Predictive Evaluation for the Preparation of a Synthetic Y-shaped DNA Nanostructure

Abstract

With the advent of deoxyribonucleic acid(DNA) nanotechnology, the Y-shaped DNA nanostructure(Y-DNA) as a basic block was first created. Due to theircharacteristic selectivity and specificity, Y-DNA-basedmaterials have been utilized in a variety of scientific fieldsincluding multiplexed nanobarcoding. Basically, the tripodDNA nanostructure was prepared by simple hybridizationof three different single stranded DNA (ssDNA). Beforethe synthetic process, the optical densities (OD) of thethree ssDNAs were measured to accurately estimate theconcentration. Through repeated temperature fluctuations,three ssDNAs were hybridized into a Y-shaped block withboth a central junction and three blunt ended arms. Afterthe reaction, the ODs of the synthesized DNA productswere measured and compared with the theoretical ODvalues calculated by a MATLAB program (‘matrix laboratory’)with different molar concentrations and volumes to predictthe presence of Y-DNA. Simultaneously, the product wasanalyzed by agarose gel electrophoresis to confirm the YDNAstructure. The measured ODs of the solutions withconfirmed Y-DNA structures were close to the theoreticalmaximum OD values. This article provides means to helpunderstand and prepare Y-DNA by performing ODmeasurements. It is highly expected that this guide will bean excellent starting point for structural DNA nanotechnology.