Computer-assisted predictions of the secondary structure in the plant virus single-stranded DNA genome

Coconut foliar decay virus (CFDV) contains the single-stranded circular DNA molecules of 1291 nucleotides which were found to replicate autonomously in the cells of the diseased palms. The special features of the CFDV DNA sequence, including putative secondary structure and the distribution of the inverted repeat motifs, are investigated with computer-assisted prediction methods. It is evident that the structural principle of the branched series of long and short double helixes interspersed by short non-helical regions is existed for CFDV virion DNA. The total degree of base pairing is near 62%. We have also predicted the presence of several sequence elements formed by inverted repeat motifs which are potentially capable of binding the eukaryotic transcriptional regulatory factors.