Chimeric DNA-templated silver nanoclusters as new fluorogenic probes for biosensing applications

Lee, Shi Ting (2019) Chimeric DNA-templated silver nanoclusters as new fluorogenic probes for biosensing applications. PhD thesis, University of Nottingham.

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Over a decade of research on DNA-templated silver nanoclusters (DNA-AgNCs), this material has now been recognised as an alternative to the conventional fluorescent probes (i.e. quantum dots and organic fluorophores). The DNA-AgNCs have been widely reported for biosensing application due to their design versatility and easy integration with functional DNA sequences. Notwithstanding, a good DNA-AgNCs design is crucial to generate a successful sensing result. Among all of the reported designs, chimeric DNA-AgNCs, i.e. placing AgNCs nucleation sequence and functional sequence in a single DNA strand, is relatively underexplored. This is because the chimeric DNA-AgNCs often exhibit fluorescence turn-off response whereby its accuracy could be affected by false results. However, the simplicity of the chimeric design deserves further investigation, considering it is more cost-effective and enables conclusive results on principles of detection.

In this thesis, the principles of chimeric DNA-AgNCs were applied on two test models of distinctive sizes, i.e. adenosine (small analyte) and telomerase (macromolecule). For both studies, an identical AgNCs nucleation sequence, termed Ct9 was integrated with different functional sequences: (1) aptamer for specific recognition of adenosine; and (2) primer for telomerase binding. For adenosine study, the sensing performance of DNA-AgNCs was evaluated by systemically positioning the AgNCs nucleation sequence across the DNA template (i.e. 5’-end, 3’-end or in the middle of DNA template). Among the three formulations, only 5’-end design showed fluorescence enhancement upon binding to adenosine, which is attributable to the structural reformation of anti-parallel G-quadruplexes. In contrast, the 3’-end design showed fluorescence quenching. The reason behind this quenching effect is not fully understand.

The study on detection of telomerase activity has indicated that parallel G-quadruplex conformation was able to induce a quenching effect. However, the microenvironment of complex buffer (e.g. TRAP buffer) is required to ensure a consistent turn-off signal, independent of the size of parallel G-quadruplex.

In summary, these studies have provided an insight on the principles of detection using DNA-AgNCs. The basic guidelines from the findings not only enable improvement on the formulation of chimeric DNA-AgNCs-derived aptasensors, but also expand their possible biosensing applications.

Item Type: Thesis (University of Nottingham only) (PhD)
Supervisors: New, Siu Yee
Lim, Kuan Hon
Su, XiaoDi
Keywords: biosensor; DNA-AgNCs; fluorescent; adenosine; telomerase
Subjects: Q Science > QP Physiology
Faculties/Schools: University of Nottingham, Malaysia > Faculty of Science and Engineering — Science > School of Pharmacy
Item ID: 56816
Depositing User: LEE, SHI TING
Date Deposited: 29 Jul 2019 04:40
Last Modified: 07 May 2020 11:16

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