메뉴 건너뛰기




Volumn 5, Issue 9, 2012, Pages 204-207

Amplicon secondary structure formation and elongation during the process of sequencing

Author keywords

DNA elongation; DNA sequencing; Mfold web server; Secondary structure; Secondary structure prediction; Single stranded DNA; Single stranded DNA folding

Indexed keywords

AGAROSE; DEOXYRIBONUCLEOSIDE TRIPHOSPHATE; DNA POLYMERASE; SINGLE STRANDED DNA;

EID: 84867665235     PISSN: None     EISSN: 0974276X     Source Type: Journal    
DOI: 10.4172/jpb.1000236     Document Type: Article
Times cited : (1)

References (26)
  • 1
    • 0038497542 scopus 로고
    • A Structure for Deoxyribose Nucleic Acid
    • Watson JD, Crick FHC (1953) A Structure for Deoxyribose Nucleic Acid. Nature 171: 737-738.
    • (1953) Nature , vol.171 , pp. 737-738
    • Watson, J.D.1    Crick, F.H.C.2
  • 2
    • 0032005902 scopus 로고    scopus 로고
    • Mechanistic parallels between DNA replication, recombination and transcription
    • Kodadek T (1998) Mechanistic parallels between DNA replication, recombination and transcription. Trends Biochem Sci 23: 79-83.
    • (1998) Trends Biochem Sci , vol.23 , pp. 79-83
    • Kodadek, T.1
  • 3
    • 0030024985 scopus 로고    scopus 로고
    • Overstretching B-DNA: The elastic response of individual double-stranded and single-stranded DNA molecules
    • Smith SB, Cui Y, Bustamante C (1996) Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules. Science 271: 795-799.
    • (1996) Science , vol.271 , pp. 795-799
    • Smith, S.B.1    Cui, Y.2    Bustamante, C.3
  • 4
    • 0034901419 scopus 로고    scopus 로고
    • Stretching single-stranded DNA: Interplay of electrostatic, base-pairing, and base-pair stacking interactions
    • Zhang Y, Zhou H, Ou-Yang ZC (2001) Stretching single-stranded DNA: interplay of electrostatic, base-pairing, and base-pair stacking interactions. Biophys J 81: 1133-1143.
    • (2001) Biophys J , vol.81 , pp. 1133-1143
    • Zhang, Y.1    Zhou, H.2    Ou-Yang, Z.C.3
  • 5
    • 0031151976 scopus 로고    scopus 로고
    • DNA aptamers and DNA enzymes
    • Breaker RR (1997) DNA aptamers and DNA enzymes. Curr Opin Chem Biol 1:26-31.
    • (1997) Curr Opin Chem Biol , vol.1 , pp. 26-31
    • Breaker, R.R.1
  • 8
    • 0242581339 scopus 로고
    • Generation of single-stranded DNA by the polymerase chain reaction and its application to direct sequencing of the HLA-DQA locus
    • Gyllensten UB, Erlich HA (1988) Generation of single-stranded DNA by the polymerase chain reaction and its application to direct sequencing of the HLA-DQA locus. Proc Natl Acad Sci U S A 85: 7652-7656.
    • (1988) Proc Natl Acad Sci U S A , vol.85 , pp. 7652-7656
    • Gyllensten, U.B.1    Erlich, H.A.2
  • 10
    • 0035420206 scopus 로고    scopus 로고
    • Secondary structure prediction and structure-specific sequence analysis of single-stranded DNA
    • Dong F, Allawi HT, Anderson T, Neri BP, Lyamichev VI (2001) Secondary structure prediction and structure-specific sequence analysis of single-stranded DNA. Nucleic Acids Res 29: 3248-3257.
    • (2001) Nucleic Acids Res , vol.29 , pp. 3248-3257
    • Dong, F.1    Allawi, H.T.2    Anderson, T.3    Neri, B.P.4    Lyamichev, V.I.5
  • 12
    • 33646172099 scopus 로고    scopus 로고
    • Monitoring single-stranded DNA secondary structure formation by determining the topological state of DNA catenanes
    • Liang X, Kuhn H, Frank-Kamenetskii MD (2006) Monitoring single-stranded DNA secondary structure formation by determining the topological state of DNA catenanes. Biophys J 90: 2877-2889.
    • (2006) Biophys J , vol.90 , pp. 2877-2889
    • Liang, X.1    Kuhn, H.2    Frank-Kamenetskii, M.D.3
  • 13
    • 0001494006 scopus 로고
    • Enzymatic synthesis of deoxyribonucleic acid, XVI. Oligonucleotides as templates and the mechanism of their replication
    • Kornberg A, Bertsch LL, Jackson JF, Khorana HG (1964) Enzymatic synthesis of deoxyribonucleic acid, XVI. Oligonucleotides as templates and the mechanism of their replication. Proc Natl Acad Sci U S A 51: 315-323.
    • (1964) Proc Natl Acad Sci U S A , vol.51 , pp. 315-323
    • Kornberg, A.1    Bertsch, L.L.2    Jackson, J.F.3    Khorana, H.G.4
  • 14
    • 78649428607 scopus 로고    scopus 로고
    • Mechanism of DNA elongation during de novo DNA synthesis
    • Liang X, Kato T, Asanuma H (2008) Mechanism of DNA elongation during de novo DNA synthesis. Nucleic Acids Symp Ser 52: 411-412.
    • (2008) Nucleic Acids Symp Ser , vol.52 , pp. 411-412
    • Liang, X.1    Kato, T.2    Asanuma, H.3
  • 15
    • 0024284028 scopus 로고
    • A simple salting out procedure for extracting DNA from human nucleated cells
    • Miller SA, Dykes DD, Polesky HF (1988) A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res 16: 1215.
    • (1988) Nucleic Acids Res , vol.16 , pp. 1215
    • Miller, S.A.1    Dykes, D.D.2    Polesky, H.F.3
  • 17
    • 0042121256 scopus 로고    scopus 로고
    • Mfold web server for nucleic acid folding and hybridization prediction
    • Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406-3415.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3406-3415
    • Zuker, M.1
  • 18
    • 0023660953 scopus 로고
    • Solution hybridization of crosslinkable DNA oligonucleotides to bacteriophage M13 DNA. Effect of secondary structure on hybridization kinetics and equilibria
    • Gamper HB, Cimino GD, Hearst JE (1987) Solution hybridization of crosslinkable DNA oligonucleotides to bacteriophage M13 DNA. Effect of secondary structure on hybridization kinetics and equilibria. J Mol Biol 197: 349-362.
    • (1987) J Mol Biol , vol.197 , pp. 349-362
    • Gamper, H.B.1    Cimino, G.D.2    Hearst, J.E.3
  • 19
    • 0026621339 scopus 로고
    • Implication of RNA structure on antisense oligonucleotide hybridization kinetics
    • Lima WF, Monia BP, Ecker DJ, Freier SM (1992) Implication of RNA structure on antisense oligonucleotide hybridization kinetics. Biochemistry 31: 12055-12061.
    • (1992) Biochemistry , vol.31 , pp. 12055-12061
    • Lima, W.F.1    Monia, B.P.2    Ecker, D.J.3    Freier, S.M.4
  • 20
    • 7444246694 scopus 로고    scopus 로고
    • Amplicon secondary structure prevents target hybridization to oligonucleotide microarrays
    • Lane S, Evermann J, Loge F, Call DR (2004) Amplicon secondary structure prevents target hybridization to oligonucleotide microarrays. Biosens Bioelectron 20: 728-735.
    • (2004) Biosens Bioelectron , vol.20 , pp. 728-735
    • Lane, S.1    Evermann, J.2    Loge, F.3    Call, D.R.4
  • 21
    • 33746207804 scopus 로고    scopus 로고
    • Secondary structure effects on DNA hybridization kinetics: A solution versus surface comparison
    • Gao Y, Wolf LK, Georgiadis RM (2006) Secondary structure effects on DNA hybridization kinetics: a solution versus surface comparison. Nucleic Acids Res 34: 3370-3377.
    • (2006) Nucleic Acids Res , vol.34 , pp. 3370-3377
    • Gao, Y.1    Wolf, L.K.2    Georgiadis, R.M.3
  • 22
    • 0031859535 scopus 로고    scopus 로고
    • Short-insert libraries as a method of problem solving in genome sequencing
    • McMurray AA, Sulston JE, Quail MA (1998) Short-insert libraries as a method of problem solving in genome sequencing. Genome Res 8: 562-566.
    • (1998) Genome Res , vol.8 , pp. 562-566
    • McMurray, A.A.1    Sulston, J.E.2    Quail, M.A.3
  • 24
    • 0024841809 scopus 로고
    • Enzymatic approaches to probing of RNA secondary and tertiary structure
    • Knapp G (1989) Enzymatic approaches to probing of RNA secondary and tertiary structure. Methods Enzymol 180: 192-212.
    • (1989) Methods Enzymol , vol.180 , pp. 192-212
    • Knapp, G.1
  • 25
    • 0025678737 scopus 로고
    • Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis
    • Michel F, Westhof E (1990) Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J Mol Biol 216: 585-610.
    • (1990) J Mol Biol , vol.216 , pp. 585-610
    • Michel, F.1    Westhof, E.2
  • 26
    • 0028823370 scopus 로고
    • An interactive framework for RNA secondary structure prediction with a dynamical treatment of constraints
    • Gaspin C, Westhof E (1995) An interactive framework for RNA secondary structure prediction with a dynamical treatment of constraints. J Mol Biol 254: 163-174.
    • (1995) J Mol Biol , vol.254 , pp. 163-174
    • Gaspin, C.1    Westhof, E.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.