Highly Sensitive Single Mutation Detection of EGFR by Bridged Nucleic Acid

Overview

Highly sensitive detection of mutations is crucial for early action against cancers and other genetic diseases. Real-time quantitative PCR (qPCR) and a newly developed bridged-nucleic acid (BNA) clamp technique together provide a means of highly sensitive single mutation detection that suggests a novel method for cancer diagnosis. One of the most recently developed DNA mimics, bridged-nucleic acid (BNA) displays exceptional hybridization with DNA, making it an effective choice for clamp design. The BNA clamp, an oligonucleotide composed of both BNA and DNA monomers, allows for detection of 1 mutant species out of 10,000 wild-type species. With optimization, a 13-mer clamp containing 9 BNA bases was deemed most effective in distinguishing the mutant genes from the wild-type genes for the single mutation of T790M of epidermal growth factor receptor (EGFR), which poses issues for cancer treatment. In order to aid with design and analysis of the mutation detection technique, molecular dynamics simulations were performed via an umbrella sampling method to approximate the free energy of binding (deltaG) between the BNA clamp and a wild-type or mutant template strand. The script, ONECLICK, was designed and written for the first time to automate the umbrella sampling process. The results showed that the deltaG values for the wild-type and mutant helices were significantly different, suggesting that molecular dynamics simulations could ease the BNA clamp designing process and increase accessibility. This BNA-clamping qPCR technology coupled with computationally predictive software may offer a promising new avenue for early detection of clinically important mutations in the future.

Awards (2)

First Award of $5,000 $5,000
Intel ISEF Best of Category Award of $5,000 $5,000

Competition history

ISEF 2016 Category not listed · Entry BCHM011

Resources

ISEF abstract page

Related projects

ISEF · 2017

Development of Novel Method Using RNA Template for Detection of Mutation with Superior Sensitivity

ISEF · 2023

Designing a Novel Primer Blocker Using Bioconjugation of Single Stranded Binding Protein and Oligonucleotides for Improved KRAS Mutation Detection

ISEF · 2026

Harnessing RNA Nanotechnology: In silico Design and Structural Modeling of RNA Aptamers Targeting BRCA1 for Early Detection of Breast and Ovarian Cancer

ISEF · 2019

Ultrasensitive Detection of Early-Stage Cancer Using ctDNA Sequencing with UMIs

Closest projects by meaning, across every fair and year in the corpus.