Strand displacement amplification: a versatile tool for molecular diagnostics

References

• Walker GT, Little MC, Nadeau JG, Shank DD. Isothermal in vitro amplification of DNA by a restriction enzyme/DNA polymerase system. Proc. Natl Acad. Sri. 89,392–396 (1992).
   PubMed Web of Science ®Google Scholar
• Walker GT, Praiser MS, Schram JL, Little MC, Nadeau JG, Malinowski DR Strand displacement amplification — an isothermal, in vitro, DNA amplification technique. Nucleic Acids Res. 20, 1691–1696 (1992). Pioneering manuscript providing the first description of the mature strand displacement amplification (SDA) concept and the mechanisms of amplification.
   Google Scholar
• Milla MA, Spears PA, Pearson RE, Walker GT. Use of restriction enzyme Aval and exo- Bst polymerase in strand displacement amplification. Biotechniques 24, 392–396 (1998).
   PubMed Web of Science ®Google Scholar
• Spargo CA, Praiser MS, Van Cleve M etal Detection of M tuberculosis DNA using thermophilic strand displacement amplification. Mal Cell. Probes 10, 247–256 (1996).
   PubMed Web of Science ®Google Scholar
• •Provides details of the important benefits of thermophilic enzymes for amplification in terms of primer specificity, amplification efficiency and time to result.
   Google Scholar
• Little MC, Andrews J, Moore R et al Strand displacement amplification and homogeneous real-time detection incorporated in a second-generation DNA probe system, BD ProbeTec ET Clin. Chem. 45,777–784 (1999).
   Web of Science ®Google Scholar
• •First manuscript to describe the use of SDA on the BD ProbeTecTm ET System.
   Google Scholar
• Hellyer TJ, DesJardin LE, Teixeira L, Perkins MD, Cave MD, Eisenach KD. Detection of viable 4cobacterium tuberculosis by reverse transcriptase-strand displacement amplification of mRNA. Clin. Mcrobiol 37,518–523 (1999).
   Google Scholar
• Hellyer TJ, DesJardin LE, Assaf MK, Bates JH, Cave MD, Eisenach KD. Specificity of IS6110-based amplification assays for Mycobacterium tuberculosis complex. j Clin. Mcrobiol 34,2843–2846 (1996).
   Google Scholar
• Hellyer TJ, Fletcher TW, Bates, JH etal Strand displacement amplification and the polymerase chain reaction for monitoring response to treatment in patients with pulmonary tuberculosis. j Infect. Dis. 173, 934–941 (1996).
   PubMed Web of Science ®Google Scholar
• Spargo CA, Haaland PD, Jurgensen SR, Shank DD, Walker GT. Chemiluminescent detection of strand displacement amplified DNA from species comprising the Mycobacterium tuberculosis complex. Mal Cell Probes 7,395–404 (1993).
   Google Scholar
• Walker GT, Linn CR Detection of Mycobacterium tuberculosis DNA with thermophilic strand displacement amplification and fluorescence polarization. Clin. Chem. 42,1604–1608 (1996).
   PubMed Web of Science ®Google Scholar
• Walker GT, Linn CP, Nadeau JG. DNA detection by strand displacement amplification and fluorescence polarization with signal enhancement using a DNA binding protein. Nucleic Acids Res. 24, 348–353 (1996).
   Google Scholar
• Walker GT, Nadeau JG, Linn CP, Devlin RF, Dandliker WB. Strand displacement amplification (SDA) and transient-state fluorescence polarization detection of Mycobacterium tuberculosis DNA. Clin. Chem. 42,9–13 (1996).
   Google Scholar
• Spears PA, Linn CP, Woodard DL, Walker GT. Simultaneous strand displacement amplification and fluorescence polarization detection of Chlamydia trachomatis DNA. Anal Biochem. 247,130–137 (1997).
   PubMed Web of Science ®Google Scholar
• Diamandis ER Automation of molecular diagnostics. Clin. Chem. 42,7–8 (1996).
   Google Scholar
• Murakami A, Nakaura M, Nakatsuji Y, Nagahara S, Tran-Cong Q, Makino K Fluorescent-labeled oligonucleotide probes: detection of hybrid formation in solution by fluorescence polarization spectroscopy. Nucleic Acids Res. 19,4097–4102 (1991).
   PubMed Web of Science ®Google Scholar
• Nadeau JG, Pitner JB, Linn CP, Schram JL, Dean CH, Nycz CM. Real-time, sequence-specific detection of nucleic acids during strand displacement amplification. Anal Biochem. 276,177–187 (1999).
   PubMed Web of Science ®Google Scholar
• ••Key paper describing energy transferprobes for use in SDA reactions as well as methods for the real-time quantification of HIV RNA.
   Google Scholar
• Wolfe DM, Wang S-S, Thornton K, Kuhn AM, Nadeau JG, Hellyer TJ. Homogeneous real-time strand displacement amplification. In: DNA Amplification: Cunent Technologies & Applications. Demidov V (Ed.), Horizon Scientific Press, Wymondham, UK (2004) (In Press).
   Google Scholar
• Nycz CM, Dean CH, Haaland PD, Spargo CA, Walker GT. Quantitative reverse transcription strand displacement amplification: quantitation of nucleic acids using an isothermal amplification technique. Anal Biochem. 259,226–234 (1998).
   PubMed Web of Science ®Google Scholar
• •First paper to describe quantitative detection of nucleic acids using SDA.
   Google Scholar
• Wang S-S, Thornton K, Kuhn AM, Nadeau JG, Hellyer TJ. Homogeneous real-time detection of single nucleotide polymorphisms by strand displacement amplification on the BD ProbeTec ET System. Clin. Chem. 49,1599–1607 (2003).
   Google Scholar
• •Illustrates the versatility of SDA for alternative applications other than infectious disease diagnosis. Includes description of a universal detection system that permits the use of the same fluorescent energy transfer probes across multiple analytes.
   Google Scholar
• Chan EL, Brandt K, Olienus K, Antonishyn N, Horsman GB. Performance characteristics of the Becton Dickinson ProbeTec system for direct detection of Chlamydia trachomatis and Neisseria gonorrhoeae in male and female urine specimens in comparison with the Roche Cobas system. Arch. Pathol Lab. Med. 124,1649–1652 (2000).
   Google Scholar
• Van Der Pol B, Ferrero DV, Buck-Barrington L etal Multicenter evaluation of the BD ProbeTec ET System for detection of Chlamydia trachomatis and Neisseria gonorrhoeae in urine specimens, female endocervical swabs and male urethral swabs. J. Clin. Mcrobiol 39, 1008–1016 (2001).
   PubMed Web of Science ®Google Scholar
• Van Dyck E, Ieven M, Pattyn S, Van Damme L, laga M. Detection of Chlamydia trachomatis and Neisseria gononhoeae by enzyme immunoassay, culture and three nucleic acid amplification tests.j Clin. Mcrobiol 39,1751–1756. (2001).
   Google Scholar
• Templeton K, Roberts J, Jeffries D, Forster G, Aitken C. The detection of Chlamydia trachomatis by DNA amplification methods in urine samples from men with urethritis. Int. J. STD AIDS 12,793–796 (2001).
   Google Scholar
• Akduman D, Ehret JM, Messina K, Ragsdale S, Judson FN. Evaluation of a strand displacement amplification assay (BD Probe Tec-SDA) for detection of Neisseria gononhoeae in urine specimens. Clin. Nlicrobiol. 40,281–283 (2002).
   Google Scholar
• Verkooyen RP, Noordhoek GT, Klapper PE etal Reliability of nucleic acid amplification methods for detection of Chlamydia trachomatis in urine: results of the First International Collaborative Quality Control Study among 96 laboratories. J. Clin. Nlicrobiol 41, 3013–3016 (2003).
   Google Scholar
• Tong CY, Mallinson H. Moving to nucleic acid-based detection of genital Chlamydia trachomatis. Expert Rev. Mal Diagn. 2, 257–266 (2002).
   PubMedGoogle Scholar
• Centers for Disease Control and Prevention. Screening tests to detect Chlamydia trachomatis and Neisseria gononhoeae infections - 2002. MMWR51, No. RR-15 (2002).
   Google Scholar
• Culler EE, Caliendo AM, Nolte FS. Reproducibility of positive test results in the BD ProbeTec ET System for detection of Chlamydia trachomatis and Neisseria gononhoeae. j Clin. Mcrobiol 41, 3911–3914 (2003).
   Google Scholar
• Schachter J, McCormack WM, Chemesky MA etal Vaginal swabs are appropriate specimens for diagnosis of genital tract infection with Chlamydia trachomatis. j Clin. Mcrobiol 41, 3784–3789 (2003).
   PubMed Web of Science ®Google Scholar
• Consentino LA, Landers DV, Hillier SL. Detection of Chlamydia trachomatis and Neisseria gononhoeae by strand displacement amplification and relevance of the amplification control for use with vaginal swab specimens. J. Clin. Nlicrobiol. 41,3592–3596 (2003).
   Google Scholar
• Bergmann JS, Keating WE, Woods GL. Clinical evaluation of the BD ProbeTec ET System for rapid detection of Mycobacterium tuberculosis. j Clin. Mcrobiol 38,863–865 (2000).
   Google Scholar
• Johansen IS, Thomsen VO, Johansen A, Andersen P, Lundgren B. Evaluation of a new commercial assay for diagnosis of pulmonary and nonpulmonary tuberculosis. Eur. j Clin. Mcmbiol. Infect. Dis. 21,455–460 (2002).
   Google Scholar
• Piersimoni C, Scarparo C, Piccoli P et al Performance assessment of two commercial amplification assays for direct detection of Mycobacterium tuberculosis complex from respiratory and extrapulmonary specimens. Clin. Microbial. 40,4138–4142 (2002).
   PubMed Web of Science ®Google Scholar
• Maugein J, Fourche J, Vacher S, Grimond C, Bebear C. Evaluation of the BD ProbeTec Tm ET DTB assay for direct detection of Mycobacterium tuberculosis complex from clinical samples. Diagn. Microbial. Infect. Dis. 44,151–155 (2002).
   Google Scholar
• Huang T-S, Huang W-K, Shin-Jung Lee S, Tu H-Z, Chang S-H, Liu Y-C. Rapid detection of pulmonary tuberculosis using the BD ProbeTec ET Mycobacterium tuberculosiscomplex Direct Detection Assay (DTB). Diagn. Mcmbiol. Infect. Dir. 46, 29–33 (2003).
   Google Scholar
• Iinuma Y, Senda K, Fujihara N etal Comparison of the BD ProbeTec ET System with the Cobas Amplicor PCR for Direct Detection of Mycobacterium tuberculosis in respiratory samples. Eur Gun. Mcrobiol Infect. Dis. 22,368–371 (2003).
   PubMed Web of Science ®Google Scholar
• Mazzarelli G, Rindi L, Piccoli P, Scarparo C, Garzelli C, Tortoli E. Evaluation of the BD ProbeTec ET System for direct detection of Mycobacterium tuberculosis in pulmonary and extrapulmonary samples: a multicenter study.j Clin. Mcrobiol 41,1779–1782 (2003).
   PubMed Web of Science ®Google Scholar
• Hellyer TJ. Detection of viable Mycobacterium tuberculosis by reverse transcriptase-strand displacement amplification of mRNA. In: Methods in Molecular Medicine. Antibiotic Resistance Methods and Protocols. Gillespie SH (Ed.), Humana Press, NJ, USA, 141–155 (2001).
   Google Scholar
• Mehrpouyan M, Bishop JE, Ostrerova N, Van Cleve M, Lohman KL. A rapid and sensitive method for non-isotopic quantitation of HIV-1 RNA using thermophilic SDA and flow cytometry. Mal Cell Probesll, 337–347 (1997).
   Google Scholar
• Nuovo GJ. In situ strand displacement amplification: an improved technique for the detection of low copy nucleic acids. Diagn. Mol Pallid 9,195–202 (2000).
   PubMed Web of Science ®Google Scholar
• •Describes use of in situ SDA and reverse transcriptase-SDA to detect nucleic acids within fixed eultaryotic cells.
   Google Scholar
• Bums MA, Johnson BN, Brahmasandra SN etal An integrated nanoliter DNA analysis device. Science 282,484–487 (1998).
   PubMed Web of Science ®Google Scholar
• Westin L, Xu X, Miller C, Wang L, Edman CF, Nerenberg M. Anchored multiplex amplification on a microelectronic chip array. Nature Biotechnol 18,199–204 (2000).
   PubMed Web of Science ®Google Scholar
• •Use of the isothermal properties of SDA for rapid amplification and detection of nucleic acid on the surface of a chip.
   Google Scholar
• Walker GT, Nadeau JG, Spears PA, Schram JL, Nycz CM, Shank DD. Multiplex strand displacement amplification and detection of DNA sequences from 4cobacterium tuberculosis and other mycobacteria. Nucleic Acids Res. 22,2670–2677 (1994).
   PubMed Web of Science ®Google Scholar
• Drysdale CM, McGraw DW, Stack CB etal Complex promoter and coding region 02-adrenergic receptor haplotypes alter receptor expression and predict in vivo responsiveness. Proc. Natl Acad. ScL 97, 10483–10488 (2000).
   Google Scholar
• Vieux EF, Kwok PY, Miller RD. Primer design for PCR and sequencing in high-throughput analysis of SNPs. Biotechniques 32 (Suppl.), 28–30 (2002).
   Google Scholar