Language：English   Publishing type：Research paper (scientific journal)  

Thrombin-binding aptamer (TBA), which forms a G-quadruplex (G4) structure with anti-parallel topology, interacts with thrombin to inhibit its enzymatic activity. Here we show that the G4-topology-altering ligand L2H2-2M2EA-6LCO (6LCO) changes the anti-parallel topology of TBA G4 to the parallel topology, thereby abrogating the thrombin-inhibitory activity of TBA. This finding suggests that G4 ligands that alter topology may be promising drug candidates for diseases involving G4-binding proteins.

DOI： 10.1039/d3cc02308g

PubMed

Publishing type：Research paper (scientific journal)  

DOI： 10.1116/6.0002732

Scopus

Publishing type：Research paper (scientific journal)  

DOI： 10.35848/1347-4065/acc53c

Scopus

Publishing type：Research paper (scientific journal)   Publisher：Royal Society of Chemistry (RSC)  

Click reactions are used for chemoselective functionalization in many research fields. Despite the utility of small, bioinert azide groups as a counterpart, applications of strain-promoted alkyne-azide cycloaddition (SPAAC) reactions for...

DOI： 10.1039/d3cc01356a

Language：English   Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

Binding between a ligand and a receptor is a fundamental step in many natural or synthetic processes. In biosensing, a tight binding with a small dissociation constant (Kd) between the probe and analyte can lead to superior specificity and sensitivity. Owing to their capability of evaluating competitors, displacement assays have been used to estimate Kd at the ensemble average level. At the more sensitive single-molecule level, displacement assays are yet to be established. Here, we developed a single-molecule displacement assay (smDA) in an optical tweezers instrument and used this innovation to evaluate the binding of the L2H2-6OTD ligands to human telomeric DNA G-quadruplexes. After measuring Kd of linear and dendrimer L2H2-6OTD ligands, we found that dendrimer ligands have enhanced binding affinity to the G-quadruplexes due to their polyvalent geometry. This increased binding affinity enhanced inhibition of telomerase elongation on a telomere template in a Telomerase Repeated Amplification Protocol (TRAP). Our experiments demonstrate that the smDA approach can efficiently evaluate binding processes in chemical and biological processes.

DOI： 10.1016/j.ab.2022.114693

DOI： 10.1016/j.ijbiomac.2023.124089_references_DOI_CMwTVJcAS3IDU8lxaqQIdCGIB4l

PubMed

CiNii Research

Language：English   Publisher：Catalyst Unit  

DOI： 10.33611/trs.2021-019

CiNii Research

Other Link： https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-19K05743/

Language：English   Publishing type：Research paper (scientific journal)   Publisher：Royal Society of Chemistry (RSC)  

The extent of thermodynamic stabilization of telomeric G-quadruplex (G4) by isomers of G4 ligand L2H2-6OTD, a telomestatin analog, is inversely correlated with susceptibility to S1 nuclease. L2H2-6OTD facilitated the S1 nuclease activities through the base flipping in G4, unlike the conventional role of G4 ligands which inhibit the protein binding to DNA/RNA upon ligand interactions.

DOI： 10.1039/d1cc03294a

DOI： 10.1021/acschembio.1c00904_references_DOI_20iOj9zyhxLD3rpSIPMQTb830dF

PubMed

CiNii Research

Other Link： https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-16H06276/

Language：English   Publishing type：Research paper (scientific journal)   Publisher：Royal Society of Chemistry (RSC)  

The selective alkylation of nucleic acids is important for a medicinal approach and biological study. We now report a novel selective alkylation of the parallel G-quadruplex structure using the conjugate of the macrocyclic hexaoxazole L2G2-6OTD-1M1PA and vinyl-quinazolinone-S(O)Me (6OTD-VQ-S(O)Me).

DOI： 10.1039/d0ob02365e

DOI： 10.1002/tcr.202200194_references_DOI_HVwHTGn0IrbVop3Jaxipb7CPFQa

PubMed

CiNii Research

Other Link： https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-20H02876/

Language：English   Publishing type：Research paper (scientific journal)   Publisher：Royal Society of Chemistry (RSC)  

G-quadruplex structures (G4s) in guanine-rich regions of DNA play critical roles in various biological phenomena, including replication, translation, and gene expression. There are three types of G4 topology, i.e., parallel, anti-parallel, and hybrid, and ligands that selectively interact with or stabilize a specific topology have been extensively explored to enable studies of topology-related functions. Here, we describe the synthesis of a new series of G4 ligands based on 6LCOs (6-linear consecutive oxazoles), i.e., L2H2-2M2EA-6LCO (2), L2A2-2M2EAc-6LCO (3), and L2G2-2M2EG-6LCO (4), which bear four aminoalkyl, acetamidealkyl, and guanidinylalkyl side chains, respectively. Among them, ligand 2 stabilized telomeric G4 and induced anti-parallel topology independently of the presence of cations. The anti-parallel topology induced by 2 was identified as chair-type by means of 19F NMR spectroscopy and fluorescence experiments with 2-aminopurine-labeled DNA.

DOI： 10.1039/d0ra09413g

DOI： 10.1039/d1cc03294a_references_DOI_X4o8svdRf8WUayKAuLMQ2tPFLh6

PubMed

CiNii Research

Other Link： https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-17H03091/

Language：English   Publishing type：Research paper (scientific journal)  

G-quadruplexes (G4s), which are structures formed in guanine-rich regions of DNA, are involved in a variety of significant biological functions, and therefore "sequence-dependent" selective G4-stabilizing agents are required as tools to investigate and modulate these functions. Here, we describe the synthesis of a new series of macrocyclic hexaoxazole-type G4 ligand (6OTD) bearing three side chains. One of these ligands, 5b, stabilizes telomeric G4 preferentially over the G4-forming DNA sequences of c-kit and K-ras, due to the interaction of its piperazinylalkyl side chain with the groove of telomeric G4.

DOI： 10.3390/molecules24020263

DOI： 10.1039/d0ra09413g_references_DOI_6huA7ev2y3uPIkQRRd5LekTJ1kD

PubMed

CiNii Research

Other Link： http://www.mdpi.com/1420-3049/24/2/263/pdf

Language：English   Publishing type：Research paper (scientific journal)   Publisher：Wiley  

Mechanical anisotropy is an essential property for biomolecules to assume structural and functional roles in mechanobiology. However, there is insufficient information on the mechanical anisotropy of ligand-biomolecule complexes. Herein, we investigated the mechanical property of individual human telomeric G-quadruplexes bound to telomestatin, using optical tweezers. Stacking of the ligand to the G-tetrad planes changes the conformation of the G-quadruplex, which resembles a balloon squeezed in certain directions. Such a squeezed balloon effect strengthens the G-tetrad planes, but dislocates and weakens the loops in the G-quadruplex upon ligand binding. These dynamic interactions indicate that the binding between the ligand and G-quadruplex follows the induced-fit model. We anticipate that the altered mechanical anisotropy of the ligand-G-quadruplex complex can add additional level of regulations on the motor enzymes that process DNA or RNA molecules.

DOI： 10.1002/anie.201811046

DOI： 10.1093/nar/gkz135_references_DOI_JkrNyDwgjpL8H3S97V7egkLdFCm

PubMed

CiNii Research

Other Link： https://onlinelibrary.wiley.com/doi/full-xml/10.1002/anie.201811046

Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

G-Quadruplexes formed in the 3' telomere overhang (∼200 nucleotides) have been shown to regulate biological functions of human telomeres. The mechanism governing the population pattern of multiple telomeric G-quadruplexes is yet to be elucidated inside the telomeric overhang in a time window shorter than thermodynamic equilibrium. Using a single-molecule force ramping assay, we quantified G-quadruplex populations in telomere overhangs over a full physiological range of 99-291 nucleotides. We found that G-quadruplexes randomly form in these overhangs within seconds, which leads to a population governed by a kinetic, rather than a thermodynamic, folding pattern. The kinetic folding gives rise to vacant G-tracts between G-quadruplexes. By targeting these vacant G-tracts using complementary DNA fragments, we demonstrated that binding to the telomeric G-quadruplexes becomes more efficient and specific for telomestatin derivatives.

DOI： 10.1021/acs.biochem.8b00957

DOI： 10.1016/j.ab.2022.114693_references_DOI_LcgHxQyf2ASwU0E4G5QcjmsKeMl

PubMed

CiNii Research

Other Link： https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-16K13094/

Language：English   Publishing type：Research paper (scientific journal)   Publisher：Royal Society of Chemistry (RSC)  

G-Quadruplex structures (G4s) in guanine-rich regions of DNA play critical roles in various biological phenomena, including replication, translation, and gene expression. The G4-forming DNAs can form three kinds of topologies, i.e., parallel, anti-parallel, and hybrid. In this paper, we present G4 ligands L2H2-2M2EA-6OTD (3) and L2G2-2M2EG-6OTD (4) bearing tetra-aminoalkyl and -guanidinylalkyl side chains, respectively, in a macrocyclic hexaoxazole structure. These ligands efficiently induce the parallel-type topology of telomeric G4 regardless of the effects of cations. Titration with 4 results in a drastic topology switch to the parallel topology from the anti-parallel structure induced by the structurally related ligand L2H2-6OTD (1).

DOI： 10.1039/c8ob01702f

DOI： 10.1016/j.bbrc.2019.12.103_references_DOI_2bQJ1vbeW0FxzRfagjmBkqM3BOE

PubMed

CiNii Research

Other Link： https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-16H06276/

Language：English   Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

G-quadruplex (G4) is a higher-order nucleic acid structure that is formed by guanine-rich sequences. G4 stabilization by small-molecule compounds called G4 ligands often causes cytotoxicity, although the potential medicinal impact of this effect has not been fully established. Here we demonstrate that a synthetic G4 ligand, Y2H2-6M(4)-oxazole telomestatin derivative (6OTD), limits the growth of intractable glioblastoma (grade IV glioma) and glioma stem cells (GSCs). Experiments involving a human cancer cell line panel and mouse xenografts revealed that 6OTD exhibits antitumor activity against glioblastoma. 6OTD inhibited the growth of GSCs more potently than it did the growth of differentiated non-stem glioma cells (NSGCs). 6OTD caused DNA damage, G1 cell cycle arrest, and apoptosis in GSCs but not in NSGCs. These DNA damage foci tended to colocalize with telomeres, which contain repetitive G4-forming sequences. Compared with temozolomide, a clinical DNA-alkylating agent against glioma, 6OTD required lower concentrations to exert anti-cancer effects and preferentially affected GSCs and telomeres. 6OTD suppressed the intracranial growth of GSC-derived tumors in a mouse xenograft model. These observations indicate that 6OTD targets GSCs through G4 stabilization and promotion of DNA damage responses. Therefore, G4s are promising therapeutic targets for glioblastoma.

DOI： 10.1038/s41598-017-03785-8

DOI： 10.1016/j.bbrc.2019.12.103_references_DOI_WKNYeLKHI7IvshhIdqiT7R4k6XH

PubMed

CiNii Research

Other Link： https://www.nature.com/articles/s41598-017-03785-8