Periodic Reporting for period 2 - DNA-FAIRYLIGHTS (DNA-Fast light dRiven data technologY with multiplexed optical encoding and readout)
Reporting period: 2022-09-01 to 2025-02-28
DNA-FAIRYLIGHTS explored different methods towards the realization of hybrid metal nanoparticle/DNA for the encoding and reconfiguration (not read-only storage) of digital information. Our goal was to demonstrate the potentiality of this novel approach where high density of digital information can be stored in a DNA template. The use of nanopore reading technology, then, ensures a fast and reliable method of data reading that avoids the time-consuming necessity to amplify the DNA for readout via sequencing.
The development of such hybrid DNA systems wanted to be a radically new point-of-view in DNA-data storage.
Digital data storage is still an area in which the current demand is rapidly outpacing the capabilities offered by semiconductor technologies.
The results obtained within DNA-FAIRYLIGHTS are also impactful in other nanobiotechnology sectors, in particular high-resolution bio-imaging, encrypted information storage in manufacturing, extreme resolution patterning and tunable photonic/plasmonic systems.
DNA-FAIRYLIGHTS contributed to the development of new technologies for data storage based on nanomaterial assembly on a biomolecule template. Although DNA data storage technologies have been already demonstrated, their high cost, slow readout and read-only nature make them not applicable in the short/mid-term. The idea behind DNA-FAIRYLIGHTS is based on the use of metallic nanoparticles (NPs) and ultrasmall light-emitting nanoclusters (NCs), together with their controlled assembly on not-synthetic DNA templates. As we demonstrated, this can enable fast electro-optical reading of the encoded information by passing the functionalized strands through nanopores.
The overall objective of DNA-FAIRYLIGHTS was the development of a proof-of-concept platform for fast and inexpensive storage and manipulation of information on not-synthetic (biological) DNA. The use of distinct NPs and NCs enables to sequentially and directly identify the sequences of the encoded data from optical signals stemming from the specifically tailored nanostructures. This approach relies on two important aspects:
A) A set of plasmonic NPs and light-emitting NCs consisting of different shapes and sizes provides several specific and well-defined resonances/transitions in the visible and near-infrared spectral range;
B) their functionalization with a library of short oligonucleotide sequences that are complementary to specific sites in biological (not-synthetic) single stranded DNA, which enables controlled NP/NC decoration of the DNA strand. The decorated DNA provides a reliable storage of information, but not less importantly, a direct strategy to read the stored information sequentially via the optical signal of the functionalized strand, thus without the need DNA amplification. We introduced, for the first time in DNA data storage technology, the use of NPs and NCs as optical nanoresonators. This approach ensures a high degree of freedom in electromagnetic field engineering and, in particular, permits the spectroscopic detection at discrete wavelengths of the encoded information.
Here, the series of engineered optical resonances is defined by different discrete elements that are used to decorate DNA molecules, resulting in a DNA hybrid system where a specific optical signal can be excited at discrete sites along the DNA strand. The size of the NPs / NCs, ranging from 1 up to 30 nm required a radically new approach for the decoration of the DNA template. The short complementary oligos consist of 20 base-pairs (bp) for the attachment to the DNA and contain other sections for the linking to the NPs or NCs.
The development of such hybrid DNA systems wanted to be a radically new point-of-view in DNA-data storage.
Digital data storage is still an area in which the current demand is rapidly outpacing the capabilities offered by semiconductor technologies.
The results obtained within DNA-FAIRYLIGHTS are also impactful in other nanobiotechnology sectors, in particular high-resolution bio-imaging, encrypted information storage in manufacturing, extreme resolution patterning and tunable photonic/plasmonic systems.
DNA-FAIRYLIGHTS contributed to the development of new technologies for data storage based on nanomaterial assembly on a biomolecule template. Although DNA data storage technologies have been already demonstrated, their high cost, slow readout and read-only nature make them not applicable in the short/mid-term. The idea behind DNA-FAIRYLIGHTS is based on the use of metallic nanoparticles (NPs) and ultrasmall light-emitting nanoclusters (NCs), together with their controlled assembly on not-synthetic DNA templates. As we demonstrated, this can enable fast electro-optical reading of the encoded information by passing the functionalized strands through nanopores.
The overall objective of DNA-FAIRYLIGHTS was the development of a proof-of-concept platform for fast and inexpensive storage and manipulation of information on not-synthetic (biological) DNA. The use of distinct NPs and NCs enables to sequentially and directly identify the sequences of the encoded data from optical signals stemming from the specifically tailored nanostructures. This approach relies on two important aspects:
A) A set of plasmonic NPs and light-emitting NCs consisting of different shapes and sizes provides several specific and well-defined resonances/transitions in the visible and near-infrared spectral range;
B) their functionalization with a library of short oligonucleotide sequences that are complementary to specific sites in biological (not-synthetic) single stranded DNA, which enables controlled NP/NC decoration of the DNA strand. The decorated DNA provides a reliable storage of information, but not less importantly, a direct strategy to read the stored information sequentially via the optical signal of the functionalized strand, thus without the need DNA amplification. We introduced, for the first time in DNA data storage technology, the use of NPs and NCs as optical nanoresonators. This approach ensures a high degree of freedom in electromagnetic field engineering and, in particular, permits the spectroscopic detection at discrete wavelengths of the encoded information.
Here, the series of engineered optical resonances is defined by different discrete elements that are used to decorate DNA molecules, resulting in a DNA hybrid system where a specific optical signal can be excited at discrete sites along the DNA strand. The size of the NPs / NCs, ranging from 1 up to 30 nm required a radically new approach for the decoration of the DNA template. The short complementary oligos consist of 20 base-pairs (bp) for the attachment to the DNA and contain other sections for the linking to the NPs or NCs.
DNA-FAIRYLIGHTS' consortium included several top-level experts in DNA nanotechnology, nanopore science, digital data storage, nanomaterials and plasmonics. As part of research institutes, universities and SME companies, they worked on multiple tasks towards the different goals of the project. In particular, the strong inter-connection between the partners and the high level of interdisciplinarity of the project, required significant collaborations with exchange of materials, samples and people.
We can summarize here below the major contributions from the different partners, stressing the cooperation within the consortium:
-IIT, as coordinator, was involved in the organization of the team, the handling of the consortium, regular online and in-presence meetings, dissemination and communication activities (web-site, conferences, talks, etc). From the scientific and technical point of view, IIT developed novel methods for the fabrication of solid state nanopores, as single and arrays. In collaboration with Elements, IIT developed an integrated device for the electrical characterization of the nanopores with optical stimuli and implemented the set-up for the electro-optical measurements used in collaboration with CAM and GUNE for the proof-of-concept demonstration of DNA data storage with nanomaterials.
-ELE, in collaboration with IIT developed the system for the in-parallel electrical reading from nanopores and a device for optical-electrical control in nanopores. The project enabled the company to fully develop novel tools they are now including in their portfolio, such as the multichannel reader.
-CAM worked on the development of a robust and modular microfluidic system for the assembly of DNA+nanoparticles, also in collaboration with GUNE and IIT.
-GUNE developed a new set of metallic nanoparticles and nanoclusters to be integrated / anchored on DNA template in collaboration with CAM, IIT and ABA.
-ETH and TUM demonstrated, theoretically, the error generation in DNA data storage based on the proposed method.
-STUTT developed, in collaboration with IIT and GUNE new systems for the controlled re-arrangement of metallic nanoparticles in DNA template with external stimuli
-DS and ABA, contributed, from the biotechnology side, to the definition of the protocols for DNA synthesis and modification to be integrated with the nanomaterials.
We can summarize here below the major contributions from the different partners, stressing the cooperation within the consortium:
-IIT, as coordinator, was involved in the organization of the team, the handling of the consortium, regular online and in-presence meetings, dissemination and communication activities (web-site, conferences, talks, etc). From the scientific and technical point of view, IIT developed novel methods for the fabrication of solid state nanopores, as single and arrays. In collaboration with Elements, IIT developed an integrated device for the electrical characterization of the nanopores with optical stimuli and implemented the set-up for the electro-optical measurements used in collaboration with CAM and GUNE for the proof-of-concept demonstration of DNA data storage with nanomaterials.
-ELE, in collaboration with IIT developed the system for the in-parallel electrical reading from nanopores and a device for optical-electrical control in nanopores. The project enabled the company to fully develop novel tools they are now including in their portfolio, such as the multichannel reader.
-CAM worked on the development of a robust and modular microfluidic system for the assembly of DNA+nanoparticles, also in collaboration with GUNE and IIT.
-GUNE developed a new set of metallic nanoparticles and nanoclusters to be integrated / anchored on DNA template in collaboration with CAM, IIT and ABA.
-ETH and TUM demonstrated, theoretically, the error generation in DNA data storage based on the proposed method.
-STUTT developed, in collaboration with IIT and GUNE new systems for the controlled re-arrangement of metallic nanoparticles in DNA template with external stimuli
-DS and ABA, contributed, from the biotechnology side, to the definition of the protocols for DNA synthesis and modification to be integrated with the nanomaterials.
As demonstrated by more than 25 publications produced during the duration of the project, several scientific results, beyond the state-of-the-art of their respective fields were achieved.
In particular, the highly interdisciplinary effort of DNA-FAIRYLIGHTS led to:
• development of advanced optical technologies based on NP and NC decorated (hybrid) DNA
• highly engineered systems for molecular functionalization
• Novel data encoding concepts based on multiplexed signals
• robust optical spectroscopic platform for single molecule reading based on solid-state nanopore arrays
• integration of the above technologies within a core multifunctional platform and
• iterative refinement of the data analysis based on assessment of instrument performance.
Finally, we are convinced that the long term vision and impacts related to the technological advances of DNA-FAIRYLIGHTS will:
• make novel technologies available for new generation of data encoding and storage based on DNA
• significantly advance the field of biophotonics, plasmonics, and bio-inspired optoelectronics
• facilitate the development of new tools to characterize heterogeneous molecular ensembles through accurate and fast data reading based on optical readouts with the major advantage to avoid the need for random access.
In particular, the highly interdisciplinary effort of DNA-FAIRYLIGHTS led to:
• development of advanced optical technologies based on NP and NC decorated (hybrid) DNA
• highly engineered systems for molecular functionalization
• Novel data encoding concepts based on multiplexed signals
• robust optical spectroscopic platform for single molecule reading based on solid-state nanopore arrays
• integration of the above technologies within a core multifunctional platform and
• iterative refinement of the data analysis based on assessment of instrument performance.
Finally, we are convinced that the long term vision and impacts related to the technological advances of DNA-FAIRYLIGHTS will:
• make novel technologies available for new generation of data encoding and storage based on DNA
• significantly advance the field of biophotonics, plasmonics, and bio-inspired optoelectronics
• facilitate the development of new tools to characterize heterogeneous molecular ensembles through accurate and fast data reading based on optical readouts with the major advantage to avoid the need for random access.