Multifunctional nanopipettes: from DNA crowding to nanoscale sensing

Al-Waqfi, Rand Ahed Mahmoud (2025). Multifunctional nanopipettes: from DNA crowding to nanoscale sensing. University of Birmingham. Ph.D.

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Abstract

This work is concerned with single-molecular detection of DNA, RNA and other target systems. First, this thesis showcases the utilisation of nanopipettes’ asymmetric geometry to capture and retain double stranded kilobase pair DNA, then subsequently release the DNA by reverse translocation into the bulk solution. By utilising different DNA lengths through multiple experiments, the accumulation of DNA inside the nanochannel has been shown to induce a crowding effect. Further, under certain circumstances no DNA translocation observed, and the pipette was reversibly blocked. This crowding effect is further correlated with the length of the translocated DNA molecules; shorter DNA occupies less space and requires more translocation events to fill the pipette compared to longer DNA molecules. Interestingly, with the introduction of functional moiety to the DNA, this thesis suggests that this newfound effect could be utilized to trap DNA as a capture probe and incubate it with certain analytes inside the nanopipettes, thus, analyte detection by ‘functionalised’ DNA can be further assessed after reverse translocation.

Beyond local trapping, carrier DNA was also explored in this thesis for long noncoding RNA (lncRNA) detection as a distinct aim. While the results in this specific aspect remained inconclusive, overall, the work highlights the importance of asymmetric geometry of nanopipettes toward opening the door to new capabilities for biophysical and bioanalytical research at the single-molecule level.

Type of Work:

Thesis (Doctorates > Ph.D.)

Award Type:

Doctorates > Ph.D.

Supervisor(s):