| Info. | Vol.16 - No.4 (2022.12.20) |
|---|---|
| Title | DNA-Wrapped CNT Sensor for Small Nucleic Acid Detection: Influence of Short Complementary Sequence |
| Authors | Shrute Kannappan1,2, Junhyuck Chang3, Priyannth Ramasami Sundharbaabu3, Jun Hyuk Heo2,3, Won-kee Sung6, Jae Chul Ro3, Kyeong Kyu Kim1, John Bosco Balaguru Rayappan4,5, Jung Heon Lee2,3
*Kyeong Kyu Kim kyeongkyu@skku.edu *John Bosco Balaguru Rayappan rjbosco@ece.sastra.edu *Jung Heon Lee jhlee7@skku.edu |
| Institutions | 1Department of Precision Medicine, School of Medicine, Sungkyunkwan University (SKKU), Suwon 16419, Korea
2Research Center for Advanced Materials Technology, Core Research Institute, Suwon 16419, Korea 3School of Advanced Materials Science and Engineering, Sungkyunkwan University (SKKU), Suwon 16419, Korea 4School of Electrical and Electronics Engineering, SASTRA Deemed University, Thanjavur 613401, India 5Centre for Nanotechnology and Advanced Biomaterials (CeNTAB), SASTRA Deemed University, Thanjavur 613401, India 6PNG Biomed, Youngin-Si 16950, Republic of Korea |
| Abstract | Carbon nanotubes (CNTs) are versatile materials that act as natural fluorescence quenchers and double scaffolds for DNA that can wrap around them based on π–π stacking. We exploited these properties of CNTs to develop a hybridization-based sensor for the detection of microRNA. We designed a fluorescein amidite (FAM)-labeled single-stranded oligonucleotide containing a CNT binding region (Poly T) followed by a sequence complementary to the target nucleic acid (probe sequence). As the DNA wraps around a CNT, FAM fluorescence is quenched in the absence of the target, whereas in the presence of the target, fluorescence emission is obtained. Experimentally, we found that one of the major issues with this sensor is its compromised sensitivity due to competition for adsorption of the probe DNA onto the CNT versus that of hybridization with the target DNA. To overcome this, we introduced a short complementary sequence (SCS) that binds to the probe sequence and found that it significantly improved the limit of detection of the sensor approximately 25-fold. To gain further insights into the mechanism of SCS in improving the sensor performance, we performed molecular dynamics (MD)-based simulations. Based on hybridization energy calculations performed using MM-GBSA, we found that the position of the SCS is key to shaping the binding affinity of the probe to the CNT. The MD-based calculations were validated using experimental results by comparing the sensor’s experimental limit of detection and the hybridization energy obtained computationally. Finally, we demonstrated the applicability of this sensor for the experimental detection of the cervical cancer-related biomarker miR-21-5p in human serum. |
| Keyword | Molecular dynamics, Carbon nanotube, Nucleic acid, Fluorescence, microRNA |
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