Periodic Reporting for period 1 - DeDNAed (Cluster decorated recognition elements on DNA origami for enhanced raman spectroscopic detection methods)
Período documentado: 2021-03-01 hasta 2022-02-28
In our project a biosensor platform will be developed, that is not limited to a special target but that can be easily adapted to a wide range of applications. The platform should not only impress in its flexibility in application, but also with its ease of use, high selectivity and sensitivity as well as the speed of detection. All above-mentioned benefits are possible based on the capabilities of DNA-Origami. The so-called DNA origami, a folded DNA single strand, enables the possibility to combine the advantages of biomolecular sensors and the high-precision optical measurement method of surface-enhanced Raman spectroscopy (SERS). Individual, exchangeable bio-recognition elements (e.g. DNA aptamer, antibodies; bio-RE) with integrated atomic clusters can be easily integrated into specially aligned nanoparticle (NP) arrangements like a pin on a (nano-)breadboard, in order to achieve a fast, sensitive and selective detection of the respective target during binding to the bio-RE through near-field coupling. The integration in higher-order sensor arrays will be done on both solid silicon-based substrates and flexible surfaces (paper, polymer or textiles).
For the development of such a biosensor the following objectives are essential:
(1) Establishment of DNA origami as “nano breadboard” for the bio-RE
(2) Proof of signal enhancement through spatial alignment of bio-Re and NP
(3) Demonstration of detection of food containments and bio markers on novel sensor platform
(4) Transfer of the sensor platform to a flexible substrate
The DNA origami structure design was adapted for optimal position of bio-RE immobilization to ensure adequate gold NP anchor points for all contemplated gap sizes. Based on this four DNA origami designs with different NP spacing were synthesized. In addition, initial experiments of NP attachment were performed considering the desired spacing.
For the subsequent integration of the biosensor, three different material systems with varying binding-resistant (BR) layers were developed by nanotechnology. Their selectivity in binding affinity towards the binding-attractive (BA) layer was investigated by immobilization tests with un-functionalized DNA templates. Two of the three systems were found to be sufficiently selective. Further process adaptations to reduce the binding affinity of the BR layer are currently in progress, as are tests to increase the binding affinity of the BA layer.
From the scientific work, three deliverables (D) regarding the design of the bio-RE (D2.1) the DNA Origami (D3.1) and the immobilization system (D5.1) have been prepared so far.
In the context of project management as well as dissemination and exploitation, next to the Consortium Agreement three other administrative documents to ensure efficient project development have been developed and published in an open-access repository (Zenodo).
(1) Project Quality Plan
(2) Data Management Plan
(3) Exploitation and dissemination plan of Results
Furthermore, a project website was created, as well as an online presence on Twitter and LinkedIn.
Further, to the best of our knowledge, a method for a surface immobilization of a (functionalized) DNA origami on paper, cotton or similar substrates has never been described in the literature. However, opens up the possibility of use as wipe tests or for wearables.
The direct detection of the analyte from the solution and the transfer to application-related surfaces represent two essential steps for the further development of current research on SERS and DNA origami-supported diagnostics, which will bring a market launch into the existing biosensor technology significantly closer. The detection of various model analytes with high research relevance such as interleukin-6 (IL-6), aflatoxin, cancer DNA and recombinant surface proteins of influenza is intended to verify the high application potential of our sensor platform in the point-of-care diagnosis. However, these new research results not only limit their application to sensors and medical technology, but can also be used for optics or telecommunications.