Highly Sensitive Detection Of Nucleic Acids Using Chiral Plasmonic Sensor Based On DNA Origami

Chiral plasmonic sensing has great application prospect in the field of biosensing.Since CD signal of biological sample is too weak,almost negligible,in visible wavelength,the detection of target molecules using plasmonic sensor with dynamic CD output possesses lower background noise than that with fluorescence output,resulting in higher specificity.To construct chiral plasmonic sensors and realize CD signal sensing,one effective method is to use DNA nanotechnology to bring noble metal plasmons,such as gold nanorods,close enough within a strong coupling distance to enhance optical near-field effects.Utilizing the programmability and addressability of DNA origami technology,people can not only precisely control the static arrangement of plasmonic elements,but also design dynamic and switchable chiral plasmonic nanostructures driven by target biomolecules.Through rational design,using target biomolecules to regulate the opening and binding of DNA strands,the configuration conversion of chiral plasmonic structure as dynamic biosensor can be easily achieved,which is especially suitable for nucleic acid sequence detection.In previous work,strand displacement reaction was used to transform the configuration of the chiral plasmonic sensor,generate dynamic CD change and realize the detection of HCV-related RNA sequence.However,due to the restriction of structure concentration,the sensitivity of the detection can only reach 100pM,which is about 10 to 50 times more than the concentration of target RNA in clinical samples.We proposed internal signal amplification to improve the detection sensitivity of the chiral plasmonic sensors.As far as we know,there are many kinds of ways to achieve signal amplification,such as polymerase chain reaction(PCR)and nucleic acid circuit.PCR can directly amplify the target strands,the concentration of which is increased exponentially until an obvious fluorescent output signal is produced.As for the nucleic acid circuits,especially circuits based on catalytic amplification,the target strand is regarded as a catalyst to cycle in cascade reaction and will not be consumed.Based on this,we constructed a DNA origami-based chiral plasmonic sensor integrated with the catalytic hairpin assembly(CHA)nucleic acid circuit to realize the amplification of chiral signal.In order to verify the effectiveness of the scheme,we selected two tumor-related RNA sequences as detection targets to detect using the plasmonic sensor.One is microRNA-21,also named MIR-21,and it is related to several kinds of cancer,such as gastric and breast cancer.The other is fragment of GPC1,a pancreatic cancer-related mRNA.It is turned out that the detection limit can reach below 10 pM,which is about an order of magnitude lower than the previous work.The chiral plasmonic sensor based on CHA signal amplification can achieve high sensitivity and specificity detection,providing novel platform for constructing intelligent biosensors.The research content of this paper mainly includes the following three aspects:1.The design and preparation of gold nanorod dimer based on DNA origami structure as a chiral plasmonic sensor,which can be triggered by a specific nucleic acid sequence to realize its configuration change and generate chiral signal output.2.Based on the signal amplification principle of catalytic hairpin assembly(CHA),two nucleic acid sequences of tumor markers were selected and the corresponding hairpin sequences were designed respectively.The hairpin sequences were assembled onto the plasmonic sensor and the highly sensitive sequence detection with signal amplification function was successfully realized.3.The sensor was designed based on the entropy-driven catalytic signal amplification nucleic acid circuit and the signal amplification system was applied to the chiral plasmonic structure to realize the highly sensitive detection of the target sequence.