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An intelligent DNA nanorobot for detection of MiRNAs cancer biomarkers using molecular programming to fabricate a logic-responsive hybrid nanostructure

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Abstract

Herein, we designed a DNA framework-based intelligent nanorobot using toehold-mediated strand displacement reaction-based molecular programming and logic gate operation for the selective and synchronous detection of miR21 and miR125b, which are known as significant cancer biomarkers. Moreover, to investigate the applicability of our design, DNA nanorobots were implemented as capping agents onto the pores of MSNs. These agents can develop a logic-responsive hybrid nanostructure capable of specific drug release in the presence of both targets. The prosperous synthesis steps were verified by FTIR, XRD, BET, UV–visible, FESEM–EDX mapping, and HRTEM analyses. Finally, the proper release of the drug in the presence of both target microRNAs was studied. This Hybrid DNA Nanostructure was designed with the possibility to respond to any target oligonucleotides with 22 nucleotides length.

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Acknowledgements

We would like to thank the Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran, which assisted in performing this study. The authors thank Hojatollah Khabazzadeh for helpful discussions.

Funding

This research was funded by Kerman University of Medical Sciences, Deputy for Research and Technology (Grant Number 98000180).

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Authors and Affiliations

  1. Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran

    Amin Mirzaiebadizi, Hadi Ravan & Arezoo Shahba

  2. Department of Pathology and Stem Cell Research Center, Kerman University of Medical Sciences, Kerman, Iran

    Shahriar Dabiri & Mahsa Ziasistani

  3. Department of Chemistry, Shahid Bahonar University of Kerman, Kerman, Iran

    Pourya Mohammadi

  4. Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran

    Mehrdad Khatami

  5. Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany

    Amin Mirzaiebadizi

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  1. Amin Mirzaiebadizi
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Supplementary file1: Table S1.

Sequences of oligonucleotides strands. Fig. S1. Optimization of formation time of S–L hybrid structure; from left to right: 45 min, 90 min, 120 min, and 180 min, respectively (S Strand is in lane 4, L strand is in lane 3, S–L hybrid is in lane 2, and lane 1 is a ladder). Fig. S2. UV–visible absorption spectroscopy of Short strands in DMSO with M2 nanoparticles before subtraction

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Mirzaiebadizi, A., Ravan, H., Dabiri, S. et al. An intelligent DNA nanorobot for detection of MiRNAs cancer biomarkers using molecular programming to fabricate a logic-responsive hybrid nanostructure. Bioprocess Biosyst Eng 45, 1781–1797 (2022). https://doi.org/10.1007/s00449-022-02785-x

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