Time-Gated FRET and DNA-Based Photonic Molecular Logic Gates: AND, OR, NAND, and NOR

Abstract

Molecular logic devices (MLDs) constructed from DNA are promising for applications in bioanalysis, computing, and other applications requiring Boolean logic. These MLDs accept oligonucleotide inputs and generate fluorescence output through changes in structure. Although fluorescent dyes are most common in MLD designs, nontraditional luminescent materials with unique optical properties can potentially enhance MLD capabilities. In this context, luminescent lanthanide complexes (LLCs) have been largely overlooked. Here, we demonstrate a set of high-contrast DNA photonic logic gates based on toehold-mediated strand displacement and time-gated FRET. The gates include NAND, NOR, OR, and AND designs that accept two unlabeled target oligonucleotide sequences as inputs. Bright "true" output states utilize time-gated, FRET-sensitized emission from an Alexa Fluor 546 (A546) dye acceptor paired with a luminescent terbium cryptate (Tb) donor. Dark "false" output states are generated through either displacement of the A546, or through competitive and sequential quenching of the Tb or A546 by a dark quencher. Time-gated FRET and the long luminescence lifetime and spectrally narrow emission lines of the Tb donor enable 4-10-fold contrast between Boolean outputs, ≤10% signal variation for a common output, multicolor implementation of two logic gates in parallel, and effective performance in buffer and serum. These metrics exceed those reported for many other logic gate designs with only fluorescent dyes and with other non-LLC materials. Preliminary three-input AND and NAND gates are also demonstrated. The powerful combination of an LLC FRET donor with DNA-based logic gates is anticipated to have many future applications in bioanalysis.

Theoretical study of the photophysical processes of a styryl‐bodipy derivative eliciting an AND molecular logic gate response

“…In most cases, these changes could then be signaled by changes in the absorption or emission intensity and/or in the wavelength, and can be related to the operation of logic gates, via the familiar Boolean logic, where the modulators correspond to the inputs and the observed changes correspond to the outputs . The field of molecular logical gates (MLG) is a subject of research in many laboratories worldwide, and while a great deal of the groundwork has been accomplished, the field is still at an early stage in terms of practical applications . However, a significant rise of information processing molecular devices is expected in the forthcoming years .…”

Utilizing the Organizational Power of DNA Scaffolds for New Nanophotonic Applications

“…The photonic modulation occurs at a much greater rate than can be obtained by strand displacement, but the modulation is limited to an ON/OFF ratio of only 1.2. In contrast to this, some of the highest ON/OFF signal ratios can be obtained by exploiting time‐gated signals from lanthanide ions in MPWs where ratios in the range of 10 have been reported for three‐input AND NAND operations (ratios are generally in the 2–4 range) . In general, use of lanthanide cryptates provide unique access to the temporal dimension with variable parameters that can extend from the nanosecond to millisecond range and this can certainly increase the richness of accessible molecule logic to include even on‐the‐fly gate transitions .…”

More Than a Light Switch: Engineering Unconventional Fluorescent Configurations for Biological Sensing

“…We recently developed a series of OR, AND, NOR, and NAND logic sensors in this format. 92 The initial sensor assemblies set up different permutations of competitive and sequential FRET between a Tb LLC donor, a fluorescent dye acceptor, and dark quencher acceptor labels on the oligonucleotides. In each sensor, binding of nucleic acid target disrupted one or more of these FRET pathways in the assembly with a Boolean-like effect on the output signal, which was time-gated dye emission sensitized by energy transfer from the Tb LLC.…”

“…The systems also functioned in serum, and, as summarized in Figure 5B, the use of a Tb LLC donor permitted multiple colors of logic gate to be used in parallel. 92 Earlier work by Yoshida and Yokobayahsi used similar design motifs to create AND and OR sensors for protein targets. 101 In this case, a fluorescent dye and dark quencher were used as the FRET pair and the sensor assembly incorporated aptamer sequences.…”