Assessment of G-quadruplex prediction tools

DNA is a long polymer being famous for its double-helix form at the lower level, and for its chromosome packaging at higher levels of detail. Nonetheless DNA exists in many possible conformations, including A-DNA, B-DNA and Z-DNA forms. B-DNA is the most common form found in cells. Non-B DNAs comprise of tetraplex (G-quadruplex), left-handed Z-DNA, and others. Several recent publications have provided significant evidence that non-B DNA structures may play a role in DNA instability and mutagenesis, leading to both DNA rearrangements and increased mutational rates, which are a hallmark of cancer related diseases. Studying the structure conformation and probability of non-B DNA structure, may help in studying diseases as well as designing of new drugs. Nevertheless, even if there are some examples of prediction tools, the topic of designing efficient prediction algorithms and tools for G-quadruplex prediction is still in its infancy. As a contribution in this new area, we present preliminary results and statistics obtained by using the state of the art software tools able to predict G-quadruplex DNA conformations starting from the primary sequence. We used existing tools as well as known structures to define the state of the art and the current value of prediction tools. We believe that our study may represent an important contribution through the definition of reliable Gquadruplex prediction tools.