Screening for mitochondrial DNA (mtDNA) point mutations using nonradioactive single strand conformation polymorphism (SSCP) analysis

Abstract

Mitochondrial cytopathies such as Leber's hereditary optic neuropathy (LHON), mitochondrial encephalomyopathy with lactic acidosis and stroke-like episodes (MELAS), and myoclonus epilepsy with red ragged fibers (MERRF) are associated with distinct mtDNA point mutations (for review see 1). LHON, for example, is related to at least 14 mtDNA point mutations within different mitochondrially encoded respiratory subunit genes. In addition, the number of newly found LHON-related mutations is increasing. In the light of the large number and the dispersed distribution of these point mutations throughout the mitochondrial genome, screening for these by sequencing all of suspected loci is laborius and time-consuming. In order to facilitate a rapid screening for mitochondrial point mutations we have evaluated the use of polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) for the analysis of the human mitochondrial genome.

In a first evaluation step we created a variety of pUC18 clones derived from mitochondrial control region amplifications with defined sequence differences and length. These clones were used as standard material for an optimization of the PCR-SSCP analysis. The optimized PCR-SSCP was then applied to large cohorts of patients with known, i.e., sequenced mtDNA point mutations and to healthy controls in order to evaluate its sensitivity.

The most common LHON-related mtDNA point mutations at nucleotide positions (nps) 11778, 14484, 4216, could be detected by SSCP analysis, as well as the heteroplasmic np 3243 MELAS associated point mutation. Several new polymorphisms and point mutations were found. A sensitivity, i.e., the ability to detect defined point mutations, of 93% (clones) and 98% (disease controls) was achieved when comparing SSCP- and direct sequencing results.

The PCR-SSCP approach using a non-radioactive silver staining method is suited for the detection of human mitochondrial point mutations, as well as a helpful screening tool for novel mt DNA mutations.