1
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Bhatt U, Cucchiarini A, Luo Y, Evans CW, Mergny JL, Iyer KS, Smith NM. Preferential formation of Z-RNA over intercalated motifs in long noncoding RNA. Genome Res 2024; 34:217-230. [PMID: 38355305 PMCID: PMC10984386 DOI: 10.1101/gr.278236.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 01/31/2024] [Indexed: 02/16/2024]
Abstract
Secondary structure is a principal determinant of lncRNA function, predominantly regarding scaffold formation and interfaces with target molecules. Noncanonical secondary structures that form in nucleic acids have known roles in regulating gene expression and include G-quadruplexes (G4s), intercalated motifs (iMs), and R-loops (RLs). In this paper, we used the computational tools G4-iM Grinder and QmRLFS-finder to predict the formation of each of these structures throughout the lncRNA transcriptome in comparison to protein-coding transcripts. The importance of the predicted structures in lncRNAs in biological contexts was assessed by combining our results with publicly available lncRNA tissue expression data followed by pathway analysis. The formation of predicted G4 (pG4) and iM (piM) structures in select lncRNA sequences was confirmed in vitro using biophysical experiments under near-physiological conditions. We find that the majority of the tested pG4s form highly stable G4 structures, and identify many previously unreported G4s in biologically important lncRNAs. In contrast, none of the piM sequences are able to form iM structures, consistent with the idea that RNA is unable to form stable iMs. Unexpectedly, these C-rich sequences instead form Z-RNA structures, which have not been previously observed in regions containing cytosine repeats and represent an interesting and underexplored target for protein-RNA interactions. Our results highlight the prevalence and potential structure-associated functions of noncanonical secondary structures in lncRNAs, and show G4 and Z-RNA structure formation in many lncRNA sequences for the first time, furthering the understanding of the structure-function relationship in lncRNAs.
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Affiliation(s)
- Uditi Bhatt
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Anne Cucchiarini
- Laboratoire d'Optique et Biosciences, École Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Yu Luo
- Laboratoire d'Optique et Biosciences, École Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Cameron W Evans
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Jean-Louis Mergny
- Laboratoire d'Optique et Biosciences, École Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - K Swaminathan Iyer
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Nicole M Smith
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia;
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2
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Li X, Wu Y, Zhang X, Liu J, Zhang Y, Yuan L, Liu M. Thermodynamic and cellular studies of doxorubicin/daunorubicin loaded by a DNA tetrahedron for diagnostic imaging, chemotherapy, and gene therapy. Int J Biol Macromol 2023; 251:126245. [PMID: 37562474 DOI: 10.1016/j.ijbiomac.2023.126245] [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: 06/02/2023] [Revised: 08/06/2023] [Accepted: 08/07/2023] [Indexed: 08/12/2023]
Abstract
The combined diagnostic imaging, chemotherapy, and gene therapy based on DNA nanocarriers can reduce the toxic side effects and overcome multidrug resistance (MDR). In this study, we designed an antisense oligonucleotides (ASOs)-linked DNA tetrahedron (ASOs-TD). The detection limit of ASOs-TD for MDR1 mRNA was 0.05 μM. By using fluorescence spectroscopy and isothermal titration calorimetry (ITC), the interactions between doxorubicin (DOX) /daunorubicin (DAU) and ASOs-TD were investigated. The number of binding sites (n), binding constant (Ka), entropy change (ΔSo), enthalpy change (ΔHo) and Gibbs free energy change (ΔGo) were obtained. The intercalation of DOX/DAU with ASOs-TD was demonstrated by differential scanning calorimetry (DSC) and quenching researches of potassium ferricyanide K4[Fe(CN)6]. The in vitro release rate of DOX/DAU loaded in ASOs-TD was accelerated by deoxyribonuclease I (DNase I). In vitro cytotoxicity proved the good gene therapy effect of ASOs-TD and the increased cytotoxicity of DOX/DAU to MCF-7/ADR cells. The results of confocal laser scanning microscope (CLSM) suggested that ASOs-TD could effectively identify drug-resistant cells due to its good imaging ability for MDR1 mRNA. This work offers theoretical significance for overcoming MDR using DNA nanostructures which combine diagnostic imaging, chemotherapy, and gene therapy.
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Affiliation(s)
- Xinyu Li
- School of Chemistry and Chemical Engineering, Liaocheng University, Hunan Road, Liaocheng 252059, China
| | - Yushu Wu
- Institute of Biopharmaceutical Research, Liaocheng University, Hunan Road, Liaocheng 252059, China
| | - Xinpeng Zhang
- Institute of Biopharmaceutical Research, Liaocheng University, Hunan Road, Liaocheng 252059, China
| | - Jie Liu
- Institute of Biopharmaceutical Research, Liaocheng University, Hunan Road, Liaocheng 252059, China
| | - Yanqing Zhang
- School of Chemistry and Chemical Engineering, Liaocheng University, Hunan Road, Liaocheng 252059, China
| | - Lixia Yuan
- Institute of Biopharmaceutical Research, Liaocheng University, Hunan Road, Liaocheng 252059, China
| | - Min Liu
- School of Chemistry and Chemical Engineering, Liaocheng University, Hunan Road, Liaocheng 252059, China; Institute of Biopharmaceutical Research, Liaocheng University, Hunan Road, Liaocheng 252059, China.
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3
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Wickhorst PJ, Ihmels H, Paululat T. Studies on the Interactions of 3,11-Difluoro-6,8,13-trimethyl-8 H-quino[4,3,2- kl]acridinium and Insulin with the Quadruplex-Forming Oligonucleotide Sequence a2 from the Insulin-Linked Polymorphic Region. Molecules 2021; 26:molecules26216595. [PMID: 34771003 PMCID: PMC8587938 DOI: 10.3390/molecules26216595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 11/16/2022] Open
Abstract
Recently, several quadruplex-DNA-forming sequences have been identified in the insulin-linked polymorphic region (ILPR), which is a guanine-rich oligonucleotide sequence in the promoter region of insulin. The formation of this non-canonical quadruplex DNA (G4-DNA) has been shown to be involved in the biological activity of the ILPR, specifically with regard to its interplay with insulin. In this context, this contribution reports on the investigation of the association of the quadruplex-forming ILPR sequence a2 with insulin as well as with the well-known G4-DNA ligand 3,11-difluoro-6,8,13-trimethyl-8H-quino[4,3,2-kl]acridinium (1), also named RHPS4, by optical and NMR spectroscopy. CD- and NMR-spectroscopic measurements confirmed the preferential formation of an antiparallel quadruplex structure of a2 with four stacked guanine quartets. Furthermore, ligand 1 has high affinity toward a2 and binds by terminal π stacking to the G1-G11-G15-G25 quartet. In addition, the spectroscopic studies pointed to an association of insulin to the deoxyribose backbone of the loops of a2.
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4
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Becher J, Berdnikova DV, Ihmels H, Stremmel C. Synthesis and investigation of quadruplex-DNA-binding, 9- O-substituted berberine derivatives. Beilstein J Org Chem 2020; 16:2795-2806. [PMID: 33281983 PMCID: PMC7684686 DOI: 10.3762/bjoc.16.230] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 11/02/2020] [Indexed: 12/20/2022] Open
Abstract
A small series of five novel berberine derivatives was synthesized by the Cu-catalyzed click reaction of 9-propargyladenine with 9-O-(azidoalkyl)berberine derivatives. The association of the resulting berberine-adenine conjugates with representative quadruplex-forming oligonucleotides 22AG dA(G3TTA)3G3 and a2 d(ACAG4TGTG4)2 was examined with photometric and fluorimetric titrations, thermal DNA denaturation analysis, and CD spectroscopy. The results from the spectrometric titrations indicated the formation of 2:1 or 1:1 complexes (ligand:G4-DNA) with log K b values of 10-11 (2:1) and 5-6 (1:1), which are typical for berberine derivatives. Notably, a clear relationship between the binding affinity of the ligands with the length of the alkyl linker chain, n, was not observed. However, depending on the structure, the ligands exhibited different effects when bound to the G4-DNA, such as fluorescent light-up effects and formation of ICD bands, which are mostly pronounced with a linker length of n = 4 (with a2) and n = 5 (with 22AG), thus indicating that each ligand-G4-DNA complex has a specific structure with respect to relative alignment and conformational flexibility of the ligand in the binding site. It was shown exemplarily with one representative ligand from the series that such berberine-adenine conjugates exhibit a selective binding, specifically a selectivity to quadruplex DNA in competition with duplex DNA, and a preferential thermal stabilization of the G4-DNA forms 22AG and KRAS. Notably, the experimental data do not provide evidence for a significant effect of the adenine unit on the binding affinity of the ligands, for example, by additional association with the loops, presumably because the adenine residue is sterically shielded by the neighboring triazole unit.
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Affiliation(s)
- Jonas Becher
- Department of Chemistry and Biology, University of Siegen and Center of Micro- and Nanochemistry and Engineering (Cμ); Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
| | - Daria V Berdnikova
- Department of Chemistry and Biology, University of Siegen and Center of Micro- and Nanochemistry and Engineering (Cμ); Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
| | - Heiko Ihmels
- Department of Chemistry and Biology, University of Siegen and Center of Micro- and Nanochemistry and Engineering (Cμ); Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
| | - Christopher Stremmel
- Department of Chemistry and Biology, University of Siegen and Center of Micro- and Nanochemistry and Engineering (Cμ); Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
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5
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Pei W, Liu M, Wu Y, Zhao Y, Liu T, Sun B, Liu Y, Wang Q, Han J. High payload and targeted release of anthracyclines by aptamer-tethered DNA nanotrains - Thermodynamic and release kinetic study. Eur J Pharm Sci 2020; 148:105319. [PMID: 32205231 DOI: 10.1016/j.ejps.2020.105319] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 02/27/2020] [Accepted: 03/19/2020] [Indexed: 01/21/2023]
Abstract
As one of the most promising drug delivery carriers, self-assembled DNA nanostructures are characterized of well-defined sizes, excellent biocompatibility, high drug loading and ability to control drug release. Studying the interactions between anticancer drugs and DNA nanostructures can help to associate microstructure-drug loading-release rate-therapeutic effect. Herein AS1411 aptamer-tethered DNA nanotrains (AS1411NTrs) were constructed and used as anthracyclines carrier with high payload for targeted delivery. The bindings of doxorubicin (DOX), epirubicin (EPI), and daunorubicin (DAU) to AS1411NTrs were investigated by isothermal titration calorimetry and fluorescence spectroscopy, and thermodynamic parameters were obtained. The high drug payload capacity of AS1411NTrs was verified by the large number of binding sites (~20). The binding mode was determined by differential scanning calorimetry and potassium iodide (KI) quenching experiments. The release experiment data showed that DNase I facilitated drug release and the release followed the first-order kinetic model. MTT cell viability assay demonstrated that the drug-loaded AS1411NTrs had significantly higher cytotoxicity against target HeLa cells than normal human liver L02 cells. These findings revealed that AS1411NTrs had high payload and targeted release capacity for DOX, EPI, and DAU. This result can provide a theoretical basis for constructing reasonable DNA nanostructures based on drug carriers.
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Affiliation(s)
- Wenxin Pei
- Institute of Biopharmaceutical Research, Liaocheng University, Hunan Road, Liaocheng 252059, China
| | - Min Liu
- Institute of Biopharmaceutical Research, Liaocheng University, Hunan Road, Liaocheng 252059, China; School of Chemistry and Chemical Engineering, Liaocheng University, Hunan Road, Liaocheng 252059, China.
| | - Yushu Wu
- Institute of Biopharmaceutical Research, Liaocheng University, Hunan Road, Liaocheng 252059, China.
| | - Yanna Zhao
- Institute of Biopharmaceutical Research, Liaocheng University, Hunan Road, Liaocheng 252059, China
| | - Tingting Liu
- Institute of Biopharmaceutical Research, Liaocheng University, Hunan Road, Liaocheng 252059, China
| | - Bin Sun
- Institute of Biopharmaceutical Research, Liaocheng University, Hunan Road, Liaocheng 252059, China
| | - Yinglin Liu
- School of Chemistry and Chemical Engineering, Liaocheng University, Hunan Road, Liaocheng 252059, China
| | - Qingpeng Wang
- Institute of Biopharmaceutical Research, Liaocheng University, Hunan Road, Liaocheng 252059, China
| | - Jun Han
- Institute of Biopharmaceutical Research, Liaocheng University, Hunan Road, Liaocheng 252059, China
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6
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McRae EKS, Davidson DE, Dupas SJ, McKenna SA. Insights into the RNA quadruplex binding specificity of DDX21. Biochim Biophys Acta Gen Subj 2018; 1862:1973-1979. [PMID: 29906500 DOI: 10.1016/j.bbagen.2018.06.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 05/28/2018] [Accepted: 06/11/2018] [Indexed: 11/20/2022]
Abstract
Guanine quadruplexes can form in both DNA and RNA and influence many biological processes through various protein interactions. The DEAD-box RNA helicase protein DDX21 has been shown to bind and remodel RNA quadruplexes but little is known about its specificity for different quadruplex species. Previous reports have suggested DDX21 may interact with telomeric repeat containing RNA quadruplex (TERRA), an integral component of the telomere that contributes to telomeric heterochromatin formation and telomere length regulation. Here we report that the C-terminus of DDX21 directly interacts with TERRA. We use, for the first time, 2D saturation transfer difference NMR to map the protein binding site on a ribonucleic acid species and show that the quadruplex binding domain of DDX21 interacts primarily with the phosphoribose backbone of quadruplexes. Furthermore, by mutating the 2'OH of loop nucleotides we can drastically reduce DDX21's affinity for quadruplex, indicating that the recognition of quadruplex and specificity for TERRA is mediated by interactions with the 2'OH of loop nucleotides.
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Affiliation(s)
- Ewan K S McRae
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - David E Davidson
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Steven J Dupas
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Sean A McKenna
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada; Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada; Manitoba Institute for Materials, University of Manitoba, Winnipeg, Manitoba, Canada.
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7
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Yoshida W, Saikyo H, Nakabayashi K, Yoshioka H, Bay DH, Iida K, Kawai T, Hata K, Ikebukuro K, Nagasawa K, Karube I. Identification of G-quadruplex clusters by high-throughput sequencing of whole-genome amplified products with a G-quadruplex ligand. Sci Rep 2018; 8:3116. [PMID: 29449667 PMCID: PMC5814564 DOI: 10.1038/s41598-018-21514-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 02/05/2018] [Indexed: 12/31/2022] Open
Abstract
G-quadruplex (G4) is a DNA secondary structure that has been found to play regulatory roles in the genome. The identification of G4-forming sequences is important to study the specific structure-function relationships of such regions. In the present study, we developed a method for identification of G4 clusters on genomic DNA by high-throughput sequencing of genomic DNA amplified via whole-genome amplification (WGA) in the presence of a G4 ligand. The G4 ligand specifically bound to G4 structures on genomic DNA; thus, DNA polymerase was arrested on the G4 structures stabilised by G4 ligand. We utilised the telomestatin derivative L1H1-7OTD as a G4 ligand and demonstrated that the efficiency of amplification of the G4 cluster regions was lower than that of the non-G4-forming regions. By high-throughput sequencing of the WGA products, 9,651 G4 clusters were identified on human genomic DNA. Among these clusters, 3,766 G4 clusters contained at least one transcriptional start site, suggesting that genes are regulated by G4 clusters rather than by one G4 structure.
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Affiliation(s)
- Wataru Yoshida
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakura-machi, Hachioji, Tokyo, 192-0982, Japan.
| | - Hiroki Saikyo
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakura-machi, Hachioji, Tokyo, 192-0982, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Ookura, Setagaya, Tokyo, 157-0074, Japan
| | - Hitomi Yoshioka
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakura-machi, Hachioji, Tokyo, 192-0982, Japan
| | - Daniyah Habiballah Bay
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakura-machi, Hachioji, Tokyo, 192-0982, Japan.,Biology Department, Umm Al-Qura University, P.O. Box 715, Makkah, 21955, Saudi Arabia
| | - Keisuke Iida
- Molecular Chirality Research Center, Synthetic Organic Chemistry, Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi, Inage, Chiba, 263-8522, Japan
| | - Tomoko Kawai
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Ookura, Setagaya, Tokyo, 157-0074, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Ookura, Setagaya, Tokyo, 157-0074, Japan
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Isao Karube
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakura-machi, Hachioji, Tokyo, 192-0982, Japan
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8
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Aptamer@Au-o-phenylenediamine modified pencil graphite electrode: A new selective electrochemical impedance biosensor for the determination of insulin. Colloids Surf B Biointerfaces 2017; 159:47-53. [DOI: 10.1016/j.colsurfb.2017.07.076] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/21/2017] [Accepted: 07/26/2017] [Indexed: 01/26/2023]
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9
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Bay DH, Busch A, Lisdat F, Iida K, Ikebukuro K, Nagasawa K, Karube I, Yoshida W. Identification of G-quadruplex structures that possess transcriptional regulating functions in the Dele and Cdc6 CpG islands. BMC Mol Biol 2017; 18:17. [PMID: 28655335 PMCID: PMC5488298 DOI: 10.1186/s12867-017-0094-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 06/23/2017] [Indexed: 12/29/2022] Open
Abstract
Background G-quadruplex is a DNA secondary structure that has been shown to play an important role in biological systems. In a previous study, we identified 1998 G-quadruplex-forming sequences using a mouse CpG islands DNA microarray with a fluorescent-labeled G-quadruplex ligand. Among these putative G-quadruplex-forming sequences, G-quadruplex formation was verified for 10 randomly selected sequences by CD spectroscopy and DMS footprinting analysis. In this study, the biological function of the 10 G-quadruplex-forming sequences in the transcriptional regulation has been analyzed using a reporter assay. Results When G-quadruplex-forming sequences from the Dele and Cdc6 genes have been cloned in reporter vectors carrying a minimal promoter and the luciferase gene, luciferase expression is activated. This has also been detected in experiments applying a promoterless reporter vector. Mutational analysis reveals that guanine bases, which form the G-tetrads, are important in the activation. In addition, the activation has been found to decrease by the telomestatin derivative L1H1-7OTD which can bind to the G-quadruplex DNA. When Dele and Cdc6 CpG islands, containing the G-quadruplex-forming sequence, have been cloned in the promoterless reporter vector, the luciferase expression is activated. Mutational analysis reveals that the expression level is decreased by mutation on Dele G-quadruplex; however, increased by mutation on Cdc6 G-quadruplex. Conclusion Dele and Cdc6 G-quadruplex formation is significant in the transcriptional regulation. Dele and Cdc6 G-quadruplex DNA alone possess enhancer and promotor function. When studied in more complex CpG islands Dele G-quadruplex also demonstrates promotor activity, whereas Cdc6 G-quadruplex may possess a dual function of transcriptional regulation. Electronic supplementary material The online version of this article (doi:10.1186/s12867-017-0094-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniyah H Bay
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan.,Biology Department, Umm Al-Qura University, Makkah, Kingdom of Saudi Arabia
| | - Annika Busch
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan.,Biosystems Technology, Institute of Applied Life Sciences, Technical University of Applied Sciences Wildau, Wildau, Germany
| | - Fred Lisdat
- Biosystems Technology, Institute of Applied Life Sciences, Technical University of Applied Sciences Wildau, Wildau, Germany
| | - Keisuke Iida
- Graduate School of Science and Engineering, Saitama University, c/o Saitama Cancer Center, Saitama, Japan
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Isao Karube
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan
| | - Wataru Yoshida
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan.
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10
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Mondal R, Ghosh N, Mukherjee S. Contrasting effects of pH on the modulation of the structural integrity of hemoglobin induced by sodium deoxycholate. Phys Chem Chem Phys 2016; 18:30867-30876. [PMID: 27801442 DOI: 10.1039/c6cp05216a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bile salt-mediated conformational modification of hemoglobin (Hb) was examined at three different pHs i.e., 3.2, 7.4 and 9.0. The added bile salt, sodium deoxycholate (NaDC), decreases the α-helicity in Hb (α-helix: 71.3% → 61.7% in the presence of 9.6 mM NaDC, and 83.2% → 66.2% in the presence of 14 mM NaDC, at pH 7.4 and 9.0, respectively), while a reverse pattern of modification in the Circular Dichroism (CD) spectra of Hb is found at pH 3.2. The acid-induced denatured Hb (pH 3.2) regains its structural integrity by changing conformation from a random coil to an α-helix rich secondary structure upon addition of NaDC (α-helix: 10.4% → 53.4%, β-sheet: 31.0% → 18.5% and random coil: 58.6% → 28.1%, in the presence of 0.65 mM NaDC). Also, a step-wise binding interaction pattern of Hb with NaDC was revealed at pH 7.4 and 9.0 upon variation of steady-state fluorescence intensity and average lifetime of Hb. From the fluorescence lifetime decay pattern, the decrement of energy transfer from Trp to a heme group was found upon the addition of NaDC at pH 7.4 and 9.0. However, at pH 3.2, the modification of the time-resolved fluorescence decay behavior of Hb within NaDC is typically reversed, where the energy transfer from Trp to heme is restored to some extent. Thermodynamic analysis suggests that the Hb-NaDC binding interaction is characterized by a dominant entropic contribution interpreted on the basis of release of ordered water molecules to the bulk aqueous phase.
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Affiliation(s)
- Ramakanta Mondal
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal Bypass Road, Bhopal 426066, Madhya Pradesh, India.
| | - Narayani Ghosh
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal Bypass Road, Bhopal 426066, Madhya Pradesh, India.
| | - Saptarshi Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal Bypass Road, Bhopal 426066, Madhya Pradesh, India.
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11
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Mondal R, Ghosh N, Mukherjee S. Enhanced Binding of Phenosafranin to Triblock Copolymer F127 Induced by Sodium Dodecyl Sulfate: A Mixed Micellar System as an Efficient Drug Delivery Vehicle. J Phys Chem B 2016; 120:2968-76. [DOI: 10.1021/acs.jpcb.6b00759] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Ramakanta Mondal
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass
Road, Bhauri, Bhopal 462
066, Madhya Pradesh, India
| | - Narayani Ghosh
- 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
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12
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A method for rapid screening of interactions of pharmacologically active compounds with albumin. Anal Chim Acta 2015; 855:51-9. [DOI: 10.1016/j.aca.2014.12.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 12/05/2014] [Accepted: 12/07/2014] [Indexed: 11/18/2022]
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13
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Dzubiel D, Ihmels H, Mahmoud MMA, Thomas L. A comparative study of the interactions of cationic hetarenes with quadruplex-DNA forming oligonucleotide sequences of the insulin-linked polymorphic region (ILPR). Beilstein J Org Chem 2014; 10:2963-74. [PMID: 25550763 PMCID: PMC4273293 DOI: 10.3762/bjoc.10.314] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Accepted: 11/26/2014] [Indexed: 11/23/2022] Open
Abstract
The interactions of the ILPR sequence (ILPR = "insulin-linked polymorphic region") a2 [d(ACAG4TGTG4ACAG4TGTG4)] with [2.2.2]heptamethinecyanine derivatives 1a–e and with the already established quadruplex ligands coralyne (2), 3,3′-[2,6-pyridinediylbis(carbonylimino)]bis[1-methylquinolinium] (3), 4,4′,4′′,4′′′-(21H,23H-porphine-5,10,15,20-tetrayl)tetrakis[1-methylpyridinium] (4), naphtho[2,1-b:3,4-b′:6,5-b′′:7,8-b′′′]tetraquinolizinium (5) and thiazole orange (6) were studied. It is demonstrated with absorption, fluorescence and CD spectroscopy that all investigated ligands bind with relatively high affinity to the ILPR-quadruplex DNA a2 (0.2–5.5 × 106 M−1) and that in most cases the binding parameters of ligand-ILPR complexes are different from the ones observed with other native quadruplex-forming DNA sequences.
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Affiliation(s)
- Darinka Dzubiel
- Department Chemie-Biologie, Universität Siegen, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
| | - Heiko Ihmels
- Department Chemie-Biologie, Universität Siegen, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
| | - Mohamed M A Mahmoud
- Department Chemie-Biologie, Universität Siegen, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
| | - Laura Thomas
- Department Chemie-Biologie, Universität Siegen, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
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