This technology uses enzymatic ligation in DNA nanoswitches to detect very short or rare DNA and RNA sequences with high sensitivity, amplifying signals by recycling targets so even single molecules can be identified for diagnostics and research.
Background: Nucleic acid detection is a cornerstone of modern molecular biology, diagnostics, and biotechnology, enabling the identification and quantification of specific DNA or RNA sequences in a wide range of applications, from disease diagnostics to genetic research. As the demand for rapid, sensitive, and specific detection methods has grown, technologies such as PCR, hybridization assays, and molecular switches have become standard tools in laboratories and clinical settings. However, as research and clinical needs evolve, there is increasing interest in detecting ever shorter nucleic acid sequences and achieving reliable results even when the target molecules are present at extremely low concentrations. This is particularly important for early disease detection, monitoring minimal residual disease, and studying rare genetic variants or pathogens, where the ability to sensitively and specifically detect short or scarce nucleic acids can be transformative. Despite significant advances, current nucleic acid detection approaches face notable limitations. Traditional DNA nanoswitches and hybridization-based assays often struggle to reliably detect very short DNA or RNA sequences, as these short targets do not form stable complexes or loops, leading to weak or transient signals that are difficult to distinguish from background noise. Furthermore, most existing methods lack efficient signal amplification mechanisms that operate at the molecular recognition level, making it challenging to detect targets present at ultra-low abundance without resorting to complex, multi-step amplification protocols such as PCR. These limitations restrict the sensitivity, specificity, and range of nucleic acid detection, particularly in applications where sample quantity is limited or targets are highly fragmented, such as in liquid biopsies or forensic samples. As a result, there is a pressing need for new approaches that can overcome these challenges by enabling robust detection of short sequences and amplifying detection signals without introducing additional complexity or risk of contamination.
Technology Overview: This technology introduces a highly sensitive nucleic acid detection platform based on enzymatic ligation within DNA nanoswitches. The core mechanism involves the covalent closure of a nanoswitch loop by ligating detector oligonucleotides. The system is compatible with both DNA and RNA targets and can utilize various ligases, making it adaptable to a wide range of detection scenarios. Notably, the platform includes a redesigned nanoswitch composition to facilitate efficient ligation and detailed methods for constructing and using these nanoswitches. A standout feature is the cycling reaction, which enables "target recycling": after a target molecule triggers loop formation and ligation in one nanoswitch, it is released and can catalyze the looping and ligation of additional nanoswitches, thereby amplifying the detection signal. This solution is differentiated by its ability to detect very short nucleic acid sequences—targets that are typically undetectable due to the instability of short loops in conventional nanoswitch systems. The covalent ligation stabilizes these loops, expanding the range of detectable targets and making the technology especially valuable for applications requiring the identification of rare or short nucleic acids. Furthermore, the target recycling mechanism provides significant signal amplification, enabling the detection of extremely low-abundance targets, potentially down to single-molecule sensitivity. This combination of expanded target range and heightened sensitivity sets the technology apart from traditional nucleic acid detection methods, making it a powerful tool for clinical diagnostics, research, and biotechnology applications.
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Advantages: • Enables detection of very short DNA and RNA sequences by stabilizing nanoswitch loops through enzymatic ligation. • Amplifies detection signals via a novel target recycling cycling reaction, allowing a single target molecule to trigger multiple nanoswitch ligations. • Increases sensitivity to detect extremely low-abundance nucleic acid targets, potentially down to the single-molecule level. • Applicable to both DNA and RNA targets using various ligases, enhancing versatility across nucleic acid detection scenarios. • Provides new nanoswitch designs and optimized protocols for ligation and cycling reactions, improving reliability and ease of use. • Supports broad applications in clinical diagnostics, single-molecule analysis, and biotechnology research requiring sensitive nucleic acid detection.
Applications: • Ultra-sensitive clinical diagnostics • Single-molecule nucleic acid detection • Detection of short RNA biomarkers • Rare mutation screening • Environmental pathogen monitoring
Intellectual Property Summary: Patent application filed
Stage of Development: TRL 4
Licensing Status: This technology is available for licensing.