Processing DNA-Based Molecular Signals into Graphical Displays

Encoding, Decoding, and Rendering Information in DNA Nanoswitch Libraries

DNA-based construction allows the creation of molecular devices that are useful in information storage and processing. Here, we combine the programmability of DNA nanoswitches and stimuli-responsive conformational changes to demonstrate information encoding and graphical readout using gel electrophoresis. We encoded information as 5-bit binary codes for alphanumeric characters using a combination of DNA and RNA inputs that can be decoded using molecular stimuli such as a ribonuclease. We also show that a similar strategy can be used for graphical visual readout of alphabets on an agarose gel, information that is encoded by nucleic acids and decoded by a ribonuclease. Our method of information encoding and processing could be combined with DNA actuation for molecular computation and diagnostics that require a nonarbitrary visual readout.

Versatile non-luminescent color palette based on guest exchange dynamics in paramagnetic cavitands

Multicolor luminescent portrayal of complexed arrays is indispensable for many aspects of science and technology. Nevertheless, challenges such as inaccessible readouts from opaque objects, a limited visible-light spectrum and restricted spectral resolution call for alternative approaches for multicolor representation. Here, we present a strategy for spatial COlor Display by Exploiting Host-guest Dynamics (CODE-HD), comprising a paramagnetic cavitand library and various guests. First, a set of lanthanide-cradled α-cyclodextrins (Ln-CDs) is designed to induce pseudo-contact shifts in the ¹⁹F-NMR spectrum of Ln-CD-bound guest. Then, capitalizing on reversible host-guest binding dynamics and using magnetization-transfer ¹⁹F-MRI, pseudo-colored maps of complexed arrays are acquired and applied in molecular-steganography scenarios, showing CODE-HD’s ability to generate versatile outputs for information encoding. By exploiting the widely shifted resonances induced by Ln-CDs, the guest versatility and supramolecular systems' reversibility, CODE-HD provides a switchable, polychromatic palette, as an advanced strategy for light-free, multicolor-mapping.

Host-guest supramolecular chemistry can be used as a tool to develop multicolor displays. Here, the authors present a system based on lanthanide-cradled cyclodextrins that allows to construct MRI-readable and erasable artificial non-luminescent color palettes.

DNA Nanoswitch Barcodes for Multiplexed Biomarker Profiling

Molecular biomarkers play a key role in the clinic, aiding in diagnostics and prognostics, and in the research laboratory, contributing to our basic understanding of diseases. Detecting multiple and diverse molecular biomarkers within a single accessible assay would have great utility, providing a more comprehensive picture for clinical evaluation and research, but is a challenge with standard methods. Here, we report programmable DNA nanoswitches for multiplexed detection of up to 6 biomarkers at once with each combination of biomarkers producing a unique barcode signature among 64 possibilities. As a defining feature of our method, we show "mixed multiplexing" for simultaneous barcoded detection of different types of biomolecules, for example, DNA, RNA, antibody, and protein in a single assay. To demonstrate clinical potential, we show multiplexed detection of a prostate cancer biomarker panel in serum that includes two microRNA sequences and prostate specific antigen.