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Volumn 94, Issue 1, 2006, Pages 54-65

Minimizing loss of sequence information in SAGE ditags by modulating the temperature dependent 3′ → 5′ exonuclease activity of DNA polymerases on 3′-terminal isoheptyl amino groups

Author keywords

DNA polymerase; Exonuclease; Phosphorothioate; Recovery of sequence information; Serial analysis of gene expression

Indexed keywords

AMINO ACIDS; AMPLIFICATION; GELS; PHOSPHORUS COMPOUNDS; PURIFICATION; RNA; THERMAL EFFECTS;

EID: 33646571251     PISSN: 00063592     EISSN: 10970290     Source Type: Journal    
DOI: 10.1002/bit.20805     Document Type: Article
Times cited : (1)

References (38)
  • 1
    • 0030131118 scopus 로고    scopus 로고
    • Serial analysis of gene expression: ESTs get smaller
    • Adams MD. 1996. Serial analysis of gene expression: ESTs get smaller. Bioessays 18(4):261-262.
    • (1996) Bioessays , vol.18 , Issue.4 , pp. 261-262
    • Adams, M.D.1
  • 2
    • 3042641339 scopus 로고    scopus 로고
    • Correction of sequence-based artifacts in serial analysis of gene expression
    • Akmaev VR, Wang CJ. 2004. Correction of sequence-based artifacts in serial analysis of gene expression. Bioinformatics 20(8):1254-1263.
    • (2004) Bioinformatics , vol.20 , Issue.8 , pp. 1254-1263
    • Akmaev, V.R.1    Wang, C.J.2
  • 3
    • 0842311287 scopus 로고    scopus 로고
    • Thermodynamic dissection of the polymerizing and editing modes of a DNA polymerase
    • Bailey MF, van der Schans EJ, Millar DP. 2004. Thermodynamic dissection of the polymerizing and editing modes of a DNA polymerase. J Mol Biol 336(3):673-693.
    • (2004) J Mol Biol , vol.336 , Issue.3 , pp. 673-693
    • Bailey, M.F.1    Van Der Schans, E.J.2    Millar, D.P.3
  • 4
    • 0036277572 scopus 로고    scopus 로고
    • Transcriptome analysis of Saccharomyces cerevisiae using serial analysis of gene expression
    • Basrai MA, Hieter P. 2002. Transcriptome analysis of Saccharomyces cerevisiae using serial analysis of gene expression. Methods Enzymol 350:414-444.
    • (2002) Methods Enzymol , vol.350 , pp. 414-444
    • Basrai, M.A.1    Hieter, P.2
  • 5
    • 0037309660 scopus 로고    scopus 로고
    • The new role of SAGE in gene discovery
    • Boheler KR, Stern MD. 2003. The new role of SAGE in gene discovery. Trends Biotechnol 21(2):55-57.
    • (2003) Trends Biotechnol , vol.21 , Issue.2 , pp. 55-57
    • Boheler, K.R.1    Stern, M.D.2
  • 6
    • 0034194135 scopus 로고    scopus 로고
    • Thermodynamic parameters for DNA sequences with dangling ends
    • Bommarito S, Peyret N, Santa Lucia J, Jr. 2000. Thermodynamic parameters for DNA sequences with dangling ends. Nucleic Acids Res 28(9):1929-1934.
    • (2000) Nucleic Acids Res , vol.28 , Issue.9 , pp. 1929-1934
    • Bommarito, S.1    Peyret, N.2    Santa Lucia Jr., J.3
  • 7
    • 0032571245 scopus 로고    scopus 로고
    • Structural principles for the inhibition of the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase I by phosphorothioates
    • Brautigam CA, Steitz TA. 1998. Structural principles for the inhibition of the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase I by phosphorothioates. J Mol Biol 277(2):363-377.
    • (1998) J Mol Biol , vol.277 , Issue.2 , pp. 363-377
    • Brautigam, C.A.1    Steitz, T.A.2
  • 8
    • 0028806638 scopus 로고
    • Catalytic editing properties of DNA polymerases
    • Canard B, Cardona B, Sarfati RS. 1995. Catalytic editing properties of DNA polymerases. Proc Natl Acad Sci USA 92(24):10859-10863.
    • (1995) Proc Natl Acad Sci USA , vol.92 , Issue.24 , pp. 10859-10863
    • Canard, B.1    Cardona, B.2    Sarfati, R.S.3
  • 10
    • 0037126025 scopus 로고    scopus 로고
    • Identifying novel transcripts and novel genes in the human genome by using novel SAGE tags
    • Chen J, Sun M, Lee S, Zhou G, Rowley JD, Wang SM. 2002. Identifying novel transcripts and novel genes in the human genome by using novel SAGE tags. Proc Natl Acad Sci USA 99(19):12257-12262.
    • (2002) Proc Natl Acad Sci USA , vol.99 , Issue.19 , pp. 12257-12262
    • Chen, J.1    Sun, M.2    Lee, S.3    Zhou, G.4    Rowley, J.D.5    Wang, S.M.6
  • 11
    • 0035991755 scopus 로고    scopus 로고
    • Computational analysis of gene identification with sage
    • Clark T, Lee S, Ridgway Scott L, Wang SM. 2002. Computational analysis of gene identification with sage. J Comput Biol 9(3):513-526.
    • (2002) J Comput Biol , vol.9 , Issue.3 , pp. 513-526
    • Clark, T.1    Lee, S.2    Ridgway Scott, L.3    Wang, S.M.4
  • 12
    • 1642332243 scopus 로고    scopus 로고
    • Single base extension (SBE) with proofreading polymerases and phosphorothioate primers: Improved fidelity in single-substrate assays
    • Di Giusto D, King GC. 2003. Single base extension (SBE) with proofreading polymerases and phosphorothioate primers: Improved fidelity in single-substrate assays. Nucleic Acids Res 31(3):e7.
    • (2003) Nucleic Acids Res , vol.31 , Issue.3
    • Di Giusto, D.1    King, G.C.2
  • 13
    • 1642506317 scopus 로고    scopus 로고
    • Robust-long SAGE (RL-SAGE): A substantially improved LongSAGE method for gene discovery and transcriptome analysis
    • Gowda M, Jantasuriyarat C, Dean RA, Wang GL. 2004. Robust-long SAGE (RL-SAGE): A substantially improved LongSAGE method for gene discovery and transcriptome analysis. Plant Physiol 134(3):890-897.
    • (2004) Plant Physiol , vol.134 , Issue.3 , pp. 890-897
    • Gowda, M.1    Jantasuriyarat, C.2    Dean, R.A.3    Wang, G.L.4
  • 14
    • 0021770756 scopus 로고
    • The effect of the 3′,5′ thiophosphoryl linkage on the exonuclease activities of T4 polymerase and the Klenow fragment
    • Gupta AP, Benkovic PA, Benkovic SJ. 1984. The effect of the 3′,5′ thiophosphoryl linkage on the exonuclease activities of T4 polymerase and the Klenow fragment. Nucleic Acids Res 12(14):5897-5911.
    • (1984) Nucleic Acids Res , vol.12 , Issue.14 , pp. 5897-5911
    • Gupta, A.P.1    Benkovic, P.A.2    Benkovic, S.J.3
  • 15
    • 23644460630 scopus 로고    scopus 로고
    • Tag-based approaches for transcriptome research and genome annotation
    • Harbers M, Carninci P. 2005. Tag-based approaches for transcriptome research and genome annotation. Nat Methods 2(7):495-502.
    • (2005) Nat Methods , vol.2 , Issue.7 , pp. 495-502
    • Harbers, M.1    Carninci, P.2
  • 16
    • 0141567644 scopus 로고    scopus 로고
    • Comparative thermal denaturation of thermus aquaticus and Escherichia coli type 1 DNA polymerases
    • Karantzeni I, Ruiz C, Liu CC, Licata VJ. 2003. Comparative thermal denaturation of thermus aquaticus and Escherichia coli type 1 DNA polymerases. Biochem J 374(Pt 3):785-792.
    • (2003) Biochem J , vol.374 , Issue.PART 3 , pp. 785-792
    • Karantzeni, I.1    Ruiz, C.2    Liu, C.C.3    Licata, V.J.4
  • 17
    • 0027391640 scopus 로고
    • Characterization of a DNA polymerase from the hyperthermophile archaea thermococcus litoralis. Vent DNA polymerase, steady state kinetics, thermal stability, processivity, strand displacement, and exonuclease activities
    • Kong H, Kucera RB, Jack WE. 1993. Characterization of a DNA polymerase from the hyperthermophile archaea thermococcus litoralis. Vent DNA polymerase, steady state kinetics, thermal stability, processivity, strand displacement, and exonuclease activities. J Biol Chem 268(3):1965-1975.
    • (1993) J Biol Chem , vol.268 , Issue.3 , pp. 1965-1975
    • Kong, H.1    Kucera, R.B.2    Jack, W.E.3
  • 19
    • 4744376550 scopus 로고    scopus 로고
    • A comparison of gene expression profiles produced by SAGE, long SAGE, and oligonucleotide chips
    • Lu J, Lal A, Merriman B, Nelson S, Riggins G. 2004. A comparison of gene expression profiles produced by SAGE, long SAGE, and oligonucleotide chips. Genomics 84(4):631-636.
    • (2004) Genomics , vol.84 , Issue.4 , pp. 631-636
    • Lu, J.1    Lal, A.2    Merriman, B.3    Nelson, S.4    Riggins, G.5
  • 22
    • 0020480166 scopus 로고
    • Sealing of gaps in duplex DNA by T4 DNA ligase
    • Nilsson SV, Magnusson G. 1982. Sealing of gaps in duplex DNA by T4 DNA ligase. Nucleic Acids Res 10(5):1425-1437.
    • (1982) Nucleic Acids Res , vol.10 , Issue.5 , pp. 1425-1437
    • Nilsson, S.V.1    Magnusson, G.2
  • 23
    • 0037803473 scopus 로고    scopus 로고
    • Assessment of SAGE in transcript identification
    • Pleasance ED, Marra MA, Jones SJ. 2003. Assessment of SAGE in transcript identification. Genome Res 13(6A):1203-12015.
    • (2003) Genome Res , vol.13 , Issue.6 A , pp. 1203-12015
    • Pleasance, E.D.1    Marra, M.A.2    Jones, S.J.3
  • 24
    • 0025121103 scopus 로고
    • Identification of residues critical for the polymerase activity of the Klenow fragment of DNA polymerase I from Escherichia coli
    • Polesky AH, Steitz TA, Grindley ND, Joyce CM. 1990. Identification of residues critical for the polymerase activity of the Klenow fragment of DNA polymerase I from Escherichia coli. J Biol Chem 265(24):14579-14591.
    • (1990) J Biol Chem , vol.265 , Issue.24 , pp. 14579-14591
    • Polesky, A.H.1    Steitz, T.A.2    Grindley, N.D.3    Joyce, C.M.4
  • 27
    • 0024290403 scopus 로고
    • Influence of dangling thymidine residues on the stability and structure of two DNA duplexes
    • Senior M, Jones RA, Breslauer KJ. 1988. Influence of dangling thymidine residues on the stability and structure of two DNA duplexes. Biochemistry 27(10):3879-3885.
    • (1988) Biochemistry , vol.27 , Issue.10 , pp. 3879-3885
    • Senior, M.1    Jones, R.A.2    Breslauer, K.J.3
  • 28
    • 0026718980 scopus 로고
    • Phosphorothioate primers improve the amplification of DNA sequences by DNA polymerases with proofreading activity
    • Skerra A. 1992. Phosphorothioate primers improve the amplification of DNA sequences by DNA polymerases with proofreading activity. Nucleic Acids Res 20(14):3551-3554.
    • (1992) Nucleic Acids Res , vol.20 , Issue.14 , pp. 3551-3554
    • Skerra, A.1
  • 29
    • 3042855520 scopus 로고    scopus 로고
    • Increasing the efficiency of SAGE adaptor ligation by directed ligation chemistry
    • So AP, Turner RF, Haynes CA. 2004. Increasing the efficiency of SAGE adaptor ligation by directed ligation chemistry. Nucleic Acids Res 32(12):e96.
    • (2004) Nucleic Acids Res , vol.32 , Issue.12
    • So, A.P.1    Turner, R.F.2    Haynes, C.A.3
  • 35
    • 1842539357 scopus 로고    scopus 로고
    • Presteady-state kinetics of RB69 DNA polymerase and its exo domain mutants: Effect of pH and thiophosphoryl linkages on 3′-5′ exonuclease activity
    • Wang CX, Zakharova E, Li J, Joyce CM, Wang J, Konigsberg W. 2004. Presteady-state kinetics of RB69 DNA polymerase and its exo domain mutants: Effect of pH and thiophosphoryl linkages on 3′-5′ exonuclease activity. Biochemistry 43(13):3853-3861.
    • (2004) Biochemistry , vol.43 , Issue.13 , pp. 3853-3861
    • Wang, C.X.1    Zakharova, E.2    Li, J.3    Joyce, C.M.4    Wang, J.5    Konigsberg, W.6
  • 36
    • 0023652090 scopus 로고
    • Mismatch and blunt to protruding-end joining by DNA ligases
    • Wiaderkiewicz R, Ruiz-Carrillo A. 1987. Mismatch and blunt to protruding-end joining by DNA ligases. Nucleic Acids Res 15(19):7831-7848.
    • (1987) Nucleic Acids Res , vol.15 , Issue.19 , pp. 7831-7848
    • Wiaderkiewicz, R.1    Ruiz-Carrillo, A.2
  • 37
    • 0035313879 scopus 로고    scopus 로고
    • Use of serial analysis of gene expression (SAGE) technology
    • Yamamoto M, Wakatsuki T, Hada A, Ryo A. 2001. Use of serial analysis of gene expression (SAGE) technology. J Immunol Meth 250(1-2):45-66.
    • (2001) J Immunol Meth , vol.250 , Issue.1-2 , pp. 45-66
    • Yamamoto, M.1    Wakatsuki, T.2    Hada, A.3    Ryo, A.4
  • 38
    • 0034548049 scopus 로고    scopus 로고
    • miniSAGE: Gene expression profiling using serial analysis of gene expression from 1 microg total RNA
    • Ye SQ, Zhang LQ, Zheng F, Virgil D, Kwiterovich PO. 2000. miniSAGE: Gene expression profiling using serial analysis of gene expression from 1 microg total RNA. Anal Biochem 287(1):144-152.
    • (2000) Anal Biochem , vol.287 , Issue.1 , pp. 144-152
    • Ye, S.Q.1    Zhang, L.Q.2    Zheng, F.3    Virgil, D.4    Kwiterovich, P.O.5


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