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Updated: Sep 9, 2025
Author Spotlight: Advancements in DNA Nanosensors – Addressing Sensitivity and Selectivity Challenges in Molecular Detection
Published on: February 9, 2024
Single-Molecule Nanopore Detection of Non-Canonical Thymine-Melamine Hydrogen Bonding Base Pair in DNA Abasic Site
Shilong Liu1,2,3, Jing Li1,2,3, Yunjiao Wang1,2,3
1School of Electronic Science and Engineering, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China.
Abstract:
The binding of small molecules to DNA may represent a mutagenic process capable of inducing genomic structural alterations and functional impairment. Melamine (MA), a toxic small molecule, exhibits a hydrogen-bonding interface structurally analogous to adenine, enabling to form non-canonical thymine-melamine (T-MA) base pairs like Watson-Crick pairing. This property allows MA to program DNA nanostructure formation. Given MA's documented biological consequences, such as kidney disease, reproductive toxicity, and central nervous system dysfunction, sensitive detection of MA-DNA interactions has become critically important. However, such subtle structural changes remain challenging to identify because of the paucity of effective detection approaches in a high-resolution manner. To overcome this limitation, nanopore measurement is employed to identify T-MA hydrogen bonding base pairing in DNA. Results demonstrate that nanopore enables unambiguous identification of T-MA hydrogen bonding via mechanically unzipping thymine-melamine-thymine (T-MA-T) triplets in DNA structures. The approach achieves single-base-pair resolution, as evidenced by nucleotide substitutions flanking the abasic site in complex DNA structures. In addition, nanopore-based kinetic analysis reveals an enhanced intramolecular stability in MA-binding DNA compared to those consisting of complete canonical DNA pairs. This research establishes a powerful platform for high-resolution interrogation of DNA-small molecule interactions and quantitative biophysical characterization of mutagenic modifications at the nanoscale.
Insights
Melamine (MA) can form non-canonical base pairs with thymine in DNA, potentially causing mutations. Nanopore technology precisely detects these MA-DNA interactions, revealing enhanced DNA stability and enabling nanoscale mutagenic analysis.
Area of Science:
- Biochemistry
- Nanotechnology
- Toxicology
Background:
- Small molecule binding to DNA can cause mutations and impair function.
- Melamine (MA), a toxicant, mimics adenine and forms non-canonical thymine-melamine (T-MA) base pairs.
- Detecting MA-DNA interactions is crucial due to MA's health effects, but high-resolution methods are lacking.
Purpose of the Study:
- To develop a high-resolution method for detecting melamine-DNA interactions.
- To investigate the structural and kinetic consequences of T-MA base pairing in DNA.
- To establish a nanopore-based platform for studying DNA-small molecule interactions.
Main Methods:
- Utilized nanopore measurements to detect T-MA hydrogen bonding.
- Employed mechanical unzipping of thymine-melamine-thymine (T-MA-T) triplets in DNA.
- Performed kinetic analysis of MA-binding DNA structures.
Main Results:
- Nanopore measurements unambiguously identified T-MA hydrogen bonding.
- Achieved single-base-pair resolution, confirmed by nucleotide substitutions.
- Observed enhanced intramolecular stability in MA-binding DNA compared to canonical DNA.
Conclusions:
- Nanopore technology provides a powerful platform for high-resolution interrogation of DNA-small molecule interactions.
- This method enables quantitative biophysical characterization of mutagenic modifications at the nanoscale.
- The findings are critical for understanding and detecting the genotoxic potential of melamine.
