Maximizing Spatial Resolution of DNA Sequencing Using Single Carbon Chain

University Of Arkansas At Fayetteville, Fayetteville AR

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Abstract

PROJECT SUMMARY Rapid DNA sequencing based on nanofluidic devices such as nanopores and nanochannels has shown tremendous promise in providing a compact sensing platform for portable, low-cost genomic analysis. To date, several devices have been developed with nanopores that show the greatest potential to achieve a true label- free sequencing technique that does not require lengthy sample pretreatment and post analysis. However, despite significant technological advancement since the first nanopore concept for was proposed over 20 years ago, nanopores continue to be hampered by two major challenges, poor spatial resolution and inaccurate ratcheting mechanism, whose resolution would elevate nanopore sequencing to the ultimate single-base accuracy level needed for clinical applications. The proposed project is designed to overcome these challenges by combining a minimal one-dimensional sensing element with a novel atomic force microscopy (AFM) assisted DNA ratcheting mechanism. The new sensing element will be fabricated from a single chain of carbon atoms or carbyne whose atomic width can resolve not only a DNA base but also the spacing between consecutive bases in a DNA strand. The sequencing principle will be based on electrical current modulation in the carbyne due to DNA physisorption. The DNA ratcheting mechanism will combine enzyme turnover with AFM nanomanipulation to synchronize the turnover rate with the DNA movement speed in order to provide precise control the DNA/carbyne interaction during the sequencing process to achieve single-base resolution. We have conducted preliminary studies to validate the core concept of the proposed project through quantum simulations of the carbyne/DNA interaction and experimental AFM nanomanipulation of a single DNA strand on a nanoelectrode chip. Our ultimate goal is to achieve single-base accuracy by using a carbyne sensor to accurately ?read? the individual bases in a single-stranded DNA attached to a moving AFM tip. We plan to use an integrated approach of device fabrication and biochemical protocol development to characterize the interaction between a single carbon chain and DNA bases with high spatial and temporal resolution. The proposed project will explore several novel technological areas including carbyne fabrication, enzyme turnover and DNA ratcheting, and AFM manipulation. Results of the project are expected to impact future designs of DNA sequencing and applications of carbyne in novel electronics and high-strength materials. The proposed research team has extensive experience in device fabrication, nanoscale bio/abio interfacing technology, and synthesis of functional nanomaterials. All the proposed works will be conducted in well-established bio-nano fabrication and testing facilities. DNA stores the genetic information of all living organisms. Consequently, successful development of a compact DNA sequencing technique with single-base accuracy, such as the proposed carbyne based approach, will provide an important tool for the future development of biomedical research and clinical diagnostics. 1