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Predictive evaluation for the preparation of a synthetic Y-shaped DNA nanostructure

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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 their characteristic selectivity and specificity, Y-DNA-based materials have been utilized in a variety of scientific fields including multiplexed nanobarcoding. Basically, the tripod DNA nanostructure was prepared by simple hybridization of three different single stranded DNA (ssDNA). Before the synthetic process, the optical densities (OD) of the three ssDNAs were measured to accurately estimate the concentration. Through repeated temperature fluctuations, three ssDNAs were hybridized into a Y-shaped block with both a central junction and three blunt ended arms. After the reaction, the ODs of the synthesized DNA products were measured and compared with the theoretical OD values calculated by a MATLAB program (‘matrix laboratory’) with different molar concentrations and volumes to predict the presence of Y-DNA. Simultaneously, the product was analyzed by agarose gel electrophoresis to confirm the YDNA structure. The measured ODs of the solutions with confirmed Y-DNA structures were close to the theoretical maximum OD values. This article provides means to help understand and prepare Y-DNA by performing OD measurements. It is highly expected that this guide will be an excellent starting point for structural DNA nanotechnology.

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Authors and Affiliations

  1. School of Chemical Engineering, Sungkyunkwan University, Suwon, 440-746, Korea

    Seung Won Shin & Soong Ho Um

  2. SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 440-746, Korea

    Soong Ho Um

  3. Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, 121-742, Korea

    Kyung Soo Park, Jin-Ha Choi, Byung-Keun Oh & Jeong-Woo Choi

  4. Research Center for Integrated Biotechnology, Sogang University, Seoul, 121-742, Korea

    Jeong-Woo Choi

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  1. Kyung Soo Park
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  2. Seung Won Shin
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  5. Jeong-Woo Choi
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Correspondence to Soong Ho Um.

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Park, K.S., Shin, S.W., Choi, JH. et al. Predictive evaluation for the preparation of a synthetic Y-shaped DNA nanostructure. Biotechnol Bioproc E 19, 262–268 (2014). https://doi.org/10.1007/s12257-013-0626-4

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  • DOI: https://doi.org/10.1007/s12257-013-0626-4

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