UCO’s Buddy Supercomputer is Accelerating Research in DNA Sequencing and Bioinformatics


The progress toward cheaper and faster sequencing has been very impressive since the Human Genome Project first sequenced the human genome using the classical Sanger method. The Sanger procedure is time consuming due to the slow throughput with DNA fragment separation in gels. The need for cheaper and faster techniques drove scientists and companies to work on new sequencing technologies. Recently, Oxford Nanopore Technologies developed a sequencing device based on protein nanopores. Despite this progress, there are still several challenges with DNA sequencing using protein nanopores such as: 1) high startup and consumables costs; 2) short read length, which limits the ability to analyze large scale structural variations; 3) sensitivity of pore to environmental conditions e.g., temperature, pH, and applied voltage; and 4) high error rate (~15%). Due to these challenges, the need for cheaper and faster approaches with the focus on label-free, single-nucleotide, long read length automated sequencing using a minimum amount of consumables is very crucial. Two-dimensional (2D) crystals such as graphene have emerged as revolutionary materials for fast, single-nucleotide, direct-read DNA sequencing with a minimum amount of consumables. Among the large family of 2D materials, graphene remains the most widely explored for DNA sequencing applications. Due to its single-layer nature (comparable to the interbase distance in single-stranded DNA), graphene has strong potentials to be used for designing nanodevices for fast, single-nucleotide resolution, label-free DNA sequencing using a limited number of consumables. Despite its remarkable properties, sequencing DNA using graphene is experimentally very challenging. One of the major hindrances is the hydrophobic nature of graphene’s surface, which causes DNA bases to stick to its surface, making it difficult to translocate DNA through graphene nanopores. Due to this challenge, the scientific community has turned its attention to other single-layer materials similar to graphene (e.g. phosphorene and silicene). Using UCO’s Buddy Supercomputer, Dr. Benjamin Tayo’s students carried out computational studies to study the interaction of DNA bases with phosphorene and silicene. These studies reveal that phosphorene and silicene show a lower tendency (less binding energy) to bind with DNA bases (see Figure), and hence are promising alternatives to graphene for use in next-generation DNA sequencing devices. Furthermore, the hydrophilicity and biocompatibility of phosphorene makes it an important material for biological applications. Dr. Tayo’s group has partnered with leading experimentalists in the field who will provide more data for benchmarking their theoretical predictions. This research has led to two peer-reviewed journal articles, one published (AIP Advances 11, 035324 (2021); https://doi.org/10.1063/5.0043000) and the other under review. The research has been also presented at several local and national conferences.