WIN Member Seminar Series: Juewen Liu Group

The Waterloo Institute for Nanotechnology (WIN) is comprized of many talented faculty members, students and researchers from various backgrounds of study. We wanted to showcase their incredible work through our Member Seminar Series! Each month a professor and 2 of their researchers will present their research to our community. This series is an opportunity for our WIN community to come together, learn about ongoing research and potentially foster new partnerships between students, faculty and labs.

"Building biosensors by combining DNA and nanoparticles" - Professor Juewen Liu

Abstract

DNA is known for its genetic functions, but since the early 1990s, its chemical functions have been gradually discovered such as molecular recognition and catalysis. These chemical functions make it possible for using DNA as biosensors. Compared to proteins such as enzymes and antibodies, DNA is more stable, more cost-effective and easier to modify. In addition, DNA has programmable structures making it very versatile for biosensor design. To signaling the molecular recognition events of DNA, various methods have been developed, and in this talk we will focus on colorimetric sensors. Gold nanoparticles have been commonly used as color labels because of their extremely high extinction coefficients and distance-dependent color. Conjugation of DNA to gold nanoparticles can convert the molecular recognition events of DNA to colorimetric signals. I will cover examples of isolating the DNA sequences that can recognize different metal ions, and the other two lab members will talk about specific examples on biochemical characterization and bioconjugation to gold nanoparticles.

"In vitro selection and characterization of a sodium-dependent DNAzyme" - Lingzi Ma

Abstract

Sodium is the one of the most abundant metal ions in biology. The interaction between Na⁺ and biomolecules is often considered as non-specific. Recently, a Na⁺-specific DNAzyme, NaA43, was reported to catalyze the RNA cleavage reaction with an apparent dissociation constant (K_d) of ~70 mM Na⁺. Later activity studies revealed a Na⁺-binding loop in the NaA43 DNAzyme which contributes to its Na selectivity. In our lab, a similar DNA sequence (NaH1) was isolated from our in vitro selection process which also contains the Na⁺-binding loop and only differs from NaA43 at two nucleotides. Interestingly, NaH1 presents a distinct pH preference compared to NaA43 with its highest activity at around pH 5, while NaA43 prefers a higher pH around 7. Meanwhile, NaH1 exhibits a faster cleavage rate especially at relatively low Na⁺ concentrations (below 10 mM) with an apparent K_d of 12.0 ± 1.6 mM. The excellent selectivity toward Na⁺ over other monovalent ions is still preserved in NaH1. Further biochemical study revealed a general acid catalysis in the NaH1, while a general base catalysis in NaA43. This is an interesting example where single point mutations can change the mechanism of cleavage from general base to general acid, and it can also explain this Na⁺-dependent DNAzyme scaffold sensitive to a broad range of metal ions and molecules.

"Attaching DNA to gold nanoparticles" - Biwu Liu

Abstract

DNA as a powerful affinity agent has been used in constructing biosensors towards metal ions, small molecules, proteins, and even whole cells. The emerging nanotechnology has provided various signaling strategies to DNA-target recognition process. To achieve a reliable DNA biosensor with high sensitivity, selectivity, and robustness, a critical step is to conjugate the recognition component (i.e. DNA) with nanomaterials. In this talk, colloidal gold nanoparticles will be used as an example to illustrate the capability of nanotechnology in transducing the targeting process of DNA. Our efforts in understanding and controlling the DNA-nano interfaces will be discussed. The major challenge in conjugating DNA with AuNPs is to control the DNA density, conformation, and functionality as well as the colloidal stability of AuNPs. The traditional method relied on the time-consuming “salt-aging” process, which also resulted in non-specific DNA adsorption on AuNPs. By modulating the buffer pH, anions, or temperature, we show that high DNA density can be achieved much faster. Moreover, we revealed that the DNA conformation can be well maintained by backfilling the AuNPs surface with certain anions. We hope our talk will give some useful thoughts in fabricating DNA-based biosensors.