1
|
Víšková P, Ištvánková E, Ryneš J, Džatko Š, Loja T, Živković ML, Rigo R, El-Khoury R, Serrano-Chacón I, Damha MJ, González C, Mergny JL, Foldynová-Trantírková S, Trantírek L. In-cell NMR suggests that DNA i-motif levels are strongly depleted in living human cells. Nat Commun 2024; 15:1992. [PMID: 38443388 PMCID: PMC10914786 DOI: 10.1038/s41467-024-46221-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 02/13/2024] [Indexed: 03/07/2024] Open
Abstract
I-Motifs (iM) are non-canonical DNA structures potentially forming in the accessible, single-stranded, cytosine-rich genomic regions with regulatory roles. Chromatin, protein interactions, and intracellular properties seem to govern iM formation at sites with i-motif formation propensity (iMFPS) in human cells, yet their specific contributions remain unclear. Using in-cell NMR with oligonucleotide iMFPS models, we monitor iM-associated structural equilibria in asynchronous and cell cycle-synchronized HeLa cells at 37 °C. Our findings show that iMFPS displaying pHT < 7 under reference in vitro conditions occur predominantly in unfolded states in cells, while those with pHT > 7 appear as a mix of folded and unfolded states depending on the cell cycle phase. Comparing these results with previous data obtained using an iM-specific antibody (iMab) reveals that cell cycle-dependent iM formation has a dual origin, and iM formation concerns only a tiny fraction (possibly 1%) of genomic sites with iM formation propensity. We propose a comprehensive model aligning observations from iMab and in-cell NMR and enabling the identification of iMFPS capable of adopting iM structures under physiological conditions in living human cells. Our results suggest that many iMFPS may have biological roles linked to their unfolded states.
Collapse
Affiliation(s)
- Pavlína Víšková
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic
- National Centre for Biomolecular Research, Masaryk University, 625 00, Brno, Czech Republic
| | - Eva Ištvánková
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic
- National Centre for Biomolecular Research, Masaryk University, 625 00, Brno, Czech Republic
| | - Jan Ryneš
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic
| | - Šimon Džatko
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic
- Centre for Advanced Materials Application, Slovak Academy of Sciences, 845 11, Bratislava, Slovakia
| | - Tomáš Loja
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic
| | - Martina Lenarčič Živković
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic
- Slovenian NMR Centre, National Institute of Chemistry, SI-1000, Ljubljana, Slovenia
| | - Riccardo Rigo
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic
- Pharmaceutical and Pharmacological Sciences Department, University of Padova, 35131, Padova, Italy
| | - Roberto El-Khoury
- Department of Chemistry, McGill University, Montreal, QC, H3A0B8, Canada
| | - Israel Serrano-Chacón
- Instituto de Química Física 'Blas Cabrera', CSIC, C/Serrano 119, 28006, Madrid, Spain
| | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, QC, H3A0B8, Canada
| | - Carlos González
- Instituto de Química Física 'Blas Cabrera', CSIC, C/Serrano 119, 28006, Madrid, Spain
| | - Jean-Louis Mergny
- Institute of Biophysics, Czech Academy of Sciences, Brno, 612 00, Czech Republic
- Laboratoire d'Optique & Biosciences, Institut Polytechnique de Paris, Inserm, CNRS, Ecole Polytechnique, Palaiseau, 91120, France
| | - Silvie Foldynová-Trantírková
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic.
- Institute of Biophysics, Czech Academy of Sciences, Brno, 612 00, Czech Republic.
| | - Lukáš Trantírek
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic.
| |
Collapse
|
2
|
Khamari L, Mukherjee S. Deciphering the Nanoconfinement Effect on the Folding Pathway of c-MYC Promoter-Based Intercalated-Motif DNA by Single-Molecule Förster Resonance Energy Transfer. J Phys Chem Lett 2022; 13:8169-8176. [PMID: 36005552 DOI: 10.1021/acs.jpclett.2c01893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Intercalated-motif (i-motif) DNA formed by cytosine (C)-rich sequences has been considered a novel target in anticancer research. Interestingly, this type of noncanonical DNA structure is highly dynamic and can display several conformational polymorphisms based on the immediate surrounding environment. However, studies regarding the folding pathway of i-motifs having disease-specific sequences under a confined environment at physiological pH are relatively scarce. This thereby warrants more explorations that will decipher their structural and functional properties inside constrained media. Herein, using the single-molecule Förster Resonance Energy Transfer (smFRET) studies, for the first time, we have illustrated the conformational dynamics of c-MYC promoter-based i-motif structures at physiological pH inside microemulsions of different dimensions. We concluded that the folding of such motifs under confined space is not a direct transition between the random coil and i-motif conformations; rather it occurs through a partially folded intermediate, depending on the confined dimension.
Collapse
Affiliation(s)
- Laxmikanta Khamari
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462 066, Madhya Pradesh, India
| | - Saptarshi Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462 066, Madhya Pradesh, India
| |
Collapse
|
3
|
Liu W, Xu Y, Li X, Meng Y, Wang H, Liu C, Liu C, Wang L. A DNA G-quadruplex converts SOD1 into fibrillar aggregates. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2021.01.045] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
|
4
|
Wang Q, Gong Y, He Y, Xin Y, Lv N, Du X, Li Y, Jeong BR, Xu J. Genome engineering of Nannochloropsis with hundred-kilobase fragment deletions by Cas9 cleavages. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1148-1162. [PMID: 33719095 DOI: 10.1111/tpj.15227] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/21/2021] [Accepted: 03/01/2021] [Indexed: 06/12/2023]
Abstract
Industrial microalgae are promising photosynthetic cell factories, yet tools for large-scale targeted genome engineering are limited. Here for the model industrial oleaginous microalga Nannochloropsis oceanica, we established a method to precisely and serially delete large genome fragments of ~100 kb from its 30.01 Mb nuclear genome. We started by identifying the 'non-essential' chromosomal regions (i.e. low expression region or LER) based on minimal gene expression under N-replete and N-depleted conditions. The largest such LER (LER1) is ~98 kb in size, located near the telomere of the 502.09-kb-long Chromosome 30 (Chr 30). We deleted 81 kb and further distal and proximal deletions of up to 110 kb (21.9% of Chr 30) in LER1 by dual targeting the boundaries with the episome-based CRISPR/Cas9 system. The telomere-deletion mutants showed normal telomeres consisting of CCCTAA repeats, revealing telomere regeneration capability after losing the distal part of Chr 30. Interestingly, the deletions caused no significant alteration in growth, lipid production or photosynthesis (transcript-abundance change for < 3% genes under N depletion). We also achieved double-deletion of both LER1 and LER2 (from Chr 9) that total ~214 kb at maximum, which can result in slightly higher growth rate and biomass productivity than the wild-type. Therefore, loss of the large, yet 'non-essential' regions does not necessarily sacrifice important traits. Such serial targeted deletions of large genomic regions had not been previously reported in microalgae, and will accelerate crafting minimal genomes as chassis for photosynthetic production.
Collapse
Affiliation(s)
- Qintao Wang
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Qingdao National Laboratory of Marine Science and Technology, Qingdao, 266237, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanhai Gong
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Qingdao National Laboratory of Marine Science and Technology, Qingdao, 266237, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuehui He
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Qingdao National Laboratory of Marine Science and Technology, Qingdao, 266237, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yi Xin
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Qingdao National Laboratory of Marine Science and Technology, Qingdao, 266237, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Nana Lv
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Qingdao National Laboratory of Marine Science and Technology, Qingdao, 266237, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuefeng Du
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Qingdao National Laboratory of Marine Science and Technology, Qingdao, 266237, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yun Li
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Qingdao National Laboratory of Marine Science and Technology, Qingdao, 266237, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Byeong-Ryool Jeong
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, Korea
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Qingdao National Laboratory of Marine Science and Technology, Qingdao, 266237, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| |
Collapse
|
5
|
Matsumoto S, Sugimoto N. New Insights into the Functions of Nucleic Acids Controlled by Cellular Microenvironments. Top Curr Chem (Cham) 2021; 379:17. [PMID: 33782792 DOI: 10.1007/s41061-021-00329-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 03/11/2021] [Indexed: 12/11/2022]
Abstract
The right-handed double-helical B-form structure (B-form duplex) has been widely recognized as the canonical structure of nucleic acids since it was first proposed by James Watson and Francis Crick in 1953. This B-form duplex model has a monochronic and static structure and codes genetic information within a sequence. Interestingly, DNA and RNA can form various non-canonical structures, such as hairpin loops, left-handed helices, triplexes, tetraplexes of G-quadruplex and i-motif, and branched junctions, in addition to the canonical structure. The formation of non-canonical structures depends not only on sequence but also on the surrounding environment. Importantly, these non-canonical structures may exhibit a wide variety of biological roles by changing their structures and stabilities in response to the surrounding environments, which undergo vast changes at specific locations and at specific times in cells. Here, we review recent progress regarding the interesting behaviors and functions of nucleic acids controlled by molecularly crowded cellular conditions. New insights gained from recent studies suggest that nucleic acids not only code genetic information in sequences but also have unknown functions regarding their structures and stabilities through drastic structural changes in cellular environments.
Collapse
Affiliation(s)
- Saki Matsumoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan. .,Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan.
| |
Collapse
|
6
|
Školáková P, Badri Z, Foldynová-Trantírková S, Ryneš J, Šponer J, Fojtová M, Fajkus J, Marek R, Vorlíčková M, Mergny JL, Trantírek L. Composite 5-methylations of cytosines modulate i-motif stability in a sequence-specific manner: Implications for DNA nanotechnology and epigenetic regulation of plant telomeric DNA. Biochim Biophys Acta Gen Subj 2020; 1864:129651. [DOI: 10.1016/j.bbagen.2020.129651] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/23/2020] [Accepted: 05/28/2020] [Indexed: 12/14/2022]
|
7
|
Jonchhe S, Pandey S, Karna D, Pokhrel P, Cui Y, Mishra S, Sugiyama H, Endo M, Mao H. Duplex DNA Is Weakened in Nanoconfinement. J Am Chem Soc 2020; 142:10042-10049. [PMID: 32383870 PMCID: PMC7295077 DOI: 10.1021/jacs.0c01978] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
For proteins and DNA secondary structures such as G-quadruplexes and i-motifs, nanoconfinement can facilitate their folding and increase structural stabilities. However, the properties of the physiologically prevalent B-DNA duplex have not been elucidated inside the nanocavity. Using a 17-bp DNA duplex in the form of a hairpin stem, here, we probed folding and unfolding transitions of the hairpin DNA duplex inside a DNA origami nanocavity. Compared to the free solution, the DNA hairpin inside the nanocage with a 15 × 15 nm cross section showed a drastic decrease in mechanical (20 → 9 pN) and thermodynamic (25 → 6 kcal/mol) stabilities. Free energy profiles revealed that the activation energy of unzipping the hairpin DNA duplex decreased dramatically (28 → 8 kcal/mol), whereas the transition state moved closer to the unfolded state inside the nanocage. All of these indicate that nanoconfinement weakens the stability of the hairpin DNA duplex to an unexpected extent. In a DNA hairpin made of a stem that contains complementary telomeric G-quadruplex (GQ) and i-motif (iM) forming sequences, formation of the Hoogsteen base pairs underlining the GQ or iM is preferred over the Watson-Crick base pairs in the DNA hairpin. These results shed light on the behavior of DNA in nanochannels, nanopores, or nanopockets of various natural or synthetic machineries. It also elucidates an alternative pathway to populate noncanonical DNA over B-DNA in the cellular environment where the nanocavity is abundant.
Collapse
Affiliation(s)
- Sagun Jonchhe
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Shankar Pandey
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Deepak Karna
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Pravin Pokhrel
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Yunxi Cui
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Shubham Mishra
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
- Institute for Integrated Cell–Material Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
- Institute for Integrated Cell–Material Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Masayuki Endo
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
- Institute for Integrated Cell–Material Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Hanbin Mao
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
| |
Collapse
|
8
|
Takahashi S, Sugimoto N. Stability prediction of canonical and non-canonical structures of nucleic acids in various molecular environments and cells. Chem Soc Rev 2020; 49:8439-8468. [DOI: 10.1039/d0cs00594k] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This review provides the biophysicochemical background and recent advances in stability prediction of canonical and non-canonical structures of nucleic acids in various molecular environments and cells.
Collapse
Affiliation(s)
- Shuntaro Takahashi
- Frontier Institute for Biomolecular Engineering Research (FIBER)
- Konan University
- Kobe
- Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER)
- Konan University
- Kobe
- Japan
- Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST)
| |
Collapse
|
9
|
Školáková P, Renčiuk D, Palacký J, Krafčík D, Dvořáková Z, Kejnovská I, Bednářová K, Vorlíčková M. Systematic investigation of sequence requirements for DNA i-motif formation. Nucleic Acids Res 2019; 47:2177-2189. [PMID: 30715498 PMCID: PMC6412112 DOI: 10.1093/nar/gkz046] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 01/16/2019] [Accepted: 01/18/2019] [Indexed: 12/13/2022] Open
Abstract
The formation of intercalated motifs (iMs) - secondary DNA structures based on hemiprotonated C.C+ pairs in suitable cytosine-rich DNA sequences, is reflected by typical changes in CD and UV absorption spectra. By means of spectroscopic methods, electrophoresis, chemical modifications and other procedures, we characterized iM formation and stability in sequences with different cytosine block lengths interrupted by various numbers and types of nucleotides. Particular attention was paid to the formation of iMs at pH conditions close to neutral. We identified the optimal conditions and minimal requirements for iM formation in DNA sequences, and addressed gaps and inaccurate data interpretations in existing studies to specify principles of iM formation and modes of their folding.
Collapse
Affiliation(s)
- Petra Školáková
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Daniel Renčiuk
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Jan Palacký
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Daniel Krafčík
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 735/5, 625 00 Brno, Czech Republic
| | - Zuzana Dvořáková
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Iva Kejnovská
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Klára Bednářová
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Michaela Vorlíčková
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| |
Collapse
|
10
|
Masuda T, Shibuya Y, Arai S, Kobayashi S, Suzuki S, Kijima J, Itoh T, Sato Y, Nishizawa S, Yamaguchi A. Effect of Cavity Size of Mesoporous Silica on Short DNA Duplex Stability. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:5545-5550. [PMID: 29715034 DOI: 10.1021/acs.langmuir.8b00437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
We studied the stabilities of short (4- and 3-bp) DNA duplexes within silica mesopores modified with a positively charged trimethyl aminopropyl (TMAP) monolayer (BJH pore diameter 1.6-7.4 nm). The DNA fragments with fluorescent dye were introduced into the pores, and their fluorescence resonance energy transfer (FRET) response was measured to estimate the structuring energies of the short DNA duplexes under cryogenic conditions (temperature 233-323 K). The results confirmed the enthalpic stability gain of the duplex within size-matched pores (1.6 and 2.3 nm). The hybridization equilibrium constants found for the size-matched pores were 2 orders of magnitude larger than those for large pores (≥3.5 nm), and this size-matching effect for the enhanced duplex stability was explained by a tight electrostatic interaction between the duplex and the surface TMAP groups. These results indicate the requirement of the precise regulation of mesopore size to ensure the stabilization of hydrogen-bonded supramolecular assemblies.
Collapse
Affiliation(s)
- Tsubasa Masuda
- Institute of Quantum Beam Science , Ibaraki University , 2-1-1 Bunkyo , Mito , Ibaraki 310-8512 , Japan
| | - Yuuta Shibuya
- Institute of Quantum Beam Science , Ibaraki University , 2-1-1 Bunkyo , Mito , Ibaraki 310-8512 , Japan
| | - Shota Arai
- Institute of Quantum Beam Science , Ibaraki University , 2-1-1 Bunkyo , Mito , Ibaraki 310-8512 , Japan
| | - Sayaka Kobayashi
- Institute of Quantum Beam Science , Ibaraki University , 2-1-1 Bunkyo , Mito , Ibaraki 310-8512 , Japan
| | - Sotaro Suzuki
- Institute of Quantum Beam Science , Ibaraki University , 2-1-1 Bunkyo , Mito , Ibaraki 310-8512 , Japan
| | - Jun Kijima
- Institute of Quantum Beam Science , Ibaraki University , 2-1-1 Bunkyo , Mito , Ibaraki 310-8512 , Japan
| | - Tetsuji Itoh
- Research Institute for Chemical Process Technology , National Institute of Advanced Industrial Science and Technology (AIST) , Nigatake 4-2-1 , Sendai 983-8551 , Japan
| | - Yusuke Sato
- Department of Chemistry, Graduate School of Science , Tohoku University , Aoba-ku, Sendai 980-8578 , Japan
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science , Tohoku University , Aoba-ku, Sendai 980-8578 , Japan
| | - Akira Yamaguchi
- Institute of Quantum Beam Science , Ibaraki University , 2-1-1 Bunkyo , Mito , Ibaraki 310-8512 , Japan
| |
Collapse
|
11
|
Dzatko S, Krafcikova M, Hänsel‐Hertsch R, Fessl T, Fiala R, Loja T, Krafcik D, Mergny J, Foldynova‐Trantirkova S, Trantirek L. Evaluation of the Stability of DNA i-Motifs in the Nuclei of Living Mammalian Cells. Angew Chem Int Ed Engl 2018; 57:2165-2169. [PMID: 29266664 PMCID: PMC5820743 DOI: 10.1002/anie.201712284] [Citation(s) in RCA: 158] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Indexed: 11/21/2022]
Abstract
C-rich DNA has the capacity to form a tetra-stranded structure known as an i-motif. The i-motifs within genomic DNA have been proposed to contribute to the regulation of DNA transcription. However, direct experimental evidence for the existence of these structures in vivo has been missing. Whether i-motif structures form in complex environment of living cells is not currently known. Herein, using state-of-the-art in-cell NMR spectroscopy, we evaluate the stabilities of i-motif structures in the complex cellular environment. We show that i-motifs formed from naturally occurring C-rich sequences in the human genome are stable and persist in the nuclei of living human cells. Our data show that i-motif stabilities in vivo are generally distinct from those in vitro. Our results are the first to interlink the stability of DNA i-motifs in vitro with their stability in vivo and provide essential information for the design and development of i-motif-based DNA biosensors for intracellular applications.
Collapse
Affiliation(s)
- Simon Dzatko
- CEITEC-Central European Institute of TechnologyMasaryk UniversityBrno625 00Czech Republic
| | - Michaela Krafcikova
- CEITEC-Central European Institute of TechnologyMasaryk UniversityBrno625 00Czech Republic
| | - Robert Hänsel‐Hertsch
- Cancer Research (UK) Cambridge InstituteUniversity of CambridgeLi Ka Shing CentreCambridgeCB2 0REUK
| | - Tomas Fessl
- Faculty of ScienceUniversity of South Bohemia370 05Ceske BudejoviceCzech Republic
| | - Radovan Fiala
- CEITEC-Central European Institute of TechnologyMasaryk UniversityBrno625 00Czech Republic
| | - Tomas Loja
- CEITEC-Central European Institute of TechnologyMasaryk UniversityBrno625 00Czech Republic
| | - Daniel Krafcik
- CEITEC-Central European Institute of TechnologyMasaryk UniversityBrno625 00Czech Republic
| | - Jean‐Louis Mergny
- Université de Bordeaux, INSERM U1212, CNRS UMR 5320ARNA LaboratoryIECBPessacFrance
- Institute of BiophysicsAcademy of Sciences of the Czech Republic612 65BrnoCzech Republic
| | - Silvie Foldynova‐Trantirkova
- CEITEC-Central European Institute of TechnologyMasaryk UniversityBrno625 00Czech Republic
- Institute of BiophysicsAcademy of Sciences of the Czech Republic612 65BrnoCzech Republic
| | - Lukas Trantirek
- CEITEC-Central European Institute of TechnologyMasaryk UniversityBrno625 00Czech Republic
| |
Collapse
|
12
|
Dzatko S, Krafcikova M, Hänsel-Hertsch R, Fessl T, Fiala R, Loja T, Krafcik D, Mergny JL, Foldynova-Trantirkova S, Trantirek L. Evaluation of the Stability of DNA i-Motifs in the Nuclei of Living Mammalian Cells. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201712284] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Simon Dzatko
- CEITEC-Central European Institute of Technology; Masaryk University; Brno 625 00 Czech Republic
| | - Michaela Krafcikova
- CEITEC-Central European Institute of Technology; Masaryk University; Brno 625 00 Czech Republic
| | - Robert Hänsel-Hertsch
- Cancer Research (UK) Cambridge Institute; University of Cambridge; Li Ka Shing Centre Cambridge CB2 0RE UK
| | - Tomas Fessl
- Faculty of Science; University of South Bohemia; 370 05 Ceske Budejovice Czech Republic
| | - Radovan Fiala
- CEITEC-Central European Institute of Technology; Masaryk University; Brno 625 00 Czech Republic
| | - Tomas Loja
- CEITEC-Central European Institute of Technology; Masaryk University; Brno 625 00 Czech Republic
| | - Daniel Krafcik
- CEITEC-Central European Institute of Technology; Masaryk University; Brno 625 00 Czech Republic
| | - Jean-Louis Mergny
- Université de Bordeaux, INSERM U1212, CNRS UMR 5320; ARNA Laboratory; IECB; Pessac France
- Institute of Biophysics; Academy of Sciences of the Czech Republic; 612 65 Brno Czech Republic
| | - Silvie Foldynova-Trantirkova
- CEITEC-Central European Institute of Technology; Masaryk University; Brno 625 00 Czech Republic
- Institute of Biophysics; Academy of Sciences of the Czech Republic; 612 65 Brno Czech Republic
| | - Lukas Trantirek
- CEITEC-Central European Institute of Technology; Masaryk University; Brno 625 00 Czech Republic
| |
Collapse
|
13
|
Manna S, Panse CH, Sontakke VA, Sangamesh S, Srivatsan SG. Probing Human Telomeric DNA and RNA Topology and Ligand Binding in a Cellular Model by Using Responsive Fluorescent Nucleoside Probes. Chembiochem 2017; 18:1604-1615. [PMID: 28569423 PMCID: PMC5724660 DOI: 10.1002/cbic.201700283] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Indexed: 01/03/2023]
Abstract
The development of biophysical systems that enable an understanding of the structure and ligand-binding properties of G-quadruplex (GQ)-forming nucleic acid sequences in cells or models that mimic the cellular environment would be highly beneficial in advancing GQ-directed therapeutic strategies. Herein, the establishment of a biophysical platform to investigate the structure and recognition properties of human telomeric (H-Telo) DNA and RNA repeats in a cell-like confined environment by using conformation-sensitive fluorescent nucleoside probes and a widely used cellular model, bis(2-ethylhexyl) sodium sulfosuccinate reverse micelles (RMs), is described. The 2'-deoxy and ribonucleoside probes, composed of a 5-benzofuran uracil base analogue, faithfully report the aqueous micellar core through changes in their fluorescence properties. The nucleoside probes incorporated into different loops of H-Telo DNA and RNA oligonucleotide repeats are minimally perturbing and photophysically signal the formation of respective GQ structures in both aqueous buffer and RMs. Furthermore, these sensors enable a direct comparison of the binding affinity of a ligand to H-Telo DNA and RNA GQ structures in the bulk and confined environment of RMs. These results demonstrate that this combination of a GQ nucleoside probe and easy-to-handle RMs could provide new opportunities to study and devise screening-compatible assays in a cell-like environment to discover GQ binders of clinical potential.
Collapse
Affiliation(s)
- Sudeshna Manna
- Department of ChemistryIndian Institute of Science Education and Research (IISER)Dr. Homi Bhabha RoadPune411008India
| | - Cornelia H. Panse
- Department of ChemistryIndian Institute of Science Education and Research (IISER)Dr. Homi Bhabha RoadPune411008India
| | - Vyankat A. Sontakke
- Department of ChemistryIndian Institute of Science Education and Research (IISER)Dr. Homi Bhabha RoadPune411008India
| | - Sarangamath Sangamesh
- Department of ChemistryIndian Institute of Science Education and Research (IISER)Dr. Homi Bhabha RoadPune411008India
| | - Seergazhi G. Srivatsan
- Department of ChemistryIndian Institute of Science Education and Research (IISER)Dr. Homi Bhabha RoadPune411008India
| |
Collapse
|
14
|
Nakano SI, Sugimoto N. Model studies of the effects of intracellular crowding on nucleic acid interactions. MOLECULAR BIOSYSTEMS 2017; 13:32-41. [PMID: 27819369 DOI: 10.1039/c6mb00654j] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Molecular interactions and reactions in living cells occur with high concentrations of background molecules and ions. Many research studies have shown that intracellular molecules have characteristics different from those obtained using simple aqueous solutions. To better understand the behavior of biomolecules in intracellular environments, biophysical experiments were conducted under cell-mimicking conditions in a test tube. It has been shown that the molecular environments at the physiological level of macromolecular crowding, spatial confinement, water activity and dielectric constant, have significant effects on the interactions of DNA and RNA for hybridization, higher-order folding, and catalytic activity. The experimental approaches using in vitro model systems are useful to reveal the origin of the environmental effects and to bridge the gap between the behaviors of nucleic acids in vitro and in vivo. This paper highlights the model experiments used to evaluate the influences of intracellular environment on nucleic acid interactions.
Collapse
Affiliation(s)
- Shu-Ichi Nakano
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan.
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan. and Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| |
Collapse
|
15
|
|
16
|
Kar B, Bardhan S, Ghosh P, Ganguly B, Kundu K, Sarkar S, Paul BK, Das S. A Fast and Additive Free C-C Homo/Cross-Coupling Reaction in Reverse Micelle: An Understanding of Role of Surfactant, Water Content and Base on the Product Yield and Reaction Site. ChemistrySelect 2017. [DOI: 10.1002/slct.201601986] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Barnali Kar
- Department of Chemistry; University of North Bengal; Darjeeling 734 013 India
| | - Soumik Bardhan
- Department of Chemistry; University of North Bengal; Darjeeling 734 013 India
| | - Prasanjit Ghosh
- Department of Chemistry; University of North Bengal; Darjeeling 734 013 India
| | - Bhaskar Ganguly
- Department of Chemistry; University of North Bengal; Darjeeling 734 013 India
| | - Kaushik Kundu
- Surface and Colloid Science Laboratory, Geological Studies Unit; Indian Statistical Institute; Kolkata 700 108 India
- Department Inorganic and Physical Chemistry; Indian Institute of Science; Bangalore- 560012 India
| | - Sonali Sarkar
- Department of Chemistry; University of North Bengal; Darjeeling 734 013 India
| | - Bidyut Kumar Paul
- Surface and Colloid Science Laboratory, Geological Studies Unit; Indian Statistical Institute; Kolkata 700 108 India
| | - Sajal Das
- Department of Chemistry; University of North Bengal; Darjeeling 734 013 India
| |
Collapse
|
17
|
Kumar H, Devaraji V, Prasath R, Jadhao M, Joshi R, Bhavana P, Ghosh SK. Groove binding mediated structural modulation and DNA cleavage by quinoline appended chalcone derivative. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 151:605-615. [PMID: 26163783 DOI: 10.1016/j.saa.2015.07.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 06/30/2015] [Accepted: 07/01/2015] [Indexed: 06/04/2023]
Abstract
The present study embodies the detail DNA binding interaction of a potential bioactive quinoline appended chalcone derivative (E)-3-(anthracen-10-yl)-1-(6,8-dibromo-2-methylquinolin-3-yl)prop-2-en-1-one (ADMQ) with calf thymus DNA (ctDNA) and its consequences by UV-Vis absorption, steady state fluorescence spectroscopy, fluorescence anisotropy, circular dichromism, helix melting, agarose gel electrophoresis, molecular docking, Induced Fit Docking (IFD) and molecular dynamics (MD) simulation. The UV-Vis absorption and fluorescence study reveal that the molecule undergoes considerable interaction with the nucleic acid. The control KI quenching experiment shows the lesser accessibility of ADMQ molecule to the ionic quencher (I(-)) in presence of ctDNA as compared to the bulk aqueous phase. Insignificant change in helix melting temperature as well as in circular dichromism (CD) spectra points toward non-covalent groove binding interaction. The moderate rotational confinement of this chalcone derivative (anisotropy=0.106) trapped in the nucleic acid environment, the comparative displacement assay with well-known minor groove binder Hoechst 33258 and intercalator Ethidium Bromide establishes the minor groove binding interactions of the probe molecule. Molecular docking, IFD and MD simulation reveal that the DNA undergoes prominent morphological changes in terms of helix unwinding and bending to accommodate ADMQ in a crescent shape at an angle of 110° in a sequence specific manner. During interaction, ADMQ rigidifies and bends the sugar phosphate backbone of the nucleic acid and thereby shortens its overall length by 3.02Å. Agarose gel electrophoresis experiment with plasmid pBR 322 reveals that the groove binded ADMQ result in a concentration dependent cleavage of plasmid DNA into its supercoiled and nicked circular form. The consolidated spectroscopic research described herein provides quantitative insight into the interaction of a heterocyclic chalcone derivative with relevant target nucleic acid, which may be useful for the future research on chalcone based therapeutic agents.
Collapse
Affiliation(s)
- Himank Kumar
- Department of Chemistry, Visvesvaraya National Institute of Technology, Nagpur, Maharashtra 440010, India
| | - Vinod Devaraji
- Department of Pharmaceutical Chemistry, College of Pharmacy, Madras Medical College, Chennai 600003, India
| | - Rangaraj Prasath
- Department of Chemistry, BITS-Pilani, K.K. Birla Goa Campus, Zuarinagar, Goa 403726, India
| | - Manojkumar Jadhao
- Department of Chemistry, Visvesvaraya National Institute of Technology, Nagpur, Maharashtra 440010, India
| | - Ritika Joshi
- Department of Chemistry, Visvesvaraya National Institute of Technology, Nagpur, Maharashtra 440010, India
| | - Purushothaman Bhavana
- Department of Chemistry, BITS-Pilani, K.K. Birla Goa Campus, Zuarinagar, Goa 403726, India
| | - Sujit Kumar Ghosh
- Department of Chemistry, Visvesvaraya National Institute of Technology, Nagpur, Maharashtra 440010, India.
| |
Collapse
|
18
|
Pramanik S, Tateishi-Karimata H, Sugimoto N. Organelle-mimicking liposome dissociates G-quadruplexes and facilitates transcription. Nucleic Acids Res 2014; 42:12949-59. [PMID: 25336617 PMCID: PMC4227800 DOI: 10.1093/nar/gku998] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Important biological reactions involving nucleic acids occur near the surface of membranes such as the nuclear membrane (NM) and rough endoplasmic reticulum (ER); however, the interactions between biomembranes and nucleic acids are poorly understood. We report here that transcription was facilitated in solution with liposomes, which mimic a biomembrane surface, relative to the reaction in a homogeneous aqueous solution when the template was able to form a G-quadruplex. The G-quadruplex is known to be an inhibitor of transcription, but the stability of the G-quadruplex was decreased at the liposome surface because of unfavourable enthalpy. The destabilization of the G-quadruplex was greater at the surface of NM- and ER-mimicking liposomes than at the surfaces of liposomes designed to mimic other organelles. Thermodynamic analyses revealed that the G-rich oligonucleotides adopted an extended structure at the liposome surface, whereas in solution the compact G-quadruplex was formed. Our data suggest that changes in structure and stability of nucleic acids regulate biological reactions at membrane surfaces.
Collapse
Affiliation(s)
- Smritimoy Pramanik
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Hisae Tateishi-Karimata
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| |
Collapse
|
19
|
Ho MC, Chang CW. Cationic and anionic reverse micelles as the molecular crowding container for G-quadruplex structure. RSC Adv 2014. [DOI: 10.1039/c4ra02141j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The d[AG3(T2AG3)3] sequence shows different molecular crowding effects in AOT and CTAB reverse micelles (RMs). Our result indicates that the CTAB RMs are ideal molecular crowding containers for G-quadruplex structure.
Collapse
Affiliation(s)
- Meng-Chieh Ho
- Department of Chemistry
- National Changhua University of Education
- Changhua 50058, Taiwan
| | - Chih-Wei Chang
- Department of Chemistry
- National Changhua University of Education
- Changhua 50058, Taiwan
| |
Collapse
|
20
|
Sugimoto N. Noncanonical structures and their thermodynamics of DNA and RNA under molecular crowding: beyond the Watson-Crick double helix. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014; 307:205-73. [PMID: 24380597 DOI: 10.1016/b978-0-12-800046-5.00008-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
How does molecular crowding affect the stability of nucleic acid structures inside cells? Water is the major solvent component in living cells, and the properties of water in the highly crowded media inside cells differ from that in buffered solution. As it is difficult to measure the thermodynamic behavior of nucleic acids in cells directly and quantitatively, we recently developed a cell-mimicking system using cosolutes as crowding reagents. The influences of molecular crowding on the structures and thermodynamics of various nucleic acid sequences have been reported. In this chapter, we discuss how the structures and thermodynamic properties of nucleic acids differ under various conditions such as highly crowded environments, compartment environments, and in the presence of ionic liquids, and the major determinants of the crowding effects on nucleic acids are discussed. The effects of molecular crowding on the activities of ribozymes and riboswitches on noncanonical structures of DNA- and RNA-like quadruplexes that play important roles in transcription and translation are also described.
Collapse
Affiliation(s)
- Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER) and Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, Japan.
| |
Collapse
|
21
|
Nakano SI, Miyoshi D, Sugimoto N. Effects of molecular crowding on the structures, interactions, and functions of nucleic acids. Chem Rev 2013; 114:2733-58. [PMID: 24364729 DOI: 10.1021/cr400113m] [Citation(s) in RCA: 367] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Shu-ichi Nakano
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST) and Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University , 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | | | | |
Collapse
|
22
|
Fujita H, Imaizumi Y, Kasahara Y, Kitadume S, Ozaki H, Kuwahara M, Sugimoto N. Structural and affinity analyses of g-quadruplex DNA aptamers for camptothecin derivatives. Pharmaceuticals (Basel) 2013; 6:1082-93. [PMID: 24276420 PMCID: PMC3818834 DOI: 10.3390/ph6091082] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 08/11/2013] [Accepted: 08/26/2013] [Indexed: 01/13/2023] Open
Abstract
We recently selected DNA aptamers that bind to camptothecin (CPT) and CPT derivatives from a 70-mer oligodeoxyribonucleotide (ODN) library using the Systematic Evolution of Ligands by EXponential enrichment (SELEX) method. The target-binding activity of the obtained 70-mer CPT-binding DNA aptamer, termed CA-70, which contains a 16-mer guanine (G)-core motif (G3TG3TG3T2G3) that forms a three-tiered G-quadruplex, was determined using fluorescence titration. In this study, truncated fragments of CA-70 that all have the G-core motif, CA-40, -20, -19, -18A, -18B, -17, and -16, were carefully analyzed. We found that CA-40 retained the target-binding activity, whereas CA-20, -19, and -18B exhibited little or no binding activities. Further, not only CA-18A but also the shorter length fragments CA-17 and -16 clearly retained the binding activity, indicating that tail strands of the G-quadruplex structure can significantly affect the target binding of G-quadruplex DNA aptamers. Further analyses using circular dichroism (CD) spectroscopy and fluorescence polarization (FP) assay were conducted to investigate the structure and affinity of G-quadruplex DNA aptamers.
Collapse
Affiliation(s)
- Hiroto Fujita
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan.
| | | | | | | | | | | | | |
Collapse
|
23
|
Endoh T, Kawasaki Y, Sugimoto N. Translational halt during elongation caused by G-quadruplex formed by mRNA. Methods 2013; 64:73-8. [PMID: 23747335 DOI: 10.1016/j.ymeth.2013.05.026] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 05/28/2013] [Accepted: 05/30/2013] [Indexed: 12/29/2022] Open
Abstract
mRNA forms various secondary and tertiary structures that affect gene expression. Although structures formed in the untranslated regions (UTRs) of mRNAs that inhibit translation have been characterized, stable mRNA structures in open reading frames (ORFs) may also cause translational halt or slow translation elongation. We previously established a method, termed a synchronized translation assay, that enables time course analysis of single turnover translation elongation. In this method, translation initiation, which is a rate determining step of the translation procedure, can be ignored because all ribosomes are synchronized on a specific position of mRNA before translation elongation is restarted from this position. In this paper, we used the synchronized translation assay to evaluate the effects of a G-quadruplex structure located at various positions within the mRNA ORF on translational halt.
Collapse
Affiliation(s)
- Tamaki Endoh
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, Kobe, Japan
| | | | | |
Collapse
|
24
|
Endoh T, Kawasaki Y, Sugimoto N. Stability of RNA quadruplex in open reading frame determines proteolysis of human estrogen receptor α. Nucleic Acids Res 2013; 41:6222-31. [PMID: 23620292 PMCID: PMC3695533 DOI: 10.1093/nar/gkt286] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
mRNAs encodes not only information that determines amino acid sequences but also additional layers of information that regulate the translational processes. Notably, translational halt at specific position caused by rare codons or stable RNA structures is one of the potential factors regulating the protein expressions and structures. In this study, a quadruplex-forming potential (QFP) sequence derived from an open reading frame of human estrogen receptor α (hERα) mRNA was revealed to form parallel G-quadruplex and halt the translation elongation in vitro. Moreover, when the full-length hERα and variants containing synonymous mutations in the QFP sequence were expressed in cells, translation products cleaved at specific site were observed in quantities dependent on the thermodynamic stability of the G-quadruplexes. These results suggest that the G-quadruplex formation in the coding region of the hERα mRNA impacts folding and proteolysis of hERα protein by slowing down or temporarily stalling the translation elongation.
Collapse
Affiliation(s)
- Tamaki Endoh
- Frontier Institute for Biomolecular Engineering Research, Konan University, 7-1-20 Minatojimaminamimachi, Kobe 650-0047, Japan
| | | | | |
Collapse
|
25
|
Suppression of Gene Expression by G-Quadruplexes in Open Reading Frames Depends on G-Quadruplex Stability. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201300058] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
|
26
|
Endoh T, Kawasaki Y, Sugimoto N. Suppression of gene expression by G-quadruplexes in open reading frames depends on G-quadruplex stability. Angew Chem Int Ed Engl 2013; 52:5522-6. [PMID: 23589400 DOI: 10.1002/anie.201300058] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 03/04/2013] [Indexed: 12/29/2022]
Affiliation(s)
- Tamaki Endoh
- Frontier Institute for Biomolecular Engineering Research, Konan University, 7-1-20 Minatojima-minamimachi, Kobe 650-0047, Japan
| | | | | |
Collapse
|
27
|
Liu G, Feng DQ, Chen T, Li D, Zheng W. DNA-templated formation of silver nanoclusters as a novel light-scattering sensor for label-free copper ions detection. ACTA ACUST UNITED AC 2012. [DOI: 10.1039/c2jm35236b] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|