Background:
Although most nucleotides in the genome form canonical double-stranded
B-DNA, many repeated sequences transiently present as non-canonical conformations (non-B
DNA) such as triplexes, quadruplexes, Z-DNA, cruciforms, and slipped/hairpins. Those noncanonical
DNAs (ncDNAs) are not only associated with many genetic events such as replication,
transcription, and recombination, but are also related to the genetic instability that results in the
predisposition to disease. Due to the crucial roles of ncDNAs in cellular and genetic functions,
various computational methods have been implemented to predict sequence motifs that generate
ncDNA.
Objective:
Here, we review strategies for the identification of ncDNA motifs across the whole
genome, which is necessary for further understanding and investigation of the structure and
function of ncDNAs.
Conclusion:
There is a great demand for computational prediction of non-canonical DNAs that
play key functional roles in gene expression and genome biology. In this study, we review the
currently available computational methods for predicting the non-canonical DNAs in the genome.
Current studies not only provide an insight into the computational methods for predicting the
secondary structures of DNA but also increase our understanding of the roles of non-canonical
DNA in the genome.
