray for the investigation of compost microbial communities. J Microbiol Methods 62: 37-56.
    • (2005) J Microbiol Methods , vol.62 , pp. 37-56
    • Franke-Whittle, I.H.1    Klammer, S.H.2    Insam, H.3
  • 23
    • 77956902264 scopus 로고    scopus 로고
    • Lambda exonuclease pretreatment for improved DNA-chip performance depends on the relative probetarget position
    • Brinker A, Schulze H, Bachmann T, Moller R (2010) Lambda exonuclease pretreatment for improved DNA-chip performance depends on the relative probetarget position. Biosens Bioelectron 26: 898-902.
    • (2010) Biosens Bioelectron , vol.26 , pp. 898-902
    • Brinker, A.1    Schulze, H.2    Bachmann, T.3    Moller, R.4
  • 24
    • 0018449850 scopus 로고
    • The use of exonuclease III for preparing single stranded DNA for use as a template in the chain terminator sequencing method
    • Smith AJ (1979) The use of exonuclease III for preparing single stranded DNA for use as a template in the chain terminator sequencing method. Nucleic Acids Res 6: 831-848.
    • (1979) Nucleic Acids Res , vol.6 , pp. 831-848
    • Smith, A.J.1
  • 26
    • 79952529043 scopus 로고    scopus 로고
    • Aptamers selected by cell-SELEX for application in cancer studies
    • Zhang Y, Chen Y, Han D, Ocsoy I, Tan W (2010) Aptamers selected by cell-SELEX for application in cancer studies. Bioanalysis 2: 907-918.
    • (2010) Bioanalysis , vol.2 , pp. 907-918
    • Zhang, Y.1    Chen, Y.2    Han, D.3    Ocsoy, I.4    Tan, W.5
  • 28
    • 33646362745 scopus 로고    scopus 로고
    • Direct amplification of single-stranded DNA for pyrosequencing using linear-after-the-exponential (LATE)-PCR
    • DOI 10.1016/j.ab.2006.02.012, PII S000326970600114X
    • Salk JJ, Sanchez JA, Pierce KE, Rice JE, Soares KC, et al. (2006) Direct amplification of single-stranded DNA for pyrosequencing using linear-after-theexponential (LATE)-PCR. Analytical Biochemistry 353: 124-132. (Pubitemid 43668947)
    • (2006) Analytical Biochemistry , vol.353 , Issue.1 , pp. 124-132
    • Salk, J.J.1    Sanchez, J.A.2    Pierce, K.E.3    Rice, J.E.4    Soares, K.C.5    Wangh, L.J.6
  • 29
    • 26444543893 scopus 로고    scopus 로고
    • Improved microarray methods for profiling the Yeast Knockout strain collection
    • Yuan DS, Pan X, Ooi SL, Peyser BD, Spencer FA, et al. (2005) Improved microarray methods for profiling the Yeast Knockout strain collection. Nucleic Acids Res 33: e103.
    • (2005) Nucleic Acids Res , vol.33
    • Yuan, D.S.1    Pan, X.2    Ooi, S.L.3    Peyser, B.D.4    Spencer, F.A.5
  • 30
    • 34948830630 scopus 로고    scopus 로고
    • Multiplex asymmetric PCR-based oligonucleotide microarray for detection of drug resistance genes containing single mutations in Enterobacteriaceae
    • DOI 10.1128/AAC.01461-06
    • Zhu LX, Zhang ZW, Liang D, Jiang D, Wang C, et al. (2007) Multiplex asymmetric PCR-based oligonucleotide microarray for detection of drug resistance genes containing single mutations in Enterobacteriaceae. Antimicrob Agents Chemother 51: 3707-3713. (Pubitemid 47519362)
    • (2007) Antimicrobial Agents and Chemotherapy , vol.51 , Issue.10 , pp. 3707-3713
    • Zhu, L.-X.1    Zhang, Z.-W.2    Liang, D.3    Jiang, D.4    Wang, C.5    Du, N.6    Zhang, Q.7    Mitchelson, K.8    Cheng, J.9
  • 31
    • 36049044392 scopus 로고    scopus 로고
    • Linear-after-the-exponential polymerase chain reaction and allied technologies. Real-time detection strategies for rapid, reliable diagnosis from single cells
    • Pierce KE, Wangh LJ (2007) Linear-after-the-exponential polymerase chain reaction and allied technologies. Real-time detection strategies for rapid, reliable diagnosis from single cells. Methods Mol Med 132: 65-85.
    • (2007) Methods Mol Med , vol.132 , pp. 65-85
    • Pierce, K.E.1    Wangh, L.J.2
  • 32
    • 0017185043 scopus 로고
    • DNA degradation during standard alkaline of thermal denaturation
    • Drozhdeniuk AP, Sulimova GE, Vaniushin BF (1976) [DNA degradation during standard alkaline of thermal denaturation]. Biokhimiia 41: 1250-1255.
    • (1976) Biokhimiia , vol.41 , pp. 1250-1255
    • Drozhdeniuk, A.P.1    Sulimova, G.E.2    Vaniushin, B.F.3
  • 34
    • 0014601924 scopus 로고
    • The alkaline denaturation of DNA
    • Ageno M, Dore E, Frontali C (1969) The alkaline denaturation of DNA. Biophys J 9: 1281-1311.
    • (1969) Biophys J , vol.9 , pp. 1281-1311
    • Ageno, M.1    Dore, E.2    Frontali, C.3
  • 36
    • 0026676158 scopus 로고
    • Viral RNA-dependent DNA polymerase
    • Baltimore D (1992) Viral RNA-dependent DNA polymerase. 1970. Biotechnology 24: 3-5.
    • (1992) 1970. Biotechnology , vol.24 , pp. 3-5
    • Baltimore, D.1
  • 37
    • 0031905292 scopus 로고    scopus 로고
    • Viral RNA-dependent DNA polymerase RNA-dependent DNA polymerase in virions of Rous sarcoma virus
    • DOI 10.1002/(SICI)1099-1654(199801/03) 8:1<3::AID-RMV218>3.0.CO;2-#
    • Weiss R (1998) Viral RNA-dependent DNA polymerase RNA-dependent DNA polymerase in virions of Rous sarcoma virus. Rev Med Virol 8: 3-11. (Pubitemid 28095677)
    • (1998) Reviews in Medical Virology , vol.8 , Issue.1 , pp. 3-11
    • Weiss, R.A.1
  • 38
    • 0023651444 scopus 로고
    • Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates
    • Milligan JF, Groebe DR, Witherell GW, Uhlenbeck OC (1987) Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res 15: 8783-8798.
    • (1987) Nucleic Acids Res , vol.15 , pp. 8783-8798
    • Milligan, J.F.1    Groebe, D.R.2    Witherell, G.W.3    Uhlenbeck, O.C.4
  • 40
    • 14944364973 scopus 로고    scopus 로고
    • The biotin-streptavidin interaction can be reversibly broken using water at elevated temperatures
    • DOI 10.1002/elps.200410070
    • Holmberg A, Blomstergren A, Nord O, Lukacs M, Lundeberg J, et al. (2005) The biotin-streptavidin interaction can be reversibly broken using water at elevated temperatures. Electrophoresis 26: 501-510. (Pubitemid 40372776)
    • (2005) Electrophoresis , vol.26 , Issue.3 , pp. 501-510
    • Holmberg, A.1    Blomstergren, A.2    Nord, O.3    Lukacs, M.4    Lundeberg, J.5    Uhlen, M.6
  • 41
    • 67649553555 scopus 로고    scopus 로고
    • Microfluidic reactor array device for massively parallel in-situ synthesis of oligonucleotides
    • Srivannavit O, Gulari M, Hua Z, Gao X, Zhou X, et al. (2009) Microfluidic Reactor Array Device for Massively Parallel In-situ Synthesis of Oligonucleotides. Sens Actuators B Chem 140: 473-481.
    • (2009) Sens Actuators B Chem , vol.140 , pp. 473-481
    • Srivannavit, O.1    Gulari, M.2    Hua, Z.3    Gao, X.4    Zhou, X.5
  • 42
    • 0030012342 scopus 로고    scopus 로고
    • High-density oligonucleotide arrays
    • DOI 10.1016/0956-5663(96)83302-1, Surface Characterization and Optical Sensing Methods in Biosensors
    • Blanchard AP, Kaiser RJ, Hood LE (1996) High-density oligonucleotide arrays. Biosensors and Bioelectronics 11: 687-690. (Pubitemid 26153677)
    • (1996) Biosensors and Bioelectronics , vol.11 , Issue.6-7 , pp. 687-690
    • Blanchard, A.P.1    Kaiser, R.J.2    Hood, L.E.3
  • 43
    • 0025748046 scopus 로고
    • Synthesis and purification of large amounts of RNA oligonucleotides
    • Wyatt JR, Chastain M, Puglisi JD (1991) Synthesis and purification of large amounts of RNA oligonucleotides. Biotechniques 11: 764-769.
    • (1991) Biotechniques , vol.11 , pp. 764-769
    • Wyatt, J.R.1    Chastain, M.2    Puglisi, J.D.3
  • 44
    • 0018355854 scopus 로고
    • Four T7 RNA polymerase promoters contain an identical 23 bp sequence
    • Rosa M.D. 1979 Four T7 RNA polymerase promoters contain an identical 23 bp sequence Cell 16 815-825. (Pubitemid 9161332)
    • (1979) Cell , vol.16 , Issue.4 , pp. 815-825
    • Rosa, M.D.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.