Projects

Most Recent Research Project:

Glucose Oxidase (GOx)

Caroline Brown is currently developing an RNA aptamer against Glucose Oxidase (GOx), which will be used in an ELONA assay as a diagnostic tool for presymptomatic Alzheimer’s. This work employs the Systematic Evolution of Ligand by Exponential Enrichment (SELEX) to isolate the RNA sequence that binds with the highest affinity to the N71 pool. That sequence is then used in an ELONA. An ELONA is a chain of molecules that traps the biomarker between two aptamers. Once the biomarker is captured, an anti-glucose oxidase aptamer is added to the mixture and binds to the main chain. Finally, glucose is introduced, and glucose oxidase attached to the anti-GOx aptamer will light up the substrate, alerting to the presence of the Alzheimer's biomarker in the blood. The project is currently on its first round of SELEX, and results are showing that stringency might have been too high in the first round, which will be taken into account when proceeding. The advantage of finding a diagnostic aptamer that can be used as an Alzheimer’s diagnostic is a cheaper and faster diagnosis of the disease, which means damage to the brain can be stopped and preventative measures taken. 

NanoLuc Luciferase (NLuc) 

Kyle Nguyen worked on identifying an RNA aptamer that can bind to NanoLuc Luciferase (NLuc). He plans to combine NLuc’s fluorescent properties with another aptamer against thyroid-stimulating hormone to create a cheaper and more accessible diagnostic for the hundreds of millions of people with undiagnosed hypothyroidism. To isolate an aptamer against NLuc, he used Systematic Evolution of Ligand by Exponential Enrichment for a total of four cycles, utilizing negative selection. After his fifth round, he planned to sequence his RNA pool and utilize an assay with NLuc to see if his RNA has a significant binding affinity towards NLuc. With both aptamers against NLuc and TSH, he plans to create an assay to detect high levels of TSH. https://doi.org/10.1016/j.jbc.2024.106538.

Daniel Fuentes worked on developing an RNA aptamer against Nanoluc Luciferase(Nluc), a bioengineered enzyme capable of producing a glow-type luminescence. The project proposes a diagnostic tool capable of detecting DENV-2 E protein domain III (ED3), an envelope protein found on the viral surface of the dengue virus. Using the luminescent properties of an Nluc-conjugated aptamer in combination with an ED3-specific aptamer, a molecular complex can be constructed for the detection of prior DENV infection. Isolation of the best binding RNA sequence from the initial synthetic N71 RNA pool is achieved through the Systematic Evolution of Ligand by Exponential Enrichment (SELEX). 6 rounds of SELEX have been completed, including a negative selection during round 3. After his 6th round, he plans to obtain readings from his enriched RNA pool through Sanger Sequencing in hopes of using the information to later conduct an affinity assay to assess the RNA sequences' binding affinity. https://doi.org/10.1016/j.jbc.2024.106616. 

Superoxide Dismutase 1 (SOD-1)

Avery Matthews is currently working on developing an oligonucleotide complex that utilizes an RNA aptamer against Superoxide Dismutase 1 (SOD-1) protein. SOD-1 protein protects cells from the harmful effects of superoxide radicals. However, the protein tends to aggregate when present in the brains of patients with Amyotrophic Lateral Sclerosis (ALS), and these aggregates have been shown to increase the rate of symptom progression of the disease. The oligonucleotide complex containing the aptamer will be used as a drug delivery system for the enzyme ubiquitin. The use of this product would lead to the degradation of these harmful protein aggregates, ultimately slowing ALS progression. The Systematic Evolution of Ligands by Exponential Enrichment (SELEX) is being used to isolate the aptamer against SOD-1. Avery has completed six rounds of SELEX, and has cloned and sequenced her aptamer pool via Sanger sequencing. She plans to clone and sequence her pool again to gather better data about the progression of her aptamer selection. https://www.jbc.org/article/S0021-9258(24)00407-1/fulltext.

Alvin Pham is currently working on developing an RNA aptamer against wild-type SOD1 protein, which is known to be implicated in a number of neurodegenerative diseases, with its mechanism remaining unknown. This work employs the Systematic Evolution of Ligand by Exponential Enrichment (SELEX) to isolate the best binding RNA sequence out of the original synthetic N71 RNA pool. Seven rounds of SELEX have been completed, and the readings of the enriched pool have been obtained using Next Generation Sequencing and Sanger Sequencing. Currently, Alvin is focusing on conducting an electrophoretic mobility shift assay (EMSA) to determine the binding affinity of the enriched aptamer sequences to the SOD1 protein. Eventually, the goal is to develop this RNA aptamer as a molecular marker that will allow the tracking of wild-type SOD1 migration intracellularly. https://doi.org/10.1016/j.jbc.2024.106550.

UTexas Aptamers Database

Dhruv Kumar, Amrut Pennaka, and Einez Wu are working on developing a fine-tuned Large Language Model (LLM) to automate literature parsing for the UTexas Aptamer Database, a centralized repository for aptamer-related data. This project utilizes GPT-4o Mini and integrates OpenAI’s API with prompt engineering to extract key aptamer information efficiently. The workflow involves aggregating aptamer sequences, extracting PubMed Central IDs (PMCIDs) from PubMed URLs, and processing XML files for analysis. An initial dataset of ~300 articles has been curated, with ~200 used for fine-tuning and 100 for evaluation, assessing model performance through precision and recall metrics. Ultimately, this approach enhances database scalability, supporting advancements in aptamer-based diagnostics, therapeutics, and drug delivery.

Ali Askari created the UTexas Aptamer database, one of the world’s largest publicly accessible and searchable aptamer databases, with over 1550 aptamer sequence entries. His methodology for information collection, curation, and review of each aptamer sequence and related data begins with searching for aptamer papers, and extracted data is added to the Google Sheet, forming the dataset, aiming to include 10-30 papers for each year since 1990. The data is housed in Google Sheets, the Database (Caspio) organizes and queries the dataset, and the UTexas Aptamer Database website increases visibility for researchers. To preserve information long-term and avoid loss of data, the dataset is downloaded several times throughout the year. All aptamer sequences and related information undergo internal review, where another researcher must confirm that the information collected is accurate and inconsistencies require additional review. Then the data cleaning process correctly formats the collected information to standardize reporting. Finally, community feedback collected through the form is monitored to validate the information. 

Ali Askari and Shriya Swamy worked on the curation and internal review of aptamer sequence information and cross-referenced aptamer entries with another aptamer database: Apta-Index, to standardize and determine the accuracy of our information (90 aptamers were shared between the UTexas Aptamer Database and Apta-Index). Any discrepancies in information were addressed. Additionally, to ensure the sustainability of the database, a course-based research experience with training protocols was implemented to ensure a team of researchers will continue to curate, review, and update the database. This project has been presented at over 10 conferences to increase the visibility of the UTexas Aptamer database to other researchers. Future applications and uses of the database include, but are not limited to, analysis of data such as nucleic acid composition, determining correlation between fields of information, and can be useful for training AI, interfacing the UTexas Aptamer DB with Large Language Models, such as ChatGPT. This database is used by researchers around the world and is contributing to the advancement of aptamer research. https://doi.org/10.1093/nar/gkad959. https://doi.org/10.1016/j.jbc.2024.106562. 

Calf Intestinal Alkaline Phosphatase (CIAP)

Lilya Ma is currently working on developing an oligonucleotide complex that utilizes an RNA aptamer against Calf Intestinal Alkaline Phosphatase used within an Enzyme-Linked Oligonucleotide Assay (ELONA) against protein deglycase-1 (DJ-1) to detect early onset of strokes. CIAP is used within an ELONA assay as a reporter molecule that produces a bioluminescent signal once the biomarker is detected. Due to the time-sensitive nature of strokes, it's imperative for early diagnosis to avoid severe disabilities, including paralysis. However, advanced brain imaging, including MRIs, for diagnosing strokes, is not accessible within lower-income communities; thus, a more accessible and affordable diagnosis for strokes is needed. Selection against CIAP is done using the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) from a pool of 112 nt RNA sequences. Lilya is currently on round 5 of selection, and sequences of the potential aptamer pool will be analyzed via Sanger sequences after round completion.