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Tanabe K, Miyazaki K, Umeno H, Takemoto M, Nakano S. Basic protein- and peptide-induced stabilization of long-loop DNA G-guadruplexes. Biochimie 2024; 219:110-117. [PMID: 37972915 DOI: 10.1016/j.biochi.2023.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/05/2023] [Accepted: 11/09/2023] [Indexed: 11/19/2023]
Abstract
The human genome contains many G-quadruplex-forming sequences, including sequences containing long single-stranded loops that are believed to be unfavorable for G-quadruplex formation. The intracellular environment of biological cells is crowded with proteins with charged surfaces. Understanding the effects of protein-rich environments is important for understanding the formation of G-quadruplexes in an intracellular environment. In this study, we investigated the structural stability of DNA G-quadruplexes in the presence of several types of globular proteins (lysozyme, cytochrome c, bovine serum albumin, myoglobin, histone proteins, and serum proteins), unstructured polypeptides (protamine and poly-l-lysine), and oligopeptides (RGG/RG-domain peptides and short repeated peptides). Thermal melting studies of G-quadruplex-forming oligonucleotides derived from the human telomeric repeat sequence revealed that environments containing high concentrations of proteins and peptides differently affected the G-quadruplex stability according to their loop lengths. We found that weak electrostatic interactions of G-quadruplex loops with basic proteins and peptides improved the stability of long-loop G-quadruplexes and the interactions were strengthened under crowded conditions simulated by dextran. The comparison of the effects of different types of proteins and peptides indicated that excluded volume interactions and structural flexibility of both DNA and polypeptide chains influenced the efficiency of their interactions. This study provides insights into long-loop G-quadruplex stability in a crowded intracellular environment and the recognition of G-quadruplexes by arginine-rich domains of G-quadruplex-binding proteins.
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Affiliation(s)
- Kazuya Tanabe
- 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
| | - Kouichi Miyazaki
- 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
| | - Hikari Umeno
- 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
| | - Marina Takemoto
- 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
| | - S 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.
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Chen YW, Satange R, Wu PC, Jhan CR, Chang CK, Chung KR, Waring MJ, Lin SW, Hsieh LC, Hou MH. Co II(Chromomycin)₂ Complex Induces a Conformational Change of CCG Repeats from i-Motif to Base-Extruded DNA Duplex. Int J Mol Sci 2018; 19:ijms19092796. [PMID: 30227633 PMCID: PMC6164834 DOI: 10.3390/ijms19092796] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 09/07/2018] [Indexed: 01/07/2023] Open
Abstract
We have reported the propensity of a DNA sequence containing CCG repeats to form a stable i-motif tetraplex structure in the absence of ligands. Here we show that an i-motif DNA sequence may transition to a base-extruded duplex structure with a GGCC tetranucleotide tract when bound to the (CoII)-mediated dimer of chromomycin A3, CoII(Chro)₂. Biophysical experiments reveal that CCG trinucleotide repeats provide favorable binding sites for CoII(Chro)₂. In addition, water hydration and divalent metal ion (CoII) interactions also play a crucial role in the stabilization of CCG trinucleotide repeats (TNRs). Our data furnish useful structural information for the design of novel therapeutic strategies to treat neurological diseases caused by repeat expansions.
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Affiliation(s)
- Yu-Wen Chen
- Institute of Biotechnology, National Chung-Hsing University, Taichung 402, Taiwan.
| | - Roshan Satange
- Institute of Genomics and Bioinformatics, National Chung-Hsing University, Taichung 402, Taiwan.
- Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung 402, Taiwan.
| | - Pei-Ching Wu
- Institute of Genomics and Bioinformatics, National Chung-Hsing University, Taichung 402, Taiwan.
| | - Cyong-Ru Jhan
- Department of Life Sciences, National Chung-Hsing University, Taichung 402, Taiwan.
| | - Chung-Ke Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan.
| | - Kuang-Ren Chung
- Department of Plant Pathology, National Chung-Hsing University, Taichung 402, Taiwan.
| | - Michael J Waring
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK.
| | - Sheng-Wei Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan.
| | - Li-Ching Hsieh
- Institute of Genomics and Bioinformatics, National Chung-Hsing University, Taichung 402, Taiwan.
- Advanced Plant Biotechnology Center, National Chung-Hsing University, Taichung 402, Taiwan.
| | - Ming-Hon Hou
- Institute of Biotechnology, National Chung-Hsing University, Taichung 402, Taiwan.
- Institute of Genomics and Bioinformatics, National Chung-Hsing University, Taichung 402, Taiwan.
- Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung 402, Taiwan.
- Department of Life Sciences, National Chung-Hsing University, Taichung 402, Taiwan.
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de Castro ACH, Kochi LT, Moço ACR, Coimbra RS, Oliveira GC, Cuadros-Orellana S, Madurro JM, Brito-Madurro AG. A new genosensor for meningococcal meningitis diagnosis using biological samples. J Solid State Electrochem 2018. [DOI: 10.1007/s10008-018-3940-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Wei Y, Liu R, Wang Y, Zhao Y, Cai Z, Gao X. Hairpin oligonucleotides anchored terbium ion: a fluorescent probe to specifically detect lead(II) at sub-nM levels. Analyst 2014; 138:2302-7. [PMID: 23446487 DOI: 10.1039/c3an36795a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A terbium based fluorescent probe was synthesized by coordinating terbium ions with a designed oligonucleotides (5'-ATATGGGGGATAT-3', termed GH5). GH5 improved the fluorescence of terbium ions by four orders of magnitude. The fluorescence enhancement of terbium ions by different oligonucleotides sequences indicated that the polyguanine loop of the hairpin GH5 is key to enhance terbium ion emission. The quantum yield of Tb-GH5 probe was 10.5% and the probe was photo-stable. The result of conductivity titration indicated that the stoichiometry of the probe is 3.5 Tb: 1 GH5, which is confirmed by fluorescence titration. This probe had high sensitivity and specificity for the detection of lead ions. The fluorescence intensity of this probe was linear with respect to lead concentration over a range 0.3-2.1 nM (R(2) = 0.99). The limit of detection for lead ions was 0.1 nM at a signal-to-noise ratio of 3.
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Affiliation(s)
- Yueteng Wei
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China
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Cranford SW. Thermal stability of idealized folded carbyne loops. NANOSCALE RESEARCH LETTERS 2013; 8:490. [PMID: 24252156 PMCID: PMC3842786 DOI: 10.1186/1556-276x-8-490] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 11/07/2013] [Indexed: 06/02/2023]
Abstract
Self-unfolding items provide a practical convenience, wherein ring-like frames are contorted into a state of equilibrium and subsequently pop up' or deploy when perturbed from a folded structure. Can the same process be exploited at the molecular scale? At the limiting scale is a closed chain of single atoms, used here to investigate the limits of stability of such folded ring structures via full atomistic molecular dynamics. Carbyne is a one-dimensional carbon allotrope composed of sp-hybridized carbon atoms. Here, we explore the stability of idealized carbyne loops as a function of chain length, curvature, and temperature, and delineate an effective phase diagram between folded and unfolded states. We find that while overall curvature is reduced, in addition to torsional and self-adhesive energy barriers, a local increase in curvature results in the largest impedance to unfolding.
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Affiliation(s)
- Steven W Cranford
- Laboratory of Nanotechnology in Civil Engineering, Department of Civil and Environmental Engineering, Northeastern University, Boston, MA 02115, USA.
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Lo YS, Tseng WH, Chuang CY, Hou MH. The structural basis of actinomycin D-binding induces nucleotide flipping out, a sharp bend and a left-handed twist in CGG triplet repeats. Nucleic Acids Res 2013; 41:4284-94. [PMID: 23408860 PMCID: PMC3627577 DOI: 10.1093/nar/gkt084] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The potent anticancer drug actinomycin D (ActD) functions by intercalating into DNA at GpC sites, thereby interrupting essential biological processes including replication and transcription. Certain neurological diseases are correlated with the expansion of (CGG)n trinucleotide sequences, which contain many contiguous GpC sites separated by a single G:G mispair. To characterize the binding of ActD to CGG triplet repeat sequences, the structural basis for the strong binding of ActD to neighbouring GpC sites flanking a G:G mismatch has been determined based on the crystal structure of ActD bound to ATGCGGCAT, which contains a CGG triplet sequence. The binding of ActD molecules to GCGGC causes many unexpected conformational changes including nucleotide flipping out, a sharp bend and a left-handed twist in the DNA helix via a two site-binding model. Heat denaturation, circular dichroism and surface plasmon resonance analyses showed that adjacent GpC sequences flanking a G:G mismatch are preferred ActD-binding sites. In addition, ActD was shown to bind the hairpin conformation of (CGG)16 in a pairwise combination and with greater stability than that of other DNA intercalators. Our results provide evidence of a possible biological consequence of ActD binding to CGG triplet repeat sequences.
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Affiliation(s)
- Yu-Sheng Lo
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
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Béhar G, Bellinzoni M, Maillasson M, Paillard-Laurance L, Alzari PM, He X, Mouratou B, Pecorari F. Tolerance of the archaeal Sac7d scaffold protein to alternative library designs: characterization of anti-immunoglobulin G Affitins. Protein Eng Des Sel 2013; 26:267-75. [PMID: 23315487 DOI: 10.1093/protein/gzs106] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Engineered protein scaffolds have received considerable attention as alternatives to antibodies in both basic and applied research, as they can offer superior biophysical properties often associated with a simpler molecular organization. Sac7d has been demonstrated as an effective scaffold for molecular recognition. Here, we used the initial L1 'flat surface' library constructed by randomization of 14 residues, to identify ligands specific for human immunoglobulin G. To challenge the plasticity of the Sac7d protein scaffold, we designed the alternative L2 'flat surface & loops' library whereof only 10 residues are randomized. Representative binders (Affitins) of the two libraries exhibited affinities in the low nanomolar range and were able to recognize different epitopes within human immunoglobulin G. These Affitins were stable up to pH 12 while largely conserving other favorable properties of Sac7d protein, such as high expression yields in Escherichia coli, solubility, thermal stability up to 80.7°C, and acidic stability (pH 0). In agreement with our library designs, mutagenesis study revealed two distinct binding areas, one including loops. Together, our results indicate that the Sac7d scaffold tolerates alternative library designs, which further expands the diversity of Affitins and may provide a general way to create tailored affinity tools for demanding applications.
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Affiliation(s)
- Ghislaine Béhar
- Université de Nantes, UMR CNRS 6204, Ingénierie de la reconnaissance, F-44322 Nantes, France
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Wang SY, Lee YL, Lai YH, Chen JJW, Wu WL, Yuann JMP, Su WL, Chuang SM, Hou MH. Spermine attenuates the action of the DNA intercalator, actinomycin D, on DNA binding and the inhibition of transcription and DNA replication. PLoS One 2012; 7:e47101. [PMID: 23144800 PMCID: PMC3493566 DOI: 10.1371/journal.pone.0047101] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Accepted: 09/10/2012] [Indexed: 12/23/2022] Open
Abstract
The anticancer activity of DNA intercalators is related to their ability to intercalate into the DNA duplex with high affinity, thereby interfering with DNA replication and transcription. Polyamines (spermine in particular) are almost exclusively bound to nucleic acids and are involved in many cellular processes that require nucleic acids. Until now, the effects of polyamines on DNA intercalator activities have remained unclear because intercalation is the most important mechanism employed by DNA-binding drugs. Herein, using actinomycin D (ACTD) as a model, we have attempted to elucidate the effects of spermine on the action of ACTD, including its DNA-binding ability, RNA and DNA polymerase interference, and its role in the transcription and replication inhibition of ACTD within cells. We found that spermine interfered with the binding and stabilization of ACTD to DNA. The presence of increasing concentrations of spermine enhanced the transcriptional and replication activities of RNA and DNA polymerases, respectively, in vitro treated with ActD. Moreover, a decrease in intracellular polyamine concentrations stimulated by methylglyoxal-bis(guanylhydrazone) (MGBG) enhanced the ACTD-induced inhibition of c-myc transcription and DNA replication in several cancer cell lines. The results indicated that spermine attenuates ACTD binding to DNA and its inhibition of transcription and DNA replication both in vitro and within cells. Finally, a synergistic antiproliferative effect of MGBG and ACTD was observed in a cell viability assay. Our findings will be of significant relevance to future developments in combination with cancer therapy by enhancing the anticancer activity of DNA interactors through polyamine depletion.
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Affiliation(s)
- Sheng-Yu Wang
- Department of Life Science, National Chung Hsing University, Taichung, Taiwan
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan
| | - Yueh-Luen Lee
- National Institute of Cancer Research, National Health Research Institutes, Miaoli, Taiwan
| | - Yi-Hua Lai
- Institute of Biomedical Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Jeremy J. W. Chen
- Institute of Biomedical Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Wen-Lin Wu
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan
| | - Jeu-Ming P. Yuann
- Department of Biotechnology, Ming Chuan University, Taoyuan County, Taiwan
| | - Wang-Lin Su
- Department of Life Science, National Chung Hsing University, Taichung, Taiwan
| | - Show-Mei Chuang
- Institute of Biomedical Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Ming-Hon Hou
- Department of Life Science, National Chung Hsing University, Taichung, Taiwan
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan
- * E-mail:
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9
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Hsu CW, Kuo CF, Chuang SM, Hou MH. Elucidation of the DNA-interacting properties and anticancer activity of a Ni(II)-coordinated mithramycin dimer complex. Biometals 2012; 26:1-12. [DOI: 10.1007/s10534-012-9589-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 10/03/2012] [Indexed: 02/03/2023]
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10
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Hsu CW, Chuang SM, Wu WL, Hou MH. The crucial role of divalent metal ions in the DNA-acting efficacy and inhibition of the transcription of dimeric chromomycin A3. PLoS One 2012; 7:e43792. [PMID: 22984445 PMCID: PMC3440418 DOI: 10.1371/journal.pone.0043792] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2012] [Accepted: 07/24/2012] [Indexed: 12/11/2022] Open
Abstract
Chromomycin A3 (Chro) is capable of forming a stable dimeric complex via chelation with Ni(II), Fe(II) and Co(II). According to the circular dichroism study, the dimer conformations are significantly different among the Fe(II)-, Co(II)-, and Ni(II)-containing dimeric Chro complexes; however, the dimer conformations were preserved at high temperatures. Furthermore, we conducted a systematic study to determine the effects of these divalent metal ions on the DNA-acting efficacy of dimeric Chro, including its DNA-binding affinity, DNA stabilization capacity, DNA cleavage activity, and the inhibition of transcription both in vitro and within cells. Kinetic analyses using surface plasmon resonance (SPR) showed that NiII(Chro)2 exhibited the highest Ka with a value of 1.26×107 M−1, which is approximately 1.6- and 3.7-fold higher than the Ka values obtained for CoII(Chro)2 and FeII(Chro)2, respectively. The Tm and ΔG values for the DNA duplex increased after the addition of drug complexes in the following order: NiII(Chro)2>CoII(Chro)2>FeII(Chro)2. In the DNA integrity assays, the DNA cleavage rate of CoII(Chro)2 (1.2×10−3 s−1) is higher than those of FeII(Chro)2 and NiII(Chro)2, which were calculated to be 1×10−4 and 3.1×10−4 s−1, respectively. Consistent with the SPR and UV melting results, NiII(Chro)2 possesses the highest inhibitory effect on in vitro transcription and c-myc transcription within cells compared to CoII(Chro)2 and FeII(Chro)2. By comparing the cytotoxicity among CoII(Chro)2, FeII(Chro)2, and NiII(Chro)2 to several cancer cell lines, our studies concluded that NiII(Chro)2 displayed more potential antitumor activities than CoII(Chro)2 and FeII(Chro)2 did due to its higher DNA-acting efficacy. Changes to the divalent metal ions in the dimeric Chro complexes have been correlated with improved anticancer profiles. The availability of new metal derivatives of Chro may introduce new possibilities for exploiting the unique properties of this class of compounds for therapeutic applications.
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Affiliation(s)
- Chun-Wei Hsu
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan
| | - Show-Mei Chuang
- Institute of Biomedical Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Wen-Ling Wu
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Department of Life Science, National Chung Hsing University, Taichung, Taiwan
- * E-mail:
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