Self-assembled DNA dendrons as signal amplifiers in a DNA probe-based chemiluminescence assay for enhanced colorimetric detection of short target cDNA

Abstract

A simple, reliable, and cost-effective method for nucleic acid detection is of increasing interest in clinical diagnostics of infectious and genetic diseases. Currently, enzyme-mediated methods such as polymerase chain reactions and loop-mediated isothermal amplification are the most widely used methods in the qualitative and quantitative diagnosis of long nucleic acid sequences with high sensitivity. However, a high detection sensitivity for short-length sequences remains a significant challenge because it is difficult for the primers to bind to their sequences. Our previous study demonstrated a simple, enzyme-free, and sequence-specific colorimetric detection of 24-nucleotide short target DNA at room temperature using a developed assay that combines catalytic hairpin assembly (CHA) and enzyme-linked immunosorbent assay (ELISA)-mimicking methods. In this follow-up study, we aim to design and develop DNA-based signal amplifiers, or DNA dendrons, to improve the colorimetric detection of short target cDNA in the CHA-mediated ELISA-mimicking assay. DNA dendrons are highly branched conformations synthesized by the molecular self-assembly of three DNA oligomers. The assay using DNA dendrons demonstrates an enhanced detection sensitivity with the detection of approximately 50 pM of 24-nucleotide short target cDNA, which is a 16.4-fold higher detection limit compared to that obtained without DNA dendrons under the same conditions. Thus, applications of the developed DNA dendrons as an effective signal amplifier in DNA probe-based chemiluminescence assays have the potential to improve the colorimetric detection of short target cDNA with high sensitivity for the diagnosis of different diseases.