메뉴 건너뛰기




Volumn 59, Issue 6, 2014, Pages 1517-1529

An investigation of PCR inhibition using plexor®-based quantitative PCR and short tandem repeat amplification

Author keywords

DNA typing; Forensic science; Inhibition; Melt curve; Plexor ; Real time polymerase chain reaction; Short tandem repeat

Indexed keywords

BILE ACID; CALCIUM PHOSPHATE; CALCIUM PHOSPHATE, DIBASIC, ANHYDROUS; COLLAGEN; EDETIC ACID; GUANIDINE DERIVATIVE; GUANIDINE THIOCYANATE; HEMIN; HYDROCHLORIC ACID; MICROSATELLITE DNA; PHENOL DERIVATIVE; TANNIN DERIVATIVE; THIOCYANIC ACID DERIVATIVE; UREA;

EID: 84911995443     PISSN: 00221198     EISSN: 15564029     Source Type: Journal    
DOI: 10.1111/1556-4029.12556     Document Type: Article
Times cited : (36)

References (55)
  • 1
    • 58149100307 scopus 로고    scopus 로고
    • An introduction to PCR inhibitors
    • Bessetti J. An introduction to PCR inhibitors. Profiles in DNA 2007;10(1):9-10.
    • (2007) Profiles in DNA , vol.10 , Issue.1 , pp. 9-10
    • Bessetti, J.1
  • 2
    • 0030748867 scopus 로고    scopus 로고
    • Inhibition and facilitation of nucleic acid amplification
    • Wilson I. Inhibition and facilitation of nucleic acid amplification. Appl Environ Microbiol 1997;63(10):3741-51.
    • (1997) Appl Environ Microbiol , vol.63 , Issue.10 , pp. 3741-3751
    • Wilson, I.1
  • 3
    • 17144421522 scopus 로고    scopus 로고
    • Effect of divalent metal ions on DNA studied by capillary electrophoresis
    • Hartzell B, McCord B. Effect of divalent metal ions on DNA studied by capillary electrophoresis. Electrophoresis 2005;26:1046-56.
    • (2005) Electrophoresis , vol.26 , pp. 1046-1056
    • Hartzell, B.1    McCord, B.2
  • 4
    • 77951298719 scopus 로고    scopus 로고
    • Influence of DNA extraction methods, PCR inhibitors and quantification methods on real-time PCR assay of biotechnology-derived traits
    • Demeke T, Jenkins GR. Influence of DNA extraction methods, PCR inhibitors and quantification methods on real-time PCR assay of biotechnology-derived traits. Anal Bioanal Chem 2010;396:1977-90.
    • (2010) Anal Bioanal Chem , vol.396 , pp. 1977-1990
    • Demeke, T.1    Jenkins, G.R.2
  • 6
    • 15744381713 scopus 로고
    • Kinetic PCR: real-time monitoring of DNA amplification reactions
    • Higuchi R, Fockler C, Dollinger G, Watson R. Kinetic PCR: real-time monitoring of DNA amplification reactions. Biotechnology 1993;11:1026-30.
    • (1993) Biotechnology , vol.11 , pp. 1026-1030
    • Higuchi, R.1    Fockler, C.2    Dollinger, G.3    Watson, R.4
  • 8
    • 0025861818 scopus 로고
    • Detection of specific polymerase chain reaction product by utilizing the 5′-3′ exonuclease activity of Thermus aquaticus DNA polymerase
    • Holland PM, Abramson RD, Watson R, Gelfand DH. Detection of specific polymerase chain reaction product by utilizing the 5′-3′ exonuclease activity of Thermus aquaticus DNA polymerase. Proc Natl Acad Sci USA 1991;88(16):7276-80.
    • (1991) Proc Natl Acad Sci USA , vol.88 , Issue.16 , pp. 7276-7280
    • Holland, P.M.1    Abramson, R.D.2    Watson, R.3    Gelfand, D.H.4
  • 9
    • 56549101793 scopus 로고    scopus 로고
    • Developmental validation of a real-time PCR assay for the simultaneous quantification of total human and male DNA
    • Krenke B, Nassif N, Sprecher C, Knox S, Schwandt M, Storts DR. Developmental validation of a real-time PCR assay for the simultaneous quantification of total human and male DNA. Forensic Sci Int Genet 2008;3:14-28.
    • (2008) Forensic Sci Int Genet , vol.3 , pp. 14-28
    • Krenke, B.1    Nassif, N.2    Sprecher, C.3    Knox, S.4    Schwandt, M.5    Storts, D.R.6
  • 11
    • 0031568919 scopus 로고    scopus 로고
    • Product differentiation by analysis of DNA melting curves during the polymerase chain reaction
    • Ririe KM, Rasmussen RP, Wittwer CT. Product differentiation by analysis of DNA melting curves during the polymerase chain reaction. Anal Biochem 1997;245(2):154-60.
    • (1997) Anal Biochem , vol.245 , Issue.2 , pp. 154-160
    • Ririe, K.M.1    Rasmussen, R.P.2    Wittwer, C.T.3
  • 12
    • 74249111651 scopus 로고    scopus 로고
    • A study of PCR inhibition mechanisms using real-time PCR
    • Opel K, Chung D, McCord BR. A study of PCR inhibition mechanisms using real-time PCR. J Forensic Sci 2010;55(1):25-33.
    • (2010) J Forensic Sci , vol.55 , Issue.1 , pp. 25-33
    • Opel, K.1    Chung, D.2    McCord, B.R.3
  • 13
    • 0028293407 scopus 로고
    • Mycobacterium smegmatis strain for detection of Mycobacterium tuberculosis by PCR used as internal control for inhibition of amplification and for quantitation of bacteria
    • Kolk AHJ, Noordhoek GT, De Leeuw O, Kuijper S, Van Embden JDA. Mycobacterium smegmatis strain for detection of Mycobacterium tuberculosis by PCR used as internal control for inhibition of amplification and for quantitation of bacteria. J Clin Microbiol 1994;32:1354-6.
    • (1994) J Clin Microbiol , vol.32 , pp. 1354-1356
    • Kolk, A.H.J.1    Noordhoek, G.T.2    De Leeuw, O.3    Kuijper, S.4    Van Embden, J.D.A.5
  • 14
    • 51349141379 scopus 로고    scopus 로고
    • A new real-time PCR method to overcome significant quantitative inaccuracy due to slight amplification inhibition
    • Guescini M, Sisti D, Rocchi M, Stocchi L, Stocchi V. A new real-time PCR method to overcome significant quantitative inaccuracy due to slight amplification inhibition. BMC Bioinformatics 2008;9(326):1-12.
    • (2008) BMC Bioinformatics , vol.9 , Issue.326 , pp. 1-12
    • Guescini, M.1    Sisti, D.2    Rocchi, M.3    Stocchi, L.4    Stocchi, V.5
  • 15
    • 4043147979 scopus 로고
    • A flexible growth function for empirical use
    • Richards FJ. A flexible growth function for empirical use. J Exp Bot 1959;10:290-300.
    • (1959) J Exp Bot , vol.10 , pp. 290-300
    • Richards, F.J.1
  • 16
    • 79954503793 scopus 로고    scopus 로고
    • A comparison of the effects of PCR inhibition in quantitative PCR and forensic STR analysis
    • Funes-Huacca ME, Opel K, Thompson R, McCord BR. A comparison of the effects of PCR inhibition in quantitative PCR and forensic STR analysis. Electrophoresis 2011;32(9):1084-9.
    • (2011) Electrophoresis , vol.32 , Issue.9 , pp. 1084-1089
    • Funes-Huacca, M.E.1    Opel, K.2    Thompson, R.3    McCord, B.R.4
  • 17
    • 0032827631 scopus 로고    scopus 로고
    • NaOH treatment to neutralize inhibitors of Taq polymerase
    • Bourke MT, Scherczinger CA, Ladd C, Lee HC. NaOH treatment to neutralize inhibitors of Taq polymerase. J Forensic Sci 1999;44(5):1046-50.
    • (1999) J Forensic Sci , vol.44 , Issue.5 , pp. 1046-1050
    • Bourke, M.T.1    Scherczinger, C.A.2    Ladd, C.3    Lee, H.C.4
  • 18
    • 0032127366 scopus 로고    scopus 로고
    • Efficient removal of PCR inhibitors using agarose-embedded DNA preparations
    • Moreira D. Efficient removal of PCR inhibitors using agarose-embedded DNA preparations. Nucleic Acids Res 1998;26:3309-10.
    • (1998) Nucleic Acids Res , vol.26 , pp. 3309-3310
    • Moreira, D.1
  • 20
    • 47349122123 scopus 로고    scopus 로고
    • ® MiniFiler™ PCR amplification kit: a MiniSTR multiplex for the analysis of degraded and/or PCR inhibited DNA
    • ® MiniFiler™ PCR amplification kit: a MiniSTR multiplex for the analysis of degraded and/or PCR inhibited DNA. J Forensic Sci 2008;53(4):838-52.
    • (2008) J Forensic Sci , vol.53 , Issue.4 , pp. 838-852
    • Mulero, J.1    Chang, C.2    Lagacé, R.E.3    Wang, D.4    Bas, J.L.5    McMahon, T.6
  • 24
    • 33745745782 scopus 로고    scopus 로고
    • Evaluation of real-time PCR amplification efficiencies to detect PCR inhibitors
    • Kontanis EJ, Reed FA. Evaluation of real-time PCR amplification efficiencies to detect PCR inhibitors. J Forensic Sci 2006;51(4):795-804.
    • (2006) J Forensic Sci , vol.51 , Issue.4 , pp. 795-804
    • Kontanis, E.J.1    Reed, F.A.2
  • 26
    • 0004237841 scopus 로고
    • Techniques for characterizing nonspecific protein DNA interactions
    • Revzin A, editor. Boca Raton, FL: CRC Press
    • Revzin A. Techniques for characterizing nonspecific protein DNA interactions. In: Revzin A, editor. The biology of nonspecific protein DNA interactions. Boca Raton, FL: CRC Press, 1990;15.
    • (1990) The biology of nonspecific protein DNA interactions , pp. 15
    • Revzin, A.1
  • 27
    • 0030070873 scopus 로고    scopus 로고
    • Polymerase chain reaction (PCR) detection of Listeria monocytogenes in diluted milk and reversal of PCR inhibition caused by calcium ions
    • Bickley J, Short JK, McDowell G, Parkes HC. Polymerase chain reaction (PCR) detection of Listeria monocytogenes in diluted milk and reversal of PCR inhibition caused by calcium ions. Lett Appl Microbiol 2008;22(2):153-8.
    • (2008) Lett Appl Microbiol , vol.22 , Issue.2 , pp. 153-158
    • Bickley, J.1    Short, J.K.2    McDowell, G.3    Parkes, H.C.4
  • 28
    • 0037394735 scopus 로고    scopus 로고
    • Mechanisms underlying the impact of humic acids on DNA quantification by SYBR Green I and consequences for the analysis of soils and aquatic sediments
    • Zipper H, Buta C, Lämmle K, Brunner H, Bernhagen J, Vitzthum F. Mechanisms underlying the impact of humic acids on DNA quantification by SYBR Green I and consequences for the analysis of soils and aquatic sediments. Nucleic Acids Res 2003;31(7):e39.
    • (2003) Nucleic Acids Res , vol.31 , Issue.7 , pp. e39
    • Zipper, H.1    Buta, C.2    Lämmle, K.3    Brunner, H.4    Bernhagen, J.5    Vitzthum, F.6
  • 30
    • 0027202733 scopus 로고
    • Interference of humic acids and DNA extracted directly from soil in detection and transformation of recombinant DNA from bacteria and a yeast
    • Tebbe CC, Vahjen W. Interference of humic acids and DNA extracted directly from soil in detection and transformation of recombinant DNA from bacteria and a yeast. Appl Environ Microbiol 1993;59(8):2657-65.
    • (1993) Appl Environ Microbiol , vol.59 , Issue.8 , pp. 2657-2665
    • Tebbe, C.C.1    Vahjen, W.2
  • 31
    • 0032101752 scopus 로고    scopus 로고
    • A polymerase chain reaction inhibitor of ancient hard and soft tissue DNA extracts is determined as human collagen type I
    • Scholz M, Giddings I, Pusch CM. A polymerase chain reaction inhibitor of ancient hard and soft tissue DNA extracts is determined as human collagen type I. Anal Biochem 1998;259(2):283-6.
    • (1998) Anal Biochem , vol.259 , Issue.2 , pp. 283-286
    • Scholz, M.1    Giddings, I.2    Pusch, C.M.3
  • 32
    • 18144405388 scopus 로고    scopus 로고
    • Complex between triple helix of collagen and double helix of DNA in aqueous solution
    • Mrevlishvili GM, Svintradze DV. Complex between triple helix of collagen and double helix of DNA in aqueous solution. Int J Biol Macromol 2005;35(5):243-5.
    • (2005) Int J Biol Macromol , vol.35 , Issue.5 , pp. 243-245
    • Mrevlishvili, G.M.1    Svintradze, D.V.2
  • 33
    • 57749180637 scopus 로고    scopus 로고
    • Optimization of hydrogen bonds for combined DNA/collagen complex
    • Pidaparti RM, Svintradze DV, Shan Y, Yokota H. Optimization of hydrogen bonds for combined DNA/collagen complex. J Theor Biol 2009;256(2):149-56.
    • (2009) J Theor Biol , vol.256 , Issue.2 , pp. 149-156
    • Pidaparti, R.M.1    Svintradze, D.V.2    Shan, Y.3    Yokota, H.4
  • 34
    • 21244469522 scopus 로고    scopus 로고
    • DNA renaturation at the water-phenol interface
    • Goldar A, Sikorav JL. DNA renaturation at the water-phenol interface. Eur Phys J E 2004;14:211-39.
    • (2004) Eur Phys J E , vol.14 , pp. 211-239
    • Goldar, A.1    Sikorav, J.L.2
  • 35
    • 0028120046 scopus 로고
    • A distinctive property of Tth DNA polymerase: enzymatic amplification in the presence of phenol
    • Katcher HL, Schwartz I. A distinctive property of Tth DNA polymerase: enzymatic amplification in the presence of phenol. Biotechniques 1994;16:84-92.
    • (1994) Biotechniques , vol.16 , pp. 84-92
    • Katcher, H.L.1    Schwartz, I.2
  • 36
    • 0029083363 scopus 로고
    • Inhibition of PCR by aqueous and vitreous fluids
    • Wiedbrauk DL, Werner JC, Drevon AM. Inhibition of PCR by aqueous and vitreous fluids. J Clin Microbiol 1995;33(10):2643-6.
    • (1995) J Clin Microbiol , vol.33 , Issue.10 , pp. 2643-2646
    • Wiedbrauk, D.L.1    Werner, J.C.2    Drevon, A.M.3
  • 37
    • 0028674028 scopus 로고
    • Identification of the heme compound copurified with deoxyribonucleic acid (DNA) from bloodstains, a major inhibitor of polymerase chain reaction (PCR) amplification
    • Akane A, Matsubara K, Nakamura H, Takahashi S, Kimura K. Identification of the heme compound copurified with deoxyribonucleic acid (DNA) from bloodstains, a major inhibitor of polymerase chain reaction (PCR) amplification. J Forensic Sci 1994;39:362-72.
    • (1994) J Forensic Sci , vol.39 , pp. 362-372
    • Akane, A.1    Matsubara, K.2    Nakamura, H.3    Takahashi, S.4    Kimura, K.5
  • 38
    • 85028123101 scopus 로고
    • Water-soluble eumelanin as a PCR-inhibitor and a simple method for its removal
    • Yoshii T, Tamura K, Taniguchi T, Akiyama K, Ishiyama I. Water-soluble eumelanin as a PCR-inhibitor and a simple method for its removal. Nihon Hoigaku Zasshi 1993;47(323):329.
    • (1993) Nihon Hoigaku Zasshi , vol.47 , Issue.323 , pp. 329
    • Yoshii, T.1    Tamura, K.2    Taniguchi, T.3    Akiyama, K.4    Ishiyama, I.5
  • 39
    • 77952090984 scopus 로고    scopus 로고
    • Bacterial melanin interacts with double-stranded DNA with high affinity and may inhibit cell metabolism in vivo
    • Geng J, Yuan P, Shao C, Yu S, Zhou B, Zhou P, et al. Bacterial melanin interacts with double-stranded DNA with high affinity and may inhibit cell metabolism in vivo. Arch Microbiol 2010;192:321-9.
    • (2010) Arch Microbiol , vol.192 , pp. 321-329
    • Geng, J.1    Yuan, P.2    Shao, C.3    Yu, S.4    Zhou, B.5    Zhou, P.6
  • 40
    • 0034685648 scopus 로고    scopus 로고
    • Melanin binds reversibly to thermostable DNA polymerase and inhibits its activity
    • Eckhart L, Bach J, Ban J, Tschachler E. Melanin binds reversibly to thermostable DNA polymerase and inhibits its activity. Biochem Biophys Res Commun 2000;271:726-30.
    • (2000) Biochem Biophys Res Commun , vol.271 , pp. 726-730
    • Eckhart, L.1    Bach, J.2    Ban, J.3    Tschachler, E.4
  • 41
    • 0030048084 scopus 로고    scopus 로고
    • Relief of amplification inhibition in PCR with bovine serum albumin or T4 gene 32 protein
    • Kreader CA. Relief of amplification inhibition in PCR with bovine serum albumin or T4 gene 32 protein. Appl Environ Microbiol 1996;62(3):1102-6.
    • (1996) Appl Environ Microbiol , vol.62 , Issue.3 , pp. 1102-1106
    • Kreader, C.A.1
  • 42
    • 73449143181 scopus 로고    scopus 로고
    • Effect of bile salts on the DNA and membrane integrity of enteric bacteria
    • Merritt ME, Donaldson JR. Effect of bile salts on the DNA and membrane integrity of enteric bacteria. J Med Microbiol 2009;58:1533-41.
    • (2009) J Med Microbiol , vol.58 , pp. 1533-1541
    • Merritt, M.E.1    Donaldson, J.R.2
  • 43
    • 0025810836 scopus 로고
    • Inhibitory effects of urine on the polymerase chain reaction for Cytomegalovirus DNA
    • Khan G, Kangro HO, Coates PJ, Heath RB. Inhibitory effects of urine on the polymerase chain reaction for Cytomegalovirus DNA. J Clin Pathol 1991;44:360-5.
    • (1991) J Clin Pathol , vol.44 , pp. 360-365
    • Khan, G.1    Kangro, H.O.2    Coates, P.J.3    Heath, R.B.4
  • 45
    • 0016290352 scopus 로고
    • Selective binding of metal ions to macromolecules using bifunctional analogs of EDTA
    • Sundberg MW, Meares CF, Goodwin DA, Diamanti CI. Selective binding of metal ions to macromolecules using bifunctional analogs of EDTA. J Med Chem 1974;17(12):1304-7.
    • (1974) J Med Chem , vol.17 , Issue.12 , pp. 1304-1307
    • Sundberg, M.W.1    Meares, C.F.2    Goodwin, D.A.3    Diamanti, C.I.4
  • 46
    • 0016192711 scopus 로고
    • Early stages in DNA binding and uptake during genetic transformation of Pneumococci
    • Seto H, Tomasz A. Early stages in DNA binding and uptake during genetic transformation of Pneumococci. Proc Natl Acad Sci USA 1977;71(4):1493-8.
    • (1977) Proc Natl Acad Sci USA , vol.71 , Issue.4 , pp. 1493-1498
    • Seto, H.1    Tomasz, A.2
  • 47
    • 0031018605 scopus 로고    scopus 로고
    • Amplification of Guthrie card DNA: effects of guanidine thiocyanate on binding of natural whole blood PCR inhibitors
    • Makowski GS, Davis EL, Hopfer SM. Amplification of Guthrie card DNA: effects of guanidine thiocyanate on binding of natural whole blood PCR inhibitors. J Clin Lab Anal 1997;11:87-93.
    • (1997) J Clin Lab Anal , vol.11 , pp. 87-93
    • Makowski, G.S.1    Davis, E.L.2    Hopfer, S.M.3
  • 48
    • 0042063753 scopus 로고    scopus 로고
    • Nonsequence-specific arginine interactions in the nucleosome core particle
    • García-Pérez M, Pinto M, Subirana JA. Nonsequence-specific arginine interactions in the nucleosome core particle. Biopolymers 2003;69(4):432-9.
    • (2003) Biopolymers , vol.69 , Issue.4 , pp. 432-439
    • García-Pérez, M.1    Pinto, M.2    Subirana, J.A.3
  • 49
    • 85028114997 scopus 로고    scopus 로고
    • ZunZun.com (accessed August 26, 2012).
    • Phillipe JR. ZunZun.com (accessed August 26, 2012).
    • Phillipe, J.R.1
  • 50
    • 84890468033 scopus 로고    scopus 로고
    • CurveExpert Professional
    • software; (accessed August 26, 2012).
    • Hyams DG. "CurveExpert Professional" software; http://www.curveexpert.net (accessed August 26, 2012).
    • Hyams, D.G.1
  • 51
    • 0038719959 scopus 로고    scopus 로고
    • Shapes and functions of species-area curves: a review of possible models
    • Tjørve E. Shapes and functions of species-area curves: a review of possible models. J Biogeogr 2003;30:827-35.
    • (2003) J Biogeogr , vol.30 , pp. 827-835
    • Tjørve, E.1
  • 52
    • 84987266075 scopus 로고
    • A statistical distribution function of wide applicability
    • Weibull W. A statistical distribution function of wide applicability. J Appl Mech 1951;18:293-6.
    • (1951) J Appl Mech , vol.18 , pp. 293-296
    • Weibull, W.1
  • 53
    • 0000839020 scopus 로고
    • The potential of Weibull-type functions as flexible growth curves
    • Yang RC, Kozak A, Smith JHG. The potential of Weibull-type functions as flexible growth curves. Can J For Res 1978;8:424-31.
    • (1978) Can J For Res , vol.8 , pp. 424-431
    • Yang, R.C.1    Kozak, A.2    Smith, J.H.G.3
  • 54
    • 84971936834 scopus 로고
    • The effects of frequency of defoliation on the yield response of a perennial ryegrass sward to a wide range of nitrogen application rates
    • Reid D. The effects of frequency of defoliation on the yield response of a perennial ryegrass sward to a wide range of nitrogen application rates. J Agric Sci 1978;90:447-57.
    • (1978) J Agric Sci , vol.90 , pp. 447-457
    • Reid, D.1
  • 55
    • 0031921276 scopus 로고    scopus 로고
    • Improved DNA extraction from ancient bones using silica based spin columns
    • Yang D, Eng B, Waye JS, Dudar JC, Saunders SR. Improved DNA extraction from ancient bones using silica based spin columns. Am J Phys Anthropol 1998;105:539-43.
    • (1998) Am J Phys Anthropol , vol.105 , pp. 539-543
    • Yang, D.1    Eng, B.2    Waye, J.S.3    Dudar, J.C.4    Saunders, S.R.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.