Both HV-I and HV-II of the human mtDNA contain homopolymeric tract of cytosines (C) (i.e., C-stretch) (Carracedo et al., 2000). In HV-I, the most common sequence between positions 16 184 and 16 193 is "CCCCCTCCCC" (the position of thymine 'T' is at 16 189). When the T undergoes mutational transition to C, length heteroplasmy (polymorphism of the number of repeated cyto-sine residues) supervenes. A similar homopolymeric region resides in HV-II at positions 303-315 (Stewart et al., 2001). These length heteroplasmies are believed to be supervened by an additional increase or decrease of cytosine residues through the replication slippage mechanism, which has been observed in poly G : C tracts (Hauswirth et al., 1984). In general, direct sequencing of DNA from these samples exhibits reading frame shifts and thereby both the exact number of cytosine residues of the C-stretch and sequences beyond the C-stretch cannot be determined (Tully and Levin, 2000). The additional reactions using primers that sit on the C-stretch provide sequence information from both strands following the C-stretch but the exact number of cytosine residues in the C-stretch still cannot be accurately determined.
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