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. 2008 Mar 12;130(10):2934-5.
doi: 10.1021/ja711192e. Epub 2008 Feb 19.

Split DNA enzyme for visual single nucleotide polymorphism typing

Dmitry M Kolpashchikov  1
Affiliations

Split DNA enzyme for visual single nucleotide polymorphism typing

Dmitry M Kolpashchikov. J Am Chem Soc. .
No abstract available

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Figures

Figure 1
Figure 1
Design of the binary DNA peroxidase for SNP analysis: A: parent peroxidase-like DNA enzyme; B: binary DNA peroxidase probe; and C: the probe forms active peroxidase upon hybridizing to the abutting positions of the analyte. The enzyme catalyzes oxidation of a colorless substrate to colored products. The triethylene glycol linkers are shown as dashed lines in panel C. The SNP site in the analyte sequence is underlined.
Figure 2
Figure 2
Binary DNA peroxidase probe reports single nucleotide substitution in tau protein coding DNA. A: Visual detection. Sample 0: reaction buffer (50 mM HEPES, pH 7.4, 50 mM MgCl2, 20 mM KCl, 120 mM NaCl, 0.03% Triton X-100, 1% DMSO, hemin (125 nM), H2O2 (1 mM), and DAB (1 mM)); Sample 1: reaction buffer in the presence of 1 μM peroxidase-like DNA enzyme (positive control). Strands α and β (1 μM) in the absence (sample 2) or presence of 1 μM rs242557-A (TGG CTT CGC CCA GGG TAC ACC AGG ACA CGG TTT T) (sample 3), or 1 μM rs242557-G (TGG CTT CGC CCA GGG TGC ACC AGG ACA CGG TTT T) (sample 4). The samples were incubated 30 min at room temperature. B: Electron spectrum of the same samples; sample 0 was used as a reference. C: Average optical densities at 500 nm of five independent measurements.
Figure 3
Figure 3
Analysis of binary DNA peroxidase probe by native 12% PAGE. All samples contained the reaction buffer (see legend to Figure 2). In addition, the following oligonucleotides were added: lane 1: peroxidase-like DNA enzyme (1 μM); lane 2: binary DNA peroxidase (1 μM both strands); lane 3: binary DNA peroxidase (1 μM both strands) and rs242557-A (1 μM); lane 4: binary DNA peroxidase (1 μM both strands) and rs242557-G (1 μM); lane 5: strand α (1 μM) only; lane 6: strand α (1 μM) and rs242557-A (1 μM); lane 7: strand α (1 μM) and rs242557-G (1 μM); and 8: 10 base pairs (10 bp) DNA ladder. The low mobility band in lane 4 is indicated by an arrow.
See this image and copyright information in PMC

References

    1. Budowle B. Forensic Sci. Int. 2004;146:139–142. - PubMed
    2. Piunno PA, Krull UJ. Anal. Bioanal. Chem. 2005;381:1004–1011. - PubMed
    3. Kwok P-Y. Annu. Rev. Genomics Hum. Genet. 2001;2:235–258. - PubMed
    4. Hacia JG. Nat. Genet. 1999;21:42–47. - PubMed
    5. Hahn S, Mergenthaler S, Zimmermann B, Holzgreve W. Bioelectrochemistry. 2005;67:151–154. - PubMed
    6. Ng JK, Liu WT. Anal. Bioanal. Chem. 2006;386:427–434. - PubMed
    7. Kim S, Misra A. Annu. Rev. Biomed. Eng. 2007;9:289–320. - PubMed
    1. Xu Y, Karalkar NB, Kool ET. Nat. Biotechnol. 2001;19:148–152. - PubMed
    2. Sando S, Abe H, Kool ET. J. Am. Chem. Soc. 2004;126:1081–1087. - PubMed
    3. Bichenkova EV, Savage HE, Sardarian AR, Douglas KT. Biochem. Biophys. Res. Commun. 2005;332:956–964. - PubMed
    4. Kolpashchikov DM. J. Am. Chem. Soc. 2005;127:12442–12443. - PubMed
    5. Kolpashchikov DM. J. Am. Chem. Soc. 2006;128:10625–10628. - PubMed
    6. Marti AA, Li X, Jockusch S, Li Z, Raveendra B, Kalachikov S, Russo JJ, Morozova I, Puthanveettil SV, Ju J, Turro NJ. Nucleic Acids Res. 2006;34:3161–3168. - PMC - PubMed
    7. Tsujimura Y, Osawa Y, Tazaki M, Jyo A. Anal. Biochem. 2006;359:259–61. - PubMed
    8. Kolpashchikov DM. ChemBioChem. 2007;8:2039–2042. - PMC - PubMed
    1. Li Y, Geyer CR, Sen D. Biochemistry. 1996;35:6911–6922. - PubMed
    1. Travascio P, Li Y, Sen D. Chem. Biol. 1998;5:505–517. - PubMed
    2. Travascio P, Bennet AJ, Wang DY, Sen D. Chem. Biol. 1999;6:779–787. - PubMed
    1. Xiao Y, Pavlov V, Niazov T, Dishon A, Kotler M, Willner I. J. Am. Chem. Soc. 2004;126:7430–7431. - PubMed
    2. Li D, Shlyahovsky B, Elbaz J, Willner I. Biosens. Bioelectron. 2007;22:2570–2576. - PubMed
    3. Pavlov V, Xiao Y, Gill R, Dishon A, Kotler M, Willner I. Anal. Chem. 2004;76:2152–2156. - PubMed
    4. Xiao Y, Pavlov V, Gill R, Bourenko T, Willner I. ChemBioChem. 2004;5:374–379. - PubMed

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