The University of Tokyo · Biochemistry, Genetics and Molecular Biology
Professor Keitaro Yoshimoto's research lab specializes in the development of functional nucleic acids and biomolecular recognition systems, with a focus on aptamers, DNA-based sensors, and molecularly engineered surfaces. The lab explores the design of selective molecular probes—such as small molecules and aptamers—that can detect nucleobases, proteins, and growth factors with high sensitivity and specificity, often leveraging fluorescence signaling or surface-based detection techniques. Key research directions include the application of abasic sites in DNA for selective nucleobase recognition, the engineering of protein-resistant surfaces using phosphorylcholine- and PEG-based polymers, and the discovery of high-affinity aptamers for therapeutic and diagnostic targets like thrombin and vascular endothelial growth factors. The lab integrates advanced analytical methods such as surface plasmon resonance, atomic force microscopy, and capillary electrophoresis to study molecular interactions at the nanoscale.
Figures are computed from collected data and may differ slightly.
Nucleobase recognition in water is successfully achieved by the use of an abasic site (AP site) as the molecular recognition field. We intentionally construct the AP site in DNA duplex so as to orient the AP site toward a target nucleobase and examine the complexation of 2-amino-7-methylnaphthyridine (AMND) with nucleobases at the AP site. AMND is found to selectively bind to cytosine (C) base with a 1:1 binding constant of >106 M-1, accompanied by remarkable quenching of its fluorescence. In ad
Abstract Poly[2‐(methacryloyloxy)ethyl phosphorylcholine] ‐modified gold surfaces, which have been newly prepared by a ‘grafting to’ method using a series of monosulfanyl‐terminated PMPC, are characterized by protein adsorption experiments based on surface plasmon resonance spectroscopy and ellipsometry measurements. The extent of BSA adsorption on PMPC‐modified surfaces was systematically reduced for thicker PMPC layers, thus the number of MPC units on the gold surface appears to be an importan
To examine the adsorption behavior of antibody fragments (Fab') directly immobilized on a gold surface through S-Au linkage, analyses by surface plasmon resonance (SPR), fluorometry, and atomic force microscopy (AFM) with an excellent blocking technique by the consecutive treatments of longer-poly(ethylene glycol) (PEG) (MW = 5k) and shorter-PEG (MW = 2k), abbreviated as mixed-PEG layer formation, were performed. The results of the SPR analysis suggest that the adsorption-induced inactivation of
We present a rapidly neutralizable and highly anticoagulant thrombin-binding aptamer with a short toehold sequence, originally discovered by systematic evolution of ligands by exponential enrichment (SELEX) with microbead-assisted capillary electrophoresis (MACE). MACE is a novel CE-partitioning method for SELEX and able to separate aptamers from a library of unbound nucleic acids, where the aptamer and target complexes can be detected reliably and partitioned with high purity even in the first
In combination with abasic site-containing oligodeoxynucleotides, 2-amino-4-oxopteridine (pterin) can selectively recognize guanine base over other nucleobases accompanied by fluorescence quenching, which allows clear detection of a guanine-adenine transition with the naked eye.
Vascular endothelial growth factors (VEGFs) are hypoxia-inducible secreted proteins to promote angiogenesis, in which VEGF-A is an important molecule that binds and activates VEGF receptor-1 (VEGFR-1) and VEGFR-2. In this study, two DNA aptamers, Apt01 and Apt02, were successfully isolated by alternating consecutive systematic evolution of ligands by exponential enrichment (SELEX) against VEGFR-1 and -2 using deep sequencing analysis in an early selection round. Their binding affinities for VEGF
We present herein the novel technique for constructing inverted cell-adhesion patternes on PEG gel modified glass surfaces by photoirradiation using the same photomask and materials. The PEG gel micropatterns were prepared by a photolithographic technique using a photomask with 100 microm aligned cavities after spin-coating of a mixed solution of alpha,omega-dimethacryloyl-PEG (PEG-DMA) and a photoinitiator on glass surfaces. When methanol was used as a casting solvent for the spin-coating (Meth
A sulfanyl-terminated poly(ethylene glycol) (PEG)-brushed layer was constructed on a gold sensor platform by consecutive treatment with a sulfanyl-ended semitelechelic PEG (2 kDa, hereafter "MeO-PEG-SH (2k)") and a sulfanyl-ended telechelic PEG (5 kDa, hereafter "SH-PEG-SH (5k)"). Our strategy of constructing the sulfanyl-terminated PEG-brushed gold surface is based on mixed-PEG-brush formation from the longer SH-PEG-SH (5k) and the shorter MeO-PEG-SH (2k), where the preimmobilized shorter MeO-P
Currently available methods for stem cell evaluation require both prior knowledge of specific markers and invasive cell lysis or staining, hampering the development of stem cell products with assured safety and quality. Here, we present a strategy using optical cross-reactive sensor arrays for markerless and noninvasive identification of differentiated stem cell lineages with common laboratory equipment. The sensor array consists of a library of polyion complexes (PICs) between anionic enzymes a
We investigated the spatial distribution of S -coda-wave energy in northeastern Honshu, Japan, where a volcanic front runs from north to south. Seismograms of a local event with a magnitude of 6.4 recorded by the Hi-net were analyzed in this study. The mean square amplitudes of coda waves at 82 seismic stations were calculated for bands with frequencies of 2–4, 4–8, 8–16, and 16–32 Hz. From these measurements, a clear spatial variation of coda-wave energy was observed across the volcanic front f
Polyion complexes with naturally occurring differentiation of enzymes serve to create receptor libraries with high differentiability and lower synthetic demands for pattern-based protein discrimination.
The adsorption properties and structure of polyamine-ended poly(ethylene glycol) (PEG) derivatives on a flat gold surface were studied by means of surface plasmon resonance (SPR) and X-ray photoelectron spectroscopy (XPS) using PEG(5k)-block-poly[2-(N,N-dimethylamino)ethyl methacrylate](7.5k) [PEG-b-PAMA(5k/7.5k)] and pentaethylenhexamine-ended PEG(5k) [N6-PEG(5k)], which had 48 and 6 amino groups at the omega-end, respectively. The SPR analysis showed that the amount of PEG-b-PAMA(5k/7.5k) adso
Chirality effects on stem cell fate were investigated in three-dimensional culture using soft fibrous hydrogels consisting of self-assembled <i>l</i>- and <i>d</i>-form Fmoc-Phe-Phe-Cys networks photo-cross-linked by poly(ethylene glycol) (<i>l</i>- and <i>d</i>-gel, respectively). Encapsulated human bone marrow-derived mesenchymal stem cells were all alive, spread, and grown in both hydrogels. Interestingly, the cells preferably spread and grew in <i>l</i>-gel compared to in <i>d</i>-gel under
Bone marrow-derived mesenchymal stem cells (BMSCs) are an important cell resource for stem cell-based therapy, which are generally isolated and enriched by the density-gradient method based on cell size and density after collection of tissue samples. Since this method has limitations with regards to purity and repeatability, development of alternative label-free methods for BMSC separation is desired. In the present study, rapid label-free separation and enrichment of BMSCs from a heterogeneous
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