論文 - 建石 寿枝
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In-Cell Stability Prediction of RNA/DNA Hybrid Duplexes for Designing Oligonucleotides Aimed at Therapeutics. 国際誌
Dipanwita Banerjee, Hisae Tateishi-Karimata, Maria Toplishek, Tatsuya Ohyama, Saptarshi Ghosh, Shuntaro Takahashi, Marko Trajkovski, Janez Plavec, Naoki Sugimoto
Journal of the American Chemical Society 145 ( 43 ) 23503 - 23518 2023年11月
In cells, the formation of RNA/DNA hybrid duplexes regulates gene expression and modification. The environment inside cellular organelles is heterogeneously crowded with high concentrations of biomolecules that affect the structure and stability of RNA/DNA hybrid duplexes. However, the detailed environmental effects remain unclear. Therefore, the mechanistic details of the effect of such molecular crowding were investigated at the molecular level by using thermodynamic and nuclear magnetic resonance analyses, revealing structure-dependent destabilization of the duplexes under crowded conditions. The transition from B- to A-like hybrid duplexes due to a change in conformation of the DNA strand guided by purine-pyrimidine asymmetry significantly increased the hydration number, which resulted in greater destabilization by the addition of cosolutes. By quantifying the individual contributions of environmental factors and the bulk structure of the duplex, we developed a set of parameters that predict the stability of hybrid duplexes with conformational dissimilarities under diverse crowding conditions. A comparison of the effects of environmental conditions in living cells and in vitro crowded solutions on hybrid duplex formation using the Förster resonance energy transfer technique established the applicability of our parameters to living cells. Moreover, our derived parameters can be used to estimate the efficiency of transcriptional inhibition, genome editing, and silencing techniques in cells. This supports the usefulness of our parameters for the visualization of cellular mechanisms of gene expression and the development of nucleic acid-based therapeutics targeting different cells.
DOI： 10.1021/jacs.3c06706
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Nearest-neighbor parameters for the prediction of RNA duplex stability in diverse in vitro and cellular-like crowding conditions. 査読あり 国際誌
Saptarshi Ghosh, Shuntaro Takahashi, Dipanwita Banerjee, Tatsuya Ohyama, Tamaki Endoh, Hisae Tateishi-Karimata, Naoki Sugimoto
Nucleic acids research 51 ( 9 ) 4101 - 4111 2023年5月
RNA performs various spatiotemporal functions in living cells. As the solution environments significantly affect the stability of RNA duplexes, a stability prediction of the RNA duplexes in diverse crowded conditions is required to understand and modulate gene expression in heterogeneously crowded intracellular conditions. Herein, we determined the nearest-neighbor (NN) parameters for RNA duplex formation when subjected to crowding conditions with an ionic concentration relevant to that found in cells. Determination of the individual contributions of excluded volume effect and water activity to each of the NN parameters in crowded environments enabled prediction of the thermodynamic parameters and their melting temperatures for plenty of tested RNA duplex formation in vitro and in cell with significant accuracy. The parameters reported herein will help predicting RNA duplex stability in different crowded environments, which will lead to an improved understanding of the stability-function relationship for RNAs in various cellular organelles with different molecular environments.
DOI： 10.1093/nar/gkad020
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Simple and fast screening for structure-selective G-quadruplex ligands 査読あり
Y. Hashimoto, Y. Imagawa, K. Nagano, R. Maeda, N. N.agahama, T. Torii, N. Kinoshita, N. Takamiya, K. Kawauchi, H. Tateishi-Karimata, N. Sugimoto and D. Miyoshi
Chem. Commun. 59 4891 - 4894 2023年4月
DOI： 10.1039/D3CC00556A
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High-temperature adaptation of an OsNRT2.3 allele is thermoregulated by small RNAs. 査読あり 国際共著 国際誌
Yong Zhang, Hisae Tateishi-Karimata, Tamaki Endoh, Qiongli Jin, Kexin Li, Xiaoru Fan, Yingjun Ma, Limin Gao, Haiyan Lu, Zhiye Wang, Art E Cho, Xuefeng Yao, Chunming Liu, Naoki Sugimoto, Shiwei Guo, Xiangdong Fu, Qirong Shen, Guohua Xu, Luis Rafael Herrera-Estrella, Xiaorong Fan
Science advances 8 ( 47 ) eadc9785 2022年11月
Climate change negatively affects crop yield, which hinders efforts to reach agricultural sustainability and food security. Here, we show that a previously unidentified allele of the nitrate transporter gene OsNRT2.3 is required to maintain high yield and high nitrogen use efficiency under high temperatures. We demonstrate that this tolerance to high temperatures in rice accessions harboring the HTNE-2 (high temperature resistant and nitrogen efficient-2) alleles from enhanced translation of the OsNRT2.3b mRNA isoform and the decreased abundance of a unique small RNA (sNRT2.3-1) derived from the 5' untranslated region of OsNRT2.3. sNRT2.3-1 binds to the OsNRT2.3a mRNA in a temperature-dependent manner. Our findings reveal that allelic variation in the 5' untranslated region of OsNRT2.3 leads to an increase in OsNRT2.3b protein levels and higher yield during high-temperature stress. Our results also provide a breeding strategy to produce rice varieties with higher grain yield and lower N fertilizer input suitable for a sustainable agriculture that is resilient against climate change.
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DNA methylation is regulated by both the stability and topology of G-quadruplex. 査読あり 国際誌
Saki Matsumoto, Hisae Tateishi-Karimata, Naoki Sugimoto
Chemical communications (Cambridge, England) 58 ( 89 ) 12459 - 12462 2022年11月
Since DNA methylation alters the chromatin state and regulates gene expression, elucidating the regulatory mechanisms of DNA methylation in response to environmental changes in the cell is crucial and urgent in understanding and regulating DNA methylation. G-quadruplex (G4) regulates transcription, translation and replication. Although it has recently been suggested that G4 regulates methylation, the detailed regulatory mechanism remains unclear. Here, we systematically analysed the effect of G4 formation on DNA methylation using G4s with various stabilities and topologies. The methylation efficiency decreased as the stability of G4 increased. Moreover, the degree of methylation suppression can be also controlled by G4 topology. Furthermore, our results showed the possibility of regulating methylation by modulating G4 stability and topology.
DOI： 10.1039/d2cc04383a
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Controlling liquid-liquid phase separation of G-quadruplex-forming RNAs in a sequence-specific manner. 査読あり 国際誌
Mitsuki Tsuruta, Takeru Torii, Kazuki Kohata, Keiko Kawauchi, Hisae Tateishi-Karimata, Naoki Sugimoto, Daisuke Miyoshi
Chemical communications (Cambridge, England) 58 ( 93 ) 12931 - 12934 2022年11月
We constructed a minimum liquid-liquid phase separation model system to form liquid droplets using only G-quadruplex-forming oligonucleotides and R- and G-rich oligopeptides. We found that the G-quadruplex structure is an essential component for RNA to form droplets with the peptide. Based on this model system and our findings, droplet redissolution via structure transition from a G-quadruplex to a duplex was achieved in a sequence-specific manner.
DOI： 10.1039/d2cc04366a
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Wataru Sugimoto, Natsuki Kinoshita, Minori Nakata, Tatsuya Ohyama, Hisae Tateishi-Karimata, Takahito Nishikata, Naoki Sugimoto, Daisuke Miyoshi, Keiko Kawauchi
Chemical Communications 58 ( 1 ) 48 - 51 2022年1月
出版者・発行元：Royal Society of Chemistry (RSC)
We identified cytosine-rich regions adjacent to guanine-rich regions in the TMPRSS2 gene, which showed structural competition between a G-quadruplex and a hairpin loop. Furthermore, this competition significantly affected transcription efficiency.
DOI： 10.1039/d1cc05523b
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Saki Matsumoto, Hisae Tateishi-Karimata, Tatsuya Ohyama, Naoki Sugimoto
RSC Advances 11 ( 59 ) 37205 - 37217 2021年11月
出版者・発行元：Royal Society of Chemistry (RSC)
The modification of DNA can regulate the transition between a duplex and quadruplexes during senescence responding to surrounding environments.
DOI： 10.1039/d1ra07201c
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Chemical Modulation of DNA Replication along G-Quadruplex Based on Topology-Dependent Ligand Binding. 査読あり 国際共著 国際誌
Shuntaro Takahashi, Anita Kotar, Hisae Tateishi-Karimata, Sudipta Bhowmik, Zi-Fu Wang, Ta-Chau Chang, Shinobu Sato, Shigeori Takenaka, Janez Plavec, Naoki Sugimoto
Journal of the American Chemical Society 143 ( 40 ) 16458 - 16469 2021年10月
共著
Ligands that bind to and stabilize guanine-quadruplex (G4) structures to regulate DNA replication have therapeutic potential for cancer and neurodegenerative diseases. Because there are several G4 topologies, ligands that bind to their specific types may have the ability to preferentially regulate the replication of only certain genes. Here, we demonstrated that binding ligands stalled the replication of template DNA at G4, depending on different topologies. For example, naphthalene diimide derivatives bound to the G-quartet of G4 with an additional interaction between the ligand and the loop region of a hybrid G4 type from human telomeres, which efficiently repressed the replication of the G4. Thus, these inhibitory effects were not only stability-dependent but also topology-selective based on the manner in which G4 structures interacted with G4 ligands. Our original method, referred to as a quantitative study of topology-dependent replication (QSTR), was developed to evaluate correlations between replication rate and G4 stability. QSTR enabled the systematic categorization of ligands based on topology-dependent binding. It also demonstrated accuracy in determining quantitatively how G4 ligands control the intermediate state of replication and the kinetics of G4 unwinding. Hence, the QSTR index would facilitate the design of new drugs capable of controlling the topology-dependent regulation of gene expression.
DOI： 10.1021/jacs.1c05468
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Roles of non-canonical structures of nucleic acids in cancer and neurodegenerative diseases. 査読あり 国際誌
Hisae Tateishi-Karimata, Naoki Sugimoto
Nucleic acids research 49 ( 14 ) 7839 - 7855 2021年8月
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Cancer and neurodegenerative diseases are caused by genetic and environmental factors. Expression of tumour suppressor genes is suppressed by mutations or epigenetic silencing, whereas for neurodegenerative disease-related genes, nucleic acid-based effects may be presented through loss of protein function due to erroneous protein sequences or gain of toxic function from extended repeat transcripts or toxic peptide production. These diseases are triggered by damaged genes and proteins due to lifestyle and exposure to radiation. Recent studies have indicated that transient, non-canonical structural changes in nucleic acids in response to the environment can regulate the expression of disease-related genes. Non-canonical structures are involved in many cellular functions, such as regulation of gene expression through transcription and translation, epigenetic regulation of chromatin, and DNA recombination. Transcripts generated from repeat sequences of neurodegenerative disease-related genes form non-canonical structures that are involved in protein transport and toxic aggregate formation. Intracellular phase separation promotes transcription and protein assembly, which are controlled by the nucleic acid structure and can influence cancer and neurodegenerative disease progression. These findings may aid in elucidating the underlying disease mechanisms. Here, we review the influence of non-canonical nucleic acid structures in disease-related genes on disease onset and progression.
DOI： 10.1093/nar/gkab580
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Naoki Sugimoto, Tamaki Endoh, Shuntaro Takahashi, Hisae Tateishi-Karimata
Bulletin of the Chemical Society of Japan 94 ( 7 ) 1970 - 1998 2021年7月
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Effect of Molecular Crowding on the Stability of RNA G-Quadruplexes with Various Numbers of Quartets and Lengths of Loops. 査読あり 国際誌
Saki Matsumoto, Hisae Tateishi-Karimata, Shuntaro Takahashi, Tatsuya Ohyama, Naoki Sugimoto
Biochemistry 59 ( 28 ) 2640 - 2649 2020年7月
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G-Quadruplexes are noncanonical structures formed by guanine-rich regions of not only DNA but also RNA. RNA G-quadruplexes are widely present in the transcriptome as mRNAs and noncoding RNAs and take part in various essential functions in cells. Furthermore, stable RNA G-quadruplexes control the extent of biological functions, such as mRNA translation and antigen presentation. To understand and regulate the functions controlled by RNA G-quadruplexes in cellular environments, which are molecularly crowded, we would be required to investigate the stability of G-quadruplexes in molecular crowding. Here, we systematically investigated the thermodynamic stability of RNA G-quadruplexes with different numbers of G-quartets and lengths of loops. The molecular crowding conditions of polyethylene glycol with an average molecular weight of 200 (PEG200) were found to stabilize RNA G-quadruplexes with three and four G-quartets, while G-quadruplexes with two G-quartets did not exhibit any stabilization upon addition of PEG200. On the other hand, no difference in stabilization by PEG200 was observed among the G-quadruplexes with different loop lengths. Thermodynamic analysis of the RNA G-quadruplexes revealed more appropriate motifs for identifying G-quadruplex-forming sequences. The informatics analysis with new motifs demonstrated that the distributions of G-quadruplexes in human noncoding RNAs differed depending on the number of G-quartets. Therefore, RNA G-quadruplexes with different numbers of G-quartets may play different roles in response to environmental changes in cells.
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Improved nearest-neighbor parameters for the stability of RNA/DNA hybrids under a physiological condition. 査読あり 国際誌
Dipanwita Banerjee, Hisae Tateishi-Karimata, Tatsuya Ohyama, Saptarshi Ghosh, Tamaki Endoh, Shuntaro Takahashi, Naoki Sugimoto
Nucleic acids research 48 ( 21 ) 12042 - 12054 2020年7月
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The stability of Watson-Crick paired RNA/DNA hybrids is important for designing optimal oligonucleotides for ASO (Antisense Oligonucleotide) and CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas9 techniques. Previous nearest-neighbour (NN) parameters for predicting hybrid stability in a 1 M NaCl solution, however, may not be applicable for predicting stability at salt concentrations closer to physiological condition (e.g. ∼100 mM Na+ or K+ in the presence or absence of Mg2+). Herein, we report measured thermodynamic parameters of 38 RNA/DNA hybrids at 100 mM NaCl and derive new NN parameters to predict duplex stability. Predicted ΔG°37 and Tm values based on the established NN parameters agreed well with the measured values with 2.9% and 1.1°C deviations, respectively. The new results can also be used to make precise predictions for duplexes formed in 100 mM KCl or 100 mM NaCl in the presence of 1 mM Mg2+, which can mimic an intracellular and extracellular salt condition, respectively. Comparisons of the predicted thermodynamic parameters with published data using ASO and CRISPR-Cas9 may allow designing shorter oligonucleotides for these techniques that will diminish the probability of non-specific binding and also improve the efficiency of target gene regulation.
DOI： 10.1093/nar/gkaa572
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Nearest-neighbor parameters for predicting DNA duplex stability in diverse molecular crowding conditions. 査読あり 国際誌
Saptarshi Ghosh, Shuntaro Takahashi, Tatsuya Ohyama, Tamaki Endoh, Hisae Tateishi-Karimata, Naoki Sugimoto
Proceedings of the National Academy of Sciences of the United States of America 117 ( 25 ) 14194 - 14201 2020年6月
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The intracellular environment is crowded and heterogeneous. Although the thermodynamic stability of nucleic acid duplexes is predictable in dilute solutions, methods of predicting such stability under specific intracellular conditions are not yet available. We recently showed that the nearest-neighbor model for self-complementary DNA is valid under molecular crowding condition of 40% polyethylene glycol with an average molecular weight of 200 (PEG 200) in 100 mM NaCl. Here, we determined nearest-neighbor parameters for DNA duplex formation under the same crowding condition to predict the thermodynamics of DNA duplexes in the intracellular environment. Preferential hydration of the nucleotides was found to be the key factor for nearest-neighbor parameters in the crowding condition. The determined parameters were shown to predict the thermodynamic parameters (∆H°, ∆S°, and ∆G°37) and melting temperatures (Tm) of the DNA duplexes in the crowding condition with significant accuracy. Moreover, we proposed a general method for predicting the stability of short DNA duplexes in different cosolutes based on the relationship between duplex stability and the water activity of the cosolute solution. The method described herein would be valuable for investigating biological processes that occur under specific intracellular crowded conditions and for the application of DNA-based biotechnologies in crowded environments.
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RNA G-Quadruplexes Facilitate RNA Accumulation in G-Rich Repeat Expansions 査読あり 国際共著 国際誌
Ye Teng, Hisae Tateishi-Karimata, Naoki Sugimoto
Biochemistry 59 ( 21 ) 1972 - 1980 2020年6月
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The regulatory mechanisms of the processes of RNA accumulation were examined from a chemical perspective in repeat-expansion disorders, which induce cytotoxicity and cause neurodegenerative diseases. We found that the accumulation, including production, gelation, and sedimentation, of RNA repeats transcribed from repeat expansions related to neurodegenerative diseases was greatly accelerated by G-quadruplex-forming RNA repeats, although no acceleration was induced by hairpin-forming RNA repeats. We also investigated the relationship between accumulation and physical solution properties, such as viscosity and water activity, and found that RNA accumulation was promoted through a decrease in the dielectric constant. Importantly, we found that the RNA accumulation required RNA G-quadruplexes and was promoted by changes in the dielectric property of the cell induced by an ion channel inhibitor. Our study is the first to show that the accumulation processes that induce toxicity in cells can be controlled via electrostatic interactions in the RNA G-quadruplex; thus, these can form the basis of guidelines for the chemical control of cell toxins.
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Thrombin binding aptamer G-quadruplex stabilized by pyrene-modified nucleotides 査読あり 国際共著 国際誌
Matic Kovačič, Peter Podbevšek, Hisae Tateishi-Karimata, Shuntaro Takahashi, Naoki Sugimoto, Janez Plavec
Nucleic acids research 48 ( 7 ) 3975 - 3986 2020年4月
共著
© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. Guanine-rich regions of the human genome can adopt non-canonical secondary structures. Their role in regulating gene expression has turned them into promising targets for therapeutic intervention. Ligands based on polyaromatic moieties are especially suitable for targeting G-quadruplexes utilizing their size complementarity to interact with the large exposed surface area of four guanine bases. A predictable way of (de)stabilizing specific G-quadruplex structures through efficient base stacking of polyaromatic functional groups could become a valuable tool in our therapeutic arsenal. We have investigated the effect of pyrene-modified uridine nucleotides incorporated at several positions of the thrombin binding aptamer (TBA) as a model system. Characterization using spectroscopic and biophysical methods provided important insights into modes of interaction between pyrene groups and the G-quadruplex core as well as (de)stabilization by enthalpic and entropic contributions. NMR data demonstrated that incorporation of pyrene group into G-rich oligonucleotide such as TBA may result in significant changes in 3D structure such as formation of novel dimeric topology. Site specific structural changes induced by stacking of the pyrene moiety on nearby nucleobases corelate with distinct thrombin binding affinities and increased resistance against nuclease degradation.
DOI： 10.1093/nar/gkaa118
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Hydroxyl groups in cosolutes regulate the G-quadruplex topology of telomeric DNA 査読あり 国際共著 国際誌
Hisae Tateishi-Karimata, Dipanwita Banerjee, Tatsuya Ohyama, Saki Matsumoto, Daisuke Miyoshi, Shu-ich Nakano, Naoki Sugimoto
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 525 ( 1 ) 177 - 183 2020年4月
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出版者・発行元：ACADEMIC PRESS INC ELSEVIER SCIENCE
Telomeric G-quadruplex topology has the ability to regulate telomerase activity, which counteracts the shortening of telomere with successive cell divisions, thereby causing genomic longevity. However, the detailed mechanism of G-quadruplexes topologies formed by telomeric sequences requires further investigation. In this study, we quantitatively investigated the effect of cosolutes, particularly the varying number of hydroxyl groups, on the structural transition between hybrid type and parallel G-quadruplexes formed by telomeric DNA sequences. Cosolutes with one or no hydroxyl groups in the vicinal position more efficiently induced the transition to parallel G-quadruplex from hybrid G-quadruplex than those with more hydroxyl groups. We also examined the effect of cosolute structures on the hydration of G-quadruplex formation; the results indicated that cosolutes with fewer hydroxyl groups lead to the release of greater amount of water during G-quadruplex formation. Molecular dynamics results showed that the parallel G-quadruplex was more dehydrated than the hybrid type G-quadruplex. Generally, a dehydrated structure is favored under crowding condition. Thus, depending on the surrounding cosolutes, the G-quadruplex topology can be controlled by the G-quadruplex hydration state. (c) 2020 Elsevier Inc. All rights reserved.
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New Modified Deoxythymine with Dibranched Tetraethylene Glycol Stabilizes G-Quadruplex Structures 査読あり
H. Tateishi-Karimata, T. Ohyama, T. Muraoka, S. Tanaka, K. Kinbara, and N. Sugimoto
Molecules 25 705 2020年2月
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Chemical biology of non-canonical structures of nucleic acids for therapeutic application 査読あり
H. Tateishi-Karimata and N. Sugimoto
Chem. Commun. 2020年2月
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Hydroxyl groups in cosolutes regulate the G-quadruplex topology of telomeric DNA 査読あり
H. Tateishi-Karimata, D. Banerjee, T. Ohyama, S. Matsumoto, D. Miyoshi, S. Nakano, and N. Sugimoto
Biochem. Biophys. Res. Commun. 523 2020年2月
単著
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New Modified Deoxythymine with Dibranched Tetraethylene Glycol Stabilizes G-Quadruplex Structures 査読あり 国際誌
Hisae Tateishi-Karimata, Tatsuya Ohyama, Takahiro Muraoka, Shigenori Tanaka, Kazushi Kinbara, Naoki Sugimoto
MOLECULES 25 ( 3 ) 2020年2月
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出版者・発行元：MDPI
Methods for stabilizing G-quadruplex formation is a promising therapeutic approach for cancer treatment and other biomedical applications because stable G-quadruplexes efficiently inhibit biological reactions. Oligo and polyethylene glycols are promising biocompatible compounds, and we have shown that linear oligoethylene glycols can stabilize G-quadruplexes. Here, we developed a new modified deoxythymine with dibranched or tribranched tetraethylene glycol (TEG) and incorporated these TEG-modified deoxythymines into a loop region that forms an antiparallel G-quadruplex. We analyzed the stability of the modified G-quadruplexes, and the results showed that the tribranched TEG destabilized G-quadruplexes through entropic contributions, likely through steric hindrance. Interestingly, the dibranched TEG modification increased G-quadruplex stability relative to the unmodified DNA structures due to favorable enthalpic contributions. Molecular dynamics calculations suggested that dibranched TEG interacts with the G-quadruplex through hydrogen bonding and CH-pi interactions. Moreover, these branched TEG-modified deoxythymine protected the DNA oligonucleotides from degradation by various nucleases in human serum. By taking advantage of the unique interactions between DNA and branched TEG, advanced DNA materials can be developed that affect the regulation of DNA structure.
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Chemical biology of non-canonical structures of nucleic acids for therapeutic applications 査読あり 国際誌
Hisae Tateishi-Karimata, Naoki Sugimoto
CHEMICAL COMMUNICATIONS 56 ( 16 ) 2379 - 2390 2020年2月
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出版者・発行元：ROYAL SOC CHEMISTRY
DNA forms not only the canonical duplex structure but also non-canonical structures. Most potential sequences that induce the formation of non-canonical structures are present in disease-related genes. Interestingly, biological reactions are inhibited or dysregulated by non-canonical structure formation in disease-related genes. To control biological reactions, methods for inducing the formation of non-canonical structures have been developed using small molecules and oligonucleotides. In this feature article, we review biological reactions such as replication, transcription, and reverse transcription controlled by non-canonical DNA structures formed by disease-related genes. Furthermore, we discuss recent studies aimed at developing methods for regulating these biological reactions using drugs targeting the DNA structure.
DOI： 10.1039/c9cc09771f
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Effect of potassium concentration on triplex stability under molecular crowding conditions 査読あり 国際共著
Y. Teng, H. Tateishi-Karimata, T. Ohyama, and N. Sugimoto
Molecules 25 387 2020年1月
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Effect of Potassium Concentration on Triplex Stability under Molecular Crowding Conditions 査読あり 国際共著 国際誌
Ye Teng, Hisae Tateishi-Karimata, Tatsuya Ohyama, Naoki Sugimoto
MOLECULES 25 ( 2 ) 2020年1月
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出版者・発行元：MDPI
The properties of non-canonical DNA structures, like G-quadruplexes and triplexes, change under cell-mimicking molecular crowding conditions relative to dilute aqueous solutions. The analysis of environmental effects on their stability is crucial since they play important roles in gene expression and regulation. In this study, three intramolecular and intermolecular triplex-forming sequences of different C(*)(+)G-C triplet content ((*): Hoogsteen base pair; - : Watson-Crick base pair) were designed and their stability measured in the absence and presence of a crowding agent with different K+ concentrations. In dilute solution, the stability of the triplexes was reduced by decreasing the concentration of KCl. This reduction became smaller as the number of C(*)(+)G-C triplets increased. Under molecular crowding conditions, Watson-Crick base pairs and Hoogsteen base pairs were destabilized and stabilized, respectively. Interestingly, with lower KCl concentrations (<= 1 M), the destabilization of the triplexes due to reduction of KCl concentration was significantly smaller than in dilute solutions. In addition, the C(*)(+)G-C content had greater influence on triplex stability under molecular crowding conditions. Our work provides quantitative information about the effects of K+ concentration on triplex stability under molecular crowding conditions and should further our understanding of the function and regulation of triplexes in bioprocesses.
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Effect of chemical environment changes in cell on DNA structures and functions 招待あり
Hisae Tateishi-Karimata and Naoki Sugimoto
Impact 2020 ( 7 ) 25 - 27 2020年
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出版者・発行元：Science Impact Ltd
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Validation of the nearest-neighbor model for Watson-Crick self-complementary DNA duplexes in molecular crowding condition. 査読あり
Ghosh S, Takahashi S, Endoh T, Tateishi-Karimata H, Hazra S, Sugimoto N
Nucleic acids research 47 ( 7 ) 3284 - 3294 2019年4月
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C-rich sequence in a non-template DNA strand regulates structure change of G-quadruplex in a template strand during transcription 査読あり
建石 寿枝
Bull. Chem. Soc. Jpn. 92 572 - 577 2019年
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A Turn-On Detection of DNA Sequences by Means of Fluorescence of DNA-Templated Silver Nanoclusters via Unique Interactions of a Hydrated Ionic Liquid. 査読あり
Teng Y, Tateishi-Karimata H, Tsuruoka T, Sugimoto N
Molecules (Basel, Switzerland) 23 ( 11 ) 2889 2018年11月
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Mirror-Image Dependence: Targeting Enantiomeric G-Quadruplex DNA Using Triplex Metallohelices. 査読あり 国際共著
Zhao C, Song H, Scott P, Zhao A, Tateishi-Karimata H, Sugimoto N, Ren J, Qu X
Angewandte Chemie (International ed. in English) 57 ( 48 ) 15723 - 15727 2018年10月
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An anionic phthalocyanine decreases NRAS expression by breaking down its RNA G-quadruplex 査読あり
Kawauchi Keiko, Sugimoto Wataru, Yasui Takatoshi, Murata Kohei, Itoh Katsuhiko, Takagi Kazuki, Tsuruoka Takaaki, Akamatsu Kensuke, Tateishi-Karimata Hisae, Sugimoto Naoki, Miyoshi Daisuke
NATURE COMMUNICATIONS 9 ( 1 ) 2271 2018年6月
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Biological and nanotechnological applications using interactions between ionic liquids and nucleic acids. 査読あり
Tateishi-Karimata H, Sugimoto N
Biophysical reviews 10 ( 3 ) 931 - 940 2018年6月
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Pursuing origins of (poly)ethylene glycol-induced G-quadruplex structural modulations 査読あり 国際共著
Trajkovski Marko, Endoh Tamaki, Tateishi-Karimata Hisae, Ohyama Tatsuya, Tanaka Shigenori, Plavec Janez, Sugimoto Naoki
NUCLEIC ACIDS RESEARCH 46 ( 8 ) 4301 - 4315 2018年5月
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Alkylating probes for the G-quadruplex structure and evaluation of the properties of the alkylated G-quadruplex DNA 査読あり
Sato Norihiro, Takahashi Shuntaro, Tateishi-Karimata Hisae, Hazemi Madoka E., Chikuni Tomoko, Onizuka Kazumitsu, Sugimoto Naoki, Nagatsugi Fumi
ORGANIC & BIOMOLECULAR CHEMISTRY 16 ( 9 ) 1436 - 1441 2018年3月
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Drastic stability change of X-X mismatch in d(CXG) trinucleotide repeat disorders under molecular crowding condition 査読あり
Teng Ye, Pramanik Smritimoy, Tateishi-Karimata Hisae, Ohyama Tatsuya, Sugimoto Naoki
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 496 ( 2 ) 601 - 607 2018年2月
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テトラエチレングリコールで修飾されたグアニン四重鎖の安定性の分子動力学計算による解析
大山達也, 建石寿枝, 田中成典, 杉本直己
日本核酸化学会誌 2 3 - 10 2018年
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Unexpected Position-Dependent Effects of Ribose G-Quartets in G-Quadruplexes 査読あり 国際共著
Zhou Jun, Amrane Samir, Rosu Frederic, Salgado Gilmar F., Bian Yunqiang, Tateishi-Karimata Hisae, Largy Eric, Korkut Dursun Nizam, Bourdoncle Anne, Miyoshi Daisuke, Zhang Jian, Ju Huangxian, Wang Wei, Sugimoto Naoki, Gabelica Valerie, Mergny Jean-Louis
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 139 ( 23 ) 7768 - 7779 2017年6月
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Through-bond effects in the ternary complexes of thrombin sandwiched by two DNA aptamers 査読あり 国際共著
Pica Andrea, Krauss Irene Russo, Parente Valeria, Tateishi-Karimata Hisae, Nagatoishi Satoru, Tsumoto Kouhei, Sugimoto Naoki, Sica Filomena
NUCLEIC ACIDS RESEARCH 45 ( 1 ) 461 - 469 2017年1月
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Local thermodynamics of the water molecules around single- and double-stranded DNA studied by grid inhomogeneous solvation theory 査読あり
Nakano Miki, Tateishi-Karimata Hisae, Tanaka Shigenori, Tama Florence, Miyashita Osamu, Nakano Shu-ichi, Sugimoto Naoki
CHEMICAL PHYSICS LETTERS 660 250 - 255 2016年9月
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G-Quadruplexes with Tetra(ethylene glycol)-Modified Deoxythymidines are Resistant to Nucleases and Inhibit HIV-1 Reverse Transcriptase 査読あり
Tateishi-Karimata Hisae, Muraoka Takahiro, Kinbara Kazushi, Sugimoto Naoki
CHEMBIOCHEM 17 ( 15 ) 1399 - 1402 2016年8月
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Expansion of the DNA Alphabet beyond Natural DNA Recognition. 査読あり
Tateishi-Karimata H, Sugimoto N
Chembiochem : a European journal of chemical biology 17 ( 14 ) 1301 - 1303 2016年7月
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Reevaluation of the stability of G-quadruplex structures under crowding conditions. 査読あり 国際共著
Zhou J, Tateishi-Karimata H, Mergny JL, Cheng M, Feng Z, Miyoshi D, Sugimoto N, Li C
Biochimie 121 204 - 208 2016年2月
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Incorporation of O(6)-methylguanine restricts the conformational conversion of the human telomere G-quadruplex under molecular crowding conditions. 査読あり 国際共著
Zhao A, Zhao C, Tateishi-Karimata H, Ren J, Sugimoto N, Qu X
Chemical communications (Cambridge, England) 52 ( 9 ) 1903 - 1906 2016年1月
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Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory. 査読あり
Nakano M, Tateishi-Karimata H, Tanaka S, Tama F, Miyashita O, Nakano S, Sugimoto N
Nucleic acids research 43 ( 21 ) 10114 - 10125 2015年12月
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Choline ions stabilize A-T Base pairs by fitting into minor groove 査読あり
M. Nakano, H. Tateishi-Karimata, S. Tanaka, and N. Sugimoto
JPS Conf. Proc. ( 5 ) 011008 2015年11月
共著
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DNA sensor's selectivity enhancement and protection from contaminating nucleases due to a hydrated ionic liquid. 査読あり
Tateishi-Karimata H, Pramanik S, Sugimoto N
The Analyst 140 ( 13 ) 4393 - 4398 2015年7月
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i-Motifs are more stable than G-quadruplexes in a hydrated ionic liquid. 査読あり 国際共著
Tateishi-Karimata H, Nakano M, Pramanik S, Tanaka S, Sugimoto N
Chemical communications (Cambridge, England) 51 ( 32 ) 6909 - 6912 2015年4月
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Structural foundation for DNA behavior in hydrated ionic liquid: An NMR study. 査読あり 国際共著
Marušič M, Tateishi-Karimata H, Sugimoto N, Plavec J
Biochimie 108 169 - 177 2015年1月
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Methyl substitution regulates the enantioselectivity of supramolecular complex binding to human telomeric G-quadruplex DNA. 査読あり 国際共著
Xu B, Zhao C, Chen Y, Tateishi-Karimata H, Ren J, Sugimoto N, Qu X
Chemistry (Weinheim an der Bergstrasse, Germany) 20 ( 50 ) 16467 - 16472 2014年12月
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Organelle-mimicking liposome dissociates G-quadruplexes and facilitates transcription. 査読あり
Pramanik S, Tateishi-Karimata H, Sugimoto N
Nucleic acids research 42 ( 20 ) 12949 - 12959 2014年11月
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Dangling ends perturb the stability of RNA duplexes responsive to surrounding conditions. 査読あり
Tateishi-Karimata H, Pramanik S, Nakano S, Miyoshi D, Sugimoto N
ChemMedChem 9 ( 9 ) 2150 - 2155 2014年9月
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Affinity of molecular ions for DNA structures is determined by solvent-accessible surface area. 査読あり
Nakano M, Tateishi-Karimata H, Tanaka S, Sugimoto N
The journal of physical chemistry. B 118 ( 32 ) 9583 - 9594 2014年8月
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Structure, stability and behaviour of nucleic acids in ionic liquids. 査読あり
Tateishi-Karimata H, Sugimoto N
Nucleic acids research 42 ( 14 ) 8831 - 8844 2014年8月
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Comparable stability of Hoogsteen and Watson-Crick base pairs in ionic liquid choline dihydrogen phosphate. 査読あり
Tateishi-Karimata H, Nakano M, Sugimoto N
Scientific reports 4 3593 2014年1月
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Control of stability and structure of nucleic acids using cosolutes 査読あり
H. Tateishi-Karimata and N. Sugimoto
Methods 67 151 - 158 2014年
共著
担当区分：筆頭著者
-
Structure, stability and behavior of nucleic acids in ionic liquids 査読あり
H. Tateishi-Karimata and N. Sugimoto
Nucleic Acids Res 42 8831 - 8844 2014年
共著
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New insights into transcription fidelity: thermal stability of non-canonical structures in template DNA regulates transcriptional arrest, pause, and slippage 査読あり
H. Tateishi-Karimata, N. Isono, and N. Sugimoto
PLOS One 9 e9058 2014年
共著
担当区分：筆頭著者
-
Choline ion interactions with DNA atoms explain unique stabilization of A-T base pairs in DNA duplexes: A microscopic view 査読あり
M. Nakano, H. Tateishi-Karimata, S. Tanaka, and N. Sugimoto
J. Phys. Chem. B. 118 379 - 389 2014年
共著
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Comparable stability of Hoogsteen and Watson–Crick base pairs in ionic liquid choline dihydrogen phosphate 査読あり
H. Tateishi-Karimata, M. Nakano, and N. Sugimoto
Sci Rep 4 3593 2014年
共著
担当区分：筆頭著者
-
Real-time monitoring of DNA hybridization kinetics on living cell surfaces. 査読あり
Rode AB, Endoh T, Tateishi-Karimata H, Takahashi S, Sugimoto N
Chemical communications (Cambridge, England) 49 ( 76 ) 8444 - 8446 2013年10月
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Quantitative Analyses of Nucleic Acid Stability under the Molecular Crowding Condition Induced by Cosolutes 招待あり 査読あり
H. Tateishi-Karimata, S. Nakano, N. Sugimoto
Current Protocols in Nucleic Acid Chemistry 2013年
共著
担当区分：筆頭著者
-
Real-time monitoring of DNA hybridization kinetics at living cell surfaces 査読あり
A. B. Rode, T. Endoh, H. Tateishi-Karimata, S. Takahashi and N. Sugimoto
Chem. Commun. 49 2013年
共著
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Study on Effects of Molecular Crowding on G-quadruplex-ligand Binding and Ligand-mediated Telomerase Inhibition 査読あり
H. Yaku, T. Murashima, H. Tateishi-Karimata S. Nakano, D. Miyoshi and N. Sugimoto
Methods 2013年
共著
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Study on effects of molecular crowding on G-quadruplex-ligand binding and ligand-mediated telomerase inhibition 査読あり
H. Yaku, T. Murashima, H. Tateishi-Karimata, S. Nakano, D. Miyoshi, and N. Sugimoto
Methods 64 19 - 27 2013年
共著
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Sequence and solvent effects on telomeric DNA bimolecular G-Quadruplex folding kinetics 査読あり 国際共著
A. Marchand, R. Ferreira, H. Tateishi-Karimata, D. Miyoshi, N. Sugimoto, and V. Gabelica
J. Phys. Chem. B 117 12391 - 12401 2013年
共著
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Hydration changes upon DNA folding studied by osmotic stress experiments. 査読あり
Nakano S, Yamaguchi D, Tateishi-Karimata H, Miyoshi D, Sugimoto N
Biophysical journal 102 ( 12 ) 2808 - 2817 2012年6月
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A-T base pairs are more stable than G-C base pairs in a hydrated ionic liquid. 査読あり
Tateishi-Karimata H, Sugimoto N
Angewandte Chemie (International ed. in English) 51 ( 6 ) 1416 - 1419 2012年2月
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Hydration Changes upon DNA Folding Studied by Osmotic Stress Experiments 査読あり
S. Nakano, D. Yamaguchi, H. Tateishi-Karimata, D. Miyoshi, N. Sugimoto
Biophysical Journal 102 2808 - 2817 2012年
共著
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Sequence and Solvent Effects on Telomeric DNA Bimolecular G-Quadruplex Folding Kinetics 査読あり 国際共著
Adrien Marchand, Ruben Ferreira, Hisae Tateishi-Karimata, Daisuke Miyoshi, Naoki Sugimoto, Valerie Gabelica
J. Phys. Chem. B 117 2012年
共著
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DNA Morphologic Changes Induced by Spermine on a Gold Surface under DNA Crowding Conditions 査読あり
K. Kobayashi, H. Tateishi-Karimata, K. Tsutsui, Y. Wada, and N. Sugimoto
Chem Lett 40 855 - 857 2011年
単著
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Thermal stability and hydration state of DNA G-quadruplex regulated by loop regions 査読あり
T. Fujimoto, D. Miyoshi, H. T. Karimata, and N. Sugimoto
Nucleic Acids Symp Ser. 53 237 - 238 2009年11月
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Hydration of Watson-Crick Base Pairs and Dehydration of Hoogsteen Base Pairs Inducing Structural Polymorphism under Molecular Crowding Conditions 査読あり
D. Miyoshi, K. Nakamura, H. Tateishi- Karimata, T. Ohmichi, and N. Sugimoto
J. Am. Chem. Soc. 131 3522 - 3531 2009年8月
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Facilitation of RNA enzyme activity in the molecular crowding media of cosolutes 査読あり
S. Nakano, H. Tateishi-Karimata, Y. Kitagawa, and N. Sugimoto
J. Am. Chem. Soc. 131 16881 - 16888 2009年8月
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Erratum: Conformation and the sodium ion condensation on DNA and RNA structures in the resence of a neutral cosolute as a mimic of the intracellular media (Molecular BioSystems (2009) DOI: 10.1039/b718806d) 査読あり
Shu Ichi Nakano, Lei Wu, Hirohito Oka, Hisae Tateishi Karimata, Toshimasa Kirihata, Yuichi Sato, Satoshi Fujii, Hiroshi Sakai, Masayuki Kuwahara, Hiroakiand Sawai, Naoki Sugimoto
Molecular BioSystems 5 ( 11 ) 1370 2009年
-
Conformation and the sodium ion condensation on DNA and RNA structures in the presence of a neutral cosolute as a mimic of the intracellular media 査読あり
S. Nakano, L. Wu, H. Oka, H. Tateishi-Karimata, T. Kirihata, Y. Sato, S. Fujii, H. Sakai, M. Kuwahara, H. Sawai, and N. Sugimoto
Molecular BioSystems 4 579 - 588 2008年11月
共著
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Molecular crowding effect on metal ion binding properties of the hammerhead ribozyme 査読あり
S. Nakano, Y. Kitagawa, H. T. Karimata, and N. Sugimoto
Nucleic Acids Symp. Ser. 52 519 - 520 2008年11月
-
ＤＮＡナノワイヤーの分子環境変化による可逆的制御
狩俣 寿枝
甲南大学 博士論文 2008年3月
単著
周辺環境に応答して構造を変化させるDNAワイヤーを構築した。
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Thermodynamics of DNA structures under molecular crowding conditions with neutral and positive charged cosolutes. 査読あり
Miyoshi D, Nakamura K, Muhuli S, Karimata HT, Sugimoto N
Nucleic acids symposium series (2004) ( 52 ) 413 - 414 2008年
-
Hydration regulates thermodynamic stability of DNA structures under molecular crowding conditions 査読あり
D. Miyoshi, H. Karimata, and N. Sugimoto
Nucleosides, Nucleotides and Nucleic Acids 26 6 - 9 2007年11月
共著
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Artificial G-wire Switch with 2,2’-Bipyridine Units Responsive to Divalent Metal Ions 査読あり 国際共著
D. Miyoshi, H. Karimata, Z.-M. Wang, K. Koumoto, and N. Sugimoto
J. Am. Chem. Soc. 129 5919 - 5925 2007年11月
共著
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Effects of Polyethylene Glycol on DNA Duplex Stability at Different NaCl Concentrations 査読あり
H. Karimata, S. Nakano, and N. Sugimoto
Bull. Chem. Soc. Jpn. 80 5919 - 5925 2007年11月
共著
担当区分：筆頭著者
-
Conformational switch of a functional nanowire based on the DNA G-quadruplex 査読あり 国際共著
H. Karimata, D. Miyoshi, T. Fujimoto, K. Koumoto, Z.-M. Wang, and N. Sugimoto
Nucleic Acids Symp. Ser. 51 251 - 252 2007年11月
共著
担当区分：筆頭著者
-
Hydration regulates the thermodynamic stability of DNA structures under molecular crowding conditions. 査読あり
Miyoshi D, Karimata H, Sugimoto N
Nucleosides, nucleotides & nucleic acids 26 ( 6-7 ) 589 - 595 2007年
-
Effects of cosolutes on the thermodynamic stability of parallel DNA duplex and triplex. 査読あり
Nakamura K, Karimata H, Ohmichi T, Miyoshi D, Sugimoto N
Nucleic acids symposium series (2004) ( 51 ) 167 - 168 2007年
-
Hydration regulates thermodynamics of G-quadruplex formation under molecular crowding conditions 査読あり
D. Miyoshi, H. Karimata, and N. Sugimoto
J. Am. Chem. Soc. 129 7957 - 7963 2006年11月
共著
-
Factors regulating thermodynamic stability of DNA structures under molecular crowding conditions. 査読あり
Miyoshi D, Karimata H, Sugimoto N
Nucleic acids symposium series (2004) ( 50 ) 203 - 204 2006年
-
The roles of cosolutes on the hammerhead ribozyme activity.
Karimata H, Nakano S, Sugimoto N
Nucleic acids symposium series ( 50 ) 81 - 82 2006年
-
Drastic Effect of a Single Base Difference between Human and Tetrahymena Telomere Sequences on Their Structures under Molecular Crowding Conditions 査読あり
D. Miyoshi, H. Karimata, and N. Sugimoto
Angew. Chem. Int. Ed. 44 3740 - 3744 2005年11月
共著
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DNA-Based Biosensor for Monitoring pH in Vitro and in Living Cell 査読あり
T. Ohmichi, Y. Kawamoto, P. Wu, D. Miyoshi, H. Karimata, and N. Sugimoto
Biochemistry 44 7125 - 7130 2005年11月
共著
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DNA-based biosensor for monitoring pH in vitro and in living cells. 査読あり
Ohmichi T, Kawamoto Y, Wu P, Miyoshi D, Karimata H, Sugimoto N
Biochemistry 44 ( 19 ) 7125 - 7130 2005年5月
-
DNA nanowire sensitive to the surrounding condition.
Miyoshi D, Wang ZM, Karimata H, Sugimoto N
Nucleic acids symposium series (2004) ( 49 ) 43 - 44 2005年
-
Structure and stability of DNA quadruplexes under molecular crowding conditions. 査読あり
Karimata H, Miyoshi D, Sugimoto N
Nucleic acids symposium series (2004) ( 49 ) 239 - 240 2005年
-
The effect of molecular crowding with nucleotide length and cosolute structure on DNA duplex stability 査読あり
S. Nakano, H. Karimata, T. Ohmichi, J. Kawakami, and N. Sugimoto
J. Am. Chem. Soc. 126 14330 - 14331 2004年11月
共著
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Stabilization of a DNA duplex under molecular crowding conditions of PEG. 査読あり
Karimata H, Nakano S, Ohmichi T, Kawakami J, Sugimoto N
Nucleic acids symposium series (2004) ( 48 ) 107 - 108 2004年
-
Effect of secondary structure of short double-stranded RNA on RNAi efficiency. 査読あり
Ohmichi T, Karimata H, Sugimoto N
Nucleic acids research. Supplement (2001) ( 2 ) 63 - 64 2002年