Acanthamoeba isolates from the patients and domestic taps were compared for their mtDNA restriction fragment length polymorphisms (RFLPs). The mtDNA was isolated from axenic trophozoites by the alkaline lysis method used for the isolation of bacterial plasmid DNA, as previously applied to
Acanthamoeba.
20 Approximately 2 to 3 μg of mtDNA was digested with the restriction endonuclease
HindIII (Roche Diagnostics, Sussex, UK) and separated by electrophoresis in a 0.75% agarose gel at 2 V/cm for 18 hours in 0.5× TBE buffer.
21 DNA standards of λ-
HindIII/ΦX-174 RF-
HaeIII digests (Amersham Pharmacia Biotech, Milton Keynes, UK) were included as size markers. The gels were stained with 1.0 μg/mL ethidium bromide in distilled water and photographed under UV transillumination (665 film; Polaroid, Cambridge, MA; and a Wratten no. 9 orange filter; Eastman Kodak, Rochester, NY).
21
PCR was used to amplify part of the cytochrome oxidase subunit-1 and -2 (
cox1/2) from purified mtDNA (Cox-PCR).
22 Primers used were forward (gaattagctgctccgggttc) and reverse (tcaggataatcggggatccttc) designed to amplify a 1.2-kbp fragment. PCR was performed in a 50-μL volume consisting of: 1×
Taq DNA polymerase buffer (20 mM (NH
4)
2SO
4, 75 mM Tris-HCl [pH 8.8] at 25°C, 0.01% vol/vol Tween 20), 1.5 mM MgCl
2, and 0.2 mM each dNTP, 0.5 μM of each primer, 1 U of
Taq DNA polymerase (Red Hot; Advanced Biotechnologies Ltd., Epsom, UK) and approximately 100 ng of template DNA. Thermal cycling conditions were: 4 minutes 96°C, followed by 35 cycles of 1 minute 95°C, 1 minute 52°C, and 1.5 minutes 72°C. After a final 10 minutes at 72°C, samples were held at 4°C. Amplified products were analyzed by agarose gel electrophoresis and sent for sequencing (MWG-Biotech, AG, Ebersberg, Germany). DNA sequences were aligned (ClustalW) and a phylogenetic tree constructed (TreeView Win32 1.6.6; Uniersity of Glasgow, UK).
23 24