Takahiro Nishimura

Fluorescence resonance energy transfer-based molecular logic circuit using a DNA scaffold

This paper presents a method of information processing using biomolecular input signals and fluorescence resonance energy transfer (FRET) signaling constructed on a DNA scaffold. Logic operations are achieved by encoding molecular inputs into an arrangement of fluorescence dyes using simple DNA reactions and by evaluating a logic expression using local photonic signaling that is much faster than DNA reactions. Experimental results verify the operation of a complete set of Boolean logic functions (AND, OR, NOT) and combinational logic operations using a FRET-signal cascade.

Self-Contained Photonically-Controlled DNA Tweezers

Photonic methodologies to access and control objects with a nano-scale resolution are important because of their attractive features including high sensitivity, remoteness, and various implementation tools. We report self-contained photonically-controlled DNA tweezers implemented using photoisomerizing molecules. This composition is effective to control objects with a nanoscale resolution using propagating light, which enables us to capture signals of multiple objects in a twinkle and control them over an area at a time. Experimental results demonstrated that the self-contained photonically-controlled DNA tweezers were alternated the open and closed states by light irradiation with almost uniform operation efficiency during repeated operations.

A Nanoscale Set--Reset Flip-Flop in Fluorescence Resonance Energy Transfer-Based Circuits

Fluorescence resonance energy transfer (FRET) is a promising method of implementing photonic circuits at a nanoscale. This letter presents a set–reset flip-flop that consists of fluorescent molecules organized by DNA hybridization. In the proposed flip-flop, the state changes according to the optical input and current state, then FRET is switched between on and off depending on its state. The experimental results demonstrate that the flip-flop can modulate the energy flow, and repeated cycle state transitions are induced.

Optically controllable molecular logic circuits

Molecular logic circuits represent a promising technology for observation and manipulation of biological systems at the molecular level. However, the implementation of molecular logic circuits for temporal and programmable operation remains challenging. In this paper, we demonstrate an optically controllable logic circuit that uses fluorescence resonance energy transfer (FRET) for signaling. The FRET-based signaling process is modulated by both molecular and optical inputs. Based on the distance dependence of FRET, the FRET pathways required to execute molecular logic operations are formed on a DNA nanostructure as a circuit based on its molecular inputs. In addition, the FRET pathways on the DNA nanostructure are controlled optically, using photoswitching fluorescent molecules to instruct the execution of the desired operation and the related timings. The behavior of the circuit can thus be controlled using external optical signals. As an example, a molecular logic circuit capable of executing two different logic operations was studied. The circuit contains functional DNAs and a DNA scaffold to construct two FRET routes for executing Input 1 AND Input 2 and Input 1 AND NOT Input 3 operations on molecular inputs. The circuit produced the correct outputs with all possible combinations of the inputs by following the light signals. Moreover, the operation execution timings were controlled based on light irradiation and the circuit responded to time-dependent inputs. The experimental results demonstrate that the circuit changes the output for the required operations following the input of temporal light signals.Molecular logic circuits represent a promising technology for observation and manipulation of biological systems at the molecular level. However, the implementation of molecular logic circuits for temporal and programmable operation remains challenging. In this paper, we demonstrate an optically controllable logic circuit that uses fluorescence resonance energy transfer (FRET) for signaling. The FRET-based signaling process is modulated by both molecular and optical inputs. Based on the distance dependence of FRET, the FRET pathways required to execute molecular logic operations are formed on a DNA nanostructure as a circuit based on its molecular inputs. In addition, the FRET pathways on the DNA nanostructure are controlled optically, using photoswitching fluorescent molecules to instruct the execution of the desired operation and the related timings. The behavior of the circuit can thus be controlled using external optical signals. As an example, a molecular logic circuit capable of executing two differ...

Biomolecule-to-fluorescent-color encoder: modulation of fluorescence emission via DNA structural changes.

A biomolecule-to-fluorescent-color (B/F) encoder for optical readout of biomolecular information is proposed. In the B/F encoder, a set of fluorescence wavelengths and their intensity levels are used for coding of a biomolecular signal. A hybridization chain reaction of hairpin DNAs labeled with fluorescent reporters was performed to generate the fluorescence color codes. The fluorescence is modulated via fluorescence resonance energy transfer, which is controlled by DNA structural changes. The results demonstrate that fluorescent color codes can be configured based on two wavelengths and five intensities using the B/F encoder, and the assigned codes can be retrieved via fluorescence measurements.

Gastric Contraction Imaging System Using a 3-D Endoscope

This paper presents a gastric contraction imaging system for assessment of gastric motility using a 3-D endoscope. Gastrointestinal diseases are mainly based on morphological abnormalities. However, gastrointestinal symptoms are sometimes apparent without visible abnormalities. One of the major factors for these diseases is abnormal gastrointestinal motility. For assessment of gastric motility, a gastric motility imaging system is needed. To assess the dynamic motility of the stomach, the proposed system measures 3-D gastric contractions derived from a 3-D profile of the stomach wall obtained with a developed 3-D endoscope. After obtaining contraction waves, their frequency, amplitude, and speed of propagation can be calculated using a Gaussian function. The proposed system was evaluated for 3-D measurements of several objects with known geometries. The results showed that the surface profiles could be obtained with an error of <;10% of the distance between two different points on images. Subsequently, we evaluated the validity of a prototype system using a wave simulated model. In the experiment, the amplitude and position of waves could be measured with 1-mm accuracy. The present results suggest that the proposed system can measure the speed and amplitude of contractions. This system has low invasiveness and can assess the motility of the stomach wall directly in a 3-D manner. Our method can be used for examination of gastric morphological and functional abnormalities.

A photonic DNA processor: concept and implementation

To deal with molecular information at a molecular level based on external signaling, a photonic DNA processor is a primal processing core of a nanoscale information system that works in molecular environment, for example, in situ. Use of photonic signals enables remote and spatio-temporal control of the processor. As an implementation example, we report a photonically-controlled DNA nanomachine which identifies and processes molecular information and implements physical processing as reporting the result using fluorescence signal. The nanomachine has two hairpin DNAs incorporating azobenzene and forms a tweezers-like structure. The hairpin structures are opened by ultraviolet-light irradiation, and a single-strand region is exposed to activate functionality in recognizing a target molecule. In contrast, visible-light irradiation makes the hairpin DNA close to inactivate the sensing function, and it releases the captured molecule. During activated term, the nanomachine changes its tweezers-like structure depending on existence or absence of the target molecule: the nanomachine transmutes into the closed state from the open state (initial state) by binding to the target molecule. Depending on the state, the nanomachine generates a fluorescence signal owing to fluorescence resonance energy transfer. In experiments, we demonstrated that the fluorescence intensities changed depending on existence and absence of the target molecule under photonic activation and inactivation. The result indicates that the nanomachine obtained information on the target molecule, changed the state, and reported the information to the outside world. In addition, we confirmed experimentally the functionality in measuring the concentration of the target molecule.image

Spatially parallel control of DNA reactions in optically manipulated microdroplets

In order to show the potential of photonic techniques for realizing nanoscale computing, we examined the operation of DNA reactions by optical manipulation of microdroplets that contain DNA. The processing procedures are reconfigurable owing to flexibility in manipulating the microdroplets. The method is effective in, for example, implementing DNA computations in limited-volumes at multiple positions in parallel, enhancing an operation rate, and decreasing sample consumption, and it can be a promising technique applicable to photonic DNA computing. A reaction scheme using a pair of hairpin DNA and linear DNA was examined to confirm the method. The reaction scheme provides exchange of the sequence of a sticky-end of a DNA conformation, and it is usable for DNA computation. Microdroplets that contain DNA components were contacted to each other to start the reaction. By observing fluorescence intensity, we confirmed the reaction of sequence-change in the optically manipulated microdroplet. The experimental result also showed that different reactions are implemented at separate positions simultaneously.

Optically controlled release of DNA based on nonradiative relaxation process of quenchers.

Optically controlled release of a DNA strand based on a nonradiative relaxation process of black hole quenchers (BHQs), which are a sort of dark quenchers, is presented. BHQs act as efficient energy sources because they relax completely via a nonradiative process, i.e., without fluorescent emission-based energy losses. A DNA strand is modified with BHQs and the release of its complementary strand is controlled by excitation of the BHQs. Experimental results showed that up to 50% of the target strands were released, and these strands were capable of inducing subsequent reactions. The controlled release was localized on a substrate within an area of no more than 5 micrometers in diameter.

Paper-based Raman spectroscopy for on-site therapeutic drug monitoring

This study proposes Raman spectroscopy of tear fluid with paper substrates for on-site therapeutic drug monitoring(TDM). In this method, the paper substrates are used for tear sample collection and measurement. The use of paper offers a minimally-invasive, simple, and inexpensive method for therapeutic drug monitoring. To demonstrate the usability of the paper substrates for this purpose, we measured Raman spectra of samples containing therapeutic drug and glucose with a filter paper. Experimental results show the ability to detect Raman signals from the samples absorbed on the paper substrate.