Browsing by Author "Niu, Chenqi"

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Binding Studies of Cationic Conjugated Polymers and DNA for Label-Free Fluorescent Biosensors
(American Chemical Society, 2022-07-19) Zhang, Pengbo; Lu, Chang; Niu, Chenqi; Wang, Xiaoyu; Li, Zhengping; Liu, Juewen
Cationic conjugated polymers (CCPs), especially polythiophene, have been extensively used as probes for developing DNA and aptamer-based biosensors. Although many interesting applications have been achieved, a fundamental understanding of this system remains quite limited. In this work, we performed systematic binding assays to understand the interactions between poly(3-(3′-N,N,N-triethylamino-1′-propyloxy)-4-methyl-2,5-thiophene) (PMNT) and DNA. The fluorescence of PMNT at 530 nm initially decreased and then a peak at 580 nm emerged after binding with single-stranded DNA (ssDNA). The binding force between PMNT and DNA was dominated by electrostatic interactions at first and then DNA base-mediated interactions also became important. Since the bases in double-stranded DNA (dsDNA) were shielded, their fluorescence changes were quite different. To best differentiate ssDNA and dsDNA, the optimal pH was between 6 and 8, and the optimal NaCl concentration was around 0.3 M. Moreover, by changing the sequence and length of ssDNA, poly-T had the largest fluorescence shift and poly-A had the smallest change. Under the optimized conditions, the PMNT-based biosensor had a detection limit of 1 nM DNA, which was similar to the SYBR Green I-based assay.
Capture-SELEX of DNA Aptamers for Estradiol Specifically and Estrogenic Compounds Collectively
(American Chemical Society, 2022-11-28) Niu, Chenqi; Zhang, Chong; Liu, Juewen
Estrogenic compounds such as estrone (E1), 17β-estradiol (E2), and 17α-ethynylestradiol (EE2) are serious environmental contaminants due to their potent biological activities. At least six selections were previously reported to obtain DNA aptamers for E2, highlighting its environmental importance. A careful analysis revealed that the previous aptamers either are too long or do not bind optimally. Herein, a series of new aptamers were obtained from the capture-SELEX method with dissociation constants down to 30 nM as determined by isothermal titration calorimetry (ITC). Two aptamers were converted to structure-switching fluorescent biosensors, which achieved a limit of detection down to 3.3 and 9.1 nM E2, respectively. One aptamer showed similar binding affinities to all the three estrogens, while the other aptamer is more selective for E2. Both aptamers required Mg2+ for binding. The proposed sensors were successfully applied in the determination of E2 in wastewater. Moreover, comparisons were made with previous aptamers based on primary sequence alignment and secondary structures. Among previously reported truncated aptamers, ITC showed binding only in one of them. The newly selected aptamers have the combined advantages of small size and high affinities.