We’re excited to share our latest work on SARS-CoV-2 where we expand on our previous publications and describe an aptamer class that binds all major variants of concern with high affinity. This is an important tool for the development of aptamer based COVID detection technologies that can be specific, sensitive and robust for the detection of current and possibly future variants. Read more about our work here. -Jim

Zhang Z, Li J, Gu J, Amini R, Stacey HD, Ang JC, White D, Filipe CDM, Mossman K, Miller MS, Salena BJ, Yamamura D, Sen P, Soleymani L, Brennan JD, Li Y. A Universal DNA Aptamer that Recognizes Spike Proteins of Diverse SARS-CoV-2 Variants of Concern. Chemistry. 2022 Feb 26:e202200524. doi: 10.1002/chem.202200524. Epub ahead of print. PMID: 35218097.

Aptamers are nucleic acids that are capable of recognizing target molecules. Over the past 30 years, thousands of aptamers have been discovered by scientists via in vitro selection technique. This review examined the range of targets as well as the affinity and specificity of ~1000 generated aptamers. By comparing the synthetic aptamers with natural riboswitches, protein-based recognition elements, a gap between synthetic aptamers and natural recognition elements was revealed.  A series of ideas for developing better aptamers were proposed to solve the real world problems. We hope these strategies can help aptamers remain high functionality in application environment. Happy reading 😊 – Shuwen Qian

Qian, S.; Chang, D.; He, S.; Li, Y. Aptamers from Random Sequence Space: Accomplishments, Gaps and Future Considerations. Analytica Chimica Acta 2022, 1196, 339511. https://doi.org/10.1016/j.aca.2022.339511

Following up on our recent report of high-affinity DNA aptamers for SARS-CoV-2, we’ve been busy working with our collaborators in the Soleymani Lab and the Biointerfaces Institute to apply them on electrochemical sensors. Read our latest COVID19 paper at Pubmed to learn more about how we achieve high sensitivity detection of SARS-CoV-2 in unprocessed human saliva to pave the way for a rapid and sample diagnostic test.

Take a quick look at our recent publication in Frontiers in Chemistry. In this paper, a simple and surfactant-free approach is presented to synthesize Pd-Ir nanocubes with atomic Ir shell thickness in an aqueous solution at room temperature. Biomolecules such as antibodies and nucleic acids have free access to the surface of Pd-Ir nanocubes. Applications of Pd-Ir nanocubes in immunoassays and aptamer-based biosensors are realized, exploiting the excellent peroxidase activity and fluorescence quenching ability of Pd-Ir nanocubes. Read more about our work at Pubmed. – Jiuxing

Li J, Li Y. Facile Synthesis of Pd-Ir Nanocubes for Biosensing. Front Chem. 2021 Nov 24;9:775220. doi: 10.3389/fchem.2021.775220. PMID: 34900937; PMCID: PMC8651546.

The Li Lab and our collaborators from across the McMaster community have published our first report on our novel aptamers for COVID19! The lab has refocused our efforts over the past year to address pressing COVID19 problems and we’re excited to finally be sharing our work. Read more about our work at Pubmed.

In a collaboration with the Didar Lab and Toyota Tsusho Canada, the Li Lab will be working towards the development of food wrap technologies for the detection of pathogenic bacteria using DNA sensors. Read more about it McMaster Brighter World.

Li Lab postdoctoral fellow Erin McConnell has been awarded the NSERC & L’Oréal-UNESCO Women in Science Supplement. Congratulations to Erin for her fantastic work as a scientist and as a role model for young scientists around the world.

Explore the following links to learn more about Erin’s work and the work of the other great researchers recently recognized.

Canadian Awarding ceremony of the L’Oréal-UNESCO For Women in Science fellowships

NSERC and L’Oréal-UNESCO For Women in Science Supplement

L’Oréal-UNESCO For Women in Science 2018: Erin McConnell

IUPAC Young Chemist

https://iupac.org/100/pt-of-chemist/#erin-mcconnell-he

Take a look at this recent publication from the Li Lab in Angewandte Chemie International Edition. In this paper, we explore a novel signal amplification strategy termed DNAzyme feedback amplification (DFA). This method takes advantage of rolling circle amplification and RNA-cleaving DNAzymes for biosensing applications, with sensitivity improvements of 3-6 orders of magnitude when compared to conventional methods. -Suraj

Checkout this recent paper from the Li Lab in Scientific Reports, “Detection of DNA Amplicons of Polymerase Chain Reaction Using Litmus Test.” Here we report on a novel DNA detection method that combines the advantages of the polymerase chain reaction with the simplicity of a litmus test. The diagnostic capabilities of the platform is demonstrated using clinically validated stool samples from C.difficile infected patients. -Suraj

Funding was recently announced to advance the Li lab’s research into rapid Legionella diagnostic technologies. Congratulations to our McMaster collaborators Dr. Carlos Filipe and Dr. John Brennan of the Biointerfaces Institute  and industry partners TGWT Clean Technologies Inc., Cytodiagnostics and Mold and Bacterial Consulting Labs. Read more about it on the McMaster News website.

Sepehr Manochehry, a PhD candidate in his 3rd year, earned the coveted CIHR doctoral scholarship this year. He was ranked 6th nationwide, putting him in the top one percentile among more than 700 other applicants. His success and the focus of his research was recently featured in a news magazine article. Read it to gain a better understanding of what motivates hard-working graduates students like Sepehr.  http://biochemrocks.freeflowdp.com/biochemrocks/2357984385961772?pg=23#pg23

Checkout the Li Lab’s latest paper in Nature Communications! In a collaborative project between the Li Lab and McMaster’s Biointerfaces Institute, we report a novel reporter system based on mechanically interlocked circular DNA, rolling circle amplification and DNAzymes for highly sensitive bacterial detection.

Read about a new highly specific Clostridium difficile catalytic DNA biosensor in the Li Lab’s latest publication in Angewandte Chemie International Edition. You can also checkout the a profile of the report on the McMaster Daily News.

Check out the Li Lab’s latest publication in Angewandte Chemie International Edition, “Biosensing by Tandem Reactions of Structure Switching, Nucleolytic Digestion, and DNA Amplification of a DNA Assembly”. Postdoc Meng Liu has developed a novel, high sensitivity DNA based signal amplification technique using an isothermal DNA polymerase and structure switching DNA aptamers. This work brings DNA aptamer based detection technologies another step closer to convenient and cost effective point of care applications.

-Jim

Evolution of an Enzyme from a Noncatalytic Nucleic Acid Sequence

Life as we know it requires thousands of biological molecules, called enzymes, which carry out chemical reactions and allow life to exist. These molecules did not appear out of thin air – they evolved out of a mixture of the Earth’s first compounds, known as prebiotic soup. One theory for how life originated is known as the “RNA World” Hypothesis: ribonucleic acid (RNA), capable of both encoding information and performing enzymatic reactions, could have been the initiator of the origins of life, bridging the gap between life and non-life.

In this project, we used a sequence of DNA as a proxy for RNA in the origins of life. Wesubjected it to a process called in vitro selection, where we randomly introduced small variations in the sequence and then obliged the sequences to carry out a reaction. The sequences were filtered – only sequences able to perform the specific reaction were permitted to survive. These unique sequences were then subjected to cycles of this process – induction of small variations, and segregation of competent sequences. Using this method, we were able to take a sequence which was incapable of an enzyme-like reaction, and evolve it with minimal changes into a sequence adept at executing the reaction. This experiment allows us a tiny peep into how RNA molecules could have acquired function at the brink of the origin of life.

-Rachel Gysbers