201
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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.
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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
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202
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Li Y, Han X, Yan Y, Cao Y, Xiang X, Wang S, Zhao B, Guo X. Label-Free Detection of Tetramolecular i-Motifs by Surface-Enhanced Raman Spectroscopy. Anal Chem 2018; 90:2996-3000. [DOI: 10.1021/acs.analchem.7b04277] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Yang Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Xiaoxia Han
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Yuting Yan
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Yanwei Cao
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Xiaoxuan Xiang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Sheng Wang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Bing Zhao
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Xinhua Guo
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, College of Life Science, Jilin University, Changchun 130012, P. R. China
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203
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Ren W, Zheng K, Liao C, Yang J, Zhao J. Charge evolution during the unfolding of a single DNA i-motif. Phys Chem Chem Phys 2018; 20:916-924. [PMID: 29230450 DOI: 10.1039/c7cp06235d] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The effective charge and evolution of single chains of a DNA i-motif during its unfolding process are investigated at the single molecule level. Using fluorescence correlation spectroscopy and photon counting histograms, the single chain dimensions and electrical potential of cytosine-rich human telomeric oligonucleotides are monitored, during their unfolding from the i-motif to the random coil state. It is discovered that the effective charge density of the DNA chain is very sensitive to conformation changes and the results remarkably expose the existence of an intermediate state of the unfolding process. A huge difference in pH value exists in the vicinity of the DNA chain and the bulk solution, depending on the salt concentration, as reflected by a down-shift in the pH value of unfolding. The presence of an external salt in the solution helps to stabilize the i-motif structure at low pH values due to the reduction of the effective charge density. It can also destabilize the folded structure in the pH range of the conformation transition due to the elevation of the local pH value, encouraging the deprotonation of the cytosine groups. These results provide new information for understanding the structure and stability of i-motif DNA, and its biological function, as well as the building blocks for smart nanomaterials.
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Affiliation(s)
- Weibin Ren
- Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
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204
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Liu L, Kim BG, Feroze U, Macgregor RB, Chalikian TV. Probing the Ionic Atmosphere and Hydration of the c-MYC i-Motif. J Am Chem Soc 2018; 140:2229-2238. [DOI: 10.1021/jacs.7b11537] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Lutan Liu
- Department of Pharmaceutical Sciences,
Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College
Street, Toronto, Ontario M5S 3M2, Canada
| | - Byul G. Kim
- Department of Pharmaceutical Sciences,
Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College
Street, Toronto, Ontario M5S 3M2, Canada
| | - Ujala Feroze
- Department of Pharmaceutical Sciences,
Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College
Street, Toronto, Ontario M5S 3M2, Canada
| | - Robert B. Macgregor
- Department of Pharmaceutical Sciences,
Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College
Street, Toronto, Ontario M5S 3M2, Canada
| | - Tigran V. Chalikian
- Department of Pharmaceutical Sciences,
Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College
Street, Toronto, Ontario M5S 3M2, Canada
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205
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Gouda AS, Amine MS, Pedersen EB. Improved i-motif thermal stability by insertion of anthraquinone monomers. Org Biomol Chem 2018; 15:6613-6621. [PMID: 28752173 DOI: 10.1039/c7ob01393k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
In order to gain insight into how to improve thermal stability of i-motifs when used in the context of biomedical and nanotechnological applications, novel anthraquinone-modified i-motifs were synthesized by insertion of 1,8-, 1,4-, 1,5- and 2,6-disubstituted anthraquinone monomers into the TAA loops of a 22mer cytosine-rich human telomeric DNA sequence. The influence of the four anthraquinone linkers on the i-motif thermal stability was investigated at 295 nm and pH 5.5. Anthraquinone monomers modulate the i-motif stability in a position-depending manner and the modulation also depends on the substitution pattern of the anthraquinone. The insertion of anthraquinone was found to stabilize the i-motif structure when replacing any one of the positions of the central TAA loop and the thermal stabilities were typically higher than those previously found for i-motifs containing pyrene-modified uracilyl unlocked nucleic acid monomers or twisted intercalating nucleic acid. The 2,6-disubstituted anthraquinone linker replacing T10 enabled a significant increase of i-motif thermal melting by 8.2 °C. A substantial increase of 5.0 °C in i-motif thermal melting was recorded when both A6 and T16 were modified with a double replacement by the 2,6-isomer into the TAA loops in the outer regions. The largest destabilization is observed for the 1,5-disubstituted anthraquinone linker upon the replacement of A18. CD curves of anthraquinone-modified variants imply no structural changes in all cases under potassium buffer conditions compared with those of the native i-motif. Molecular modeling studies explained the increased thermal stabilities of anthraquinone-modified i-motifs.
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Affiliation(s)
- Alaa S Gouda
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
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206
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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
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207
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Ma W, Yan L, He X, Qing T, Lei Y, Qiao Z, He D, Huang K, Wang K. Hairpin-Contained i-Motif Based Fluorescent Ratiometric Probe for High-Resolution and Sensitive Response of Small pH Variations. Anal Chem 2018; 90:1889-1896. [DOI: 10.1021/acs.analchem.7b03972] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Wenjie Ma
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Biology, College of Chemistry and Chemical
Engineering, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Changsha 410082, China
| | - Lv’an Yan
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Biology, College of Chemistry and Chemical
Engineering, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Changsha 410082, China
| | - Xiaoxiao He
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Biology, College of Chemistry and Chemical
Engineering, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Changsha 410082, China
| | - Taiping Qing
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Biology, College of Chemistry and Chemical
Engineering, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Changsha 410082, China
| | - Yanli Lei
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Biology, College of Chemistry and Chemical
Engineering, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Changsha 410082, China
| | - Zhenzhen Qiao
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Biology, College of Chemistry and Chemical
Engineering, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Changsha 410082, China
| | - Dinggeng He
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Biology, College of Chemistry and Chemical
Engineering, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Changsha 410082, China
| | - Kaihang Huang
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Biology, College of Chemistry and Chemical
Engineering, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Changsha 410082, China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Biology, College of Chemistry and Chemical
Engineering, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Changsha 410082, China
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208
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Obata S, Asamitsu S, Hashiya K, Bando T, Sugiyama H. G-Quadruplex Induction by the Hairpin Pyrrole-Imidazole Polyamide Dimer. Biochemistry 2017; 57:498-502. [PMID: 29236465 DOI: 10.1021/acs.biochem.7b01059] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The G-quadruplex (G4) is one type of higher-order structure of nucleic acids and is thought to play important roles in various biological events such as regulation of transcription and inhibition of DNA replication. Pyrrole-imidazole polyamides (PIPs) are programmable small molecules that can sequence-specifically bind with high affinity to the minor groove of double-stranded DNA (dsDNA). Herein, we designed head-to-head hairpin PIP dimers and their target dsDNA in a model G4-forming sequence. Using an electrophoresis mobility shift assay and transcription arrest assay, we found that PIP dimers could induce the structural change to G4 DNA from dsDNA through the recognition by one PIP dimer molecule of two duplex-binding sites flanking both ends of the G4-forming sequence. This induction ability was dependent on linker length. This is the first study to induce G4 formation using PIPs, which are known to be dsDNA binders. The results reported here suggest that selective G4 induction in native sequences may be achieved with PIP dimers by applying the same design strategy.
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Affiliation(s)
- Shunsuke Obata
- Department of Chemistry, Graduate School of Science, Kyoto University , Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Sefan Asamitsu
- Department of Chemistry, Graduate School of Science, Kyoto University , Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kaori Hashiya
- Department of Chemistry, Graduate School of Science, Kyoto University , Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University , Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University , Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan.,Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University , Yoshida-Ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan
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209
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Abou Assi H, Lin YC, Serrano I, González C, Damha MJ. Probing Synergistic Effects of DNA Methylation and 2′-β-Fluorination on i-Motif Stability. Chemistry 2017; 24:471-477. [PMID: 29096420 DOI: 10.1002/chem.201704591] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Hala Abou Assi
- Department of Chemistry; McGill University; 801 Sherbrooke St. West Montreal QC H3A 0B8 Canada
| | - Yu Chen Lin
- Department of Chemistry; McGill University; 801 Sherbrooke St. West Montreal QC H3A 0B8 Canada
| | - Israel Serrano
- Instituto de Química Física “Rocasolano”; CSIC; Serrano 119 28006 Madrid Spain
| | - Carlos González
- Instituto de Química Física “Rocasolano”; CSIC; Serrano 119 28006 Madrid Spain
| | - Masad J. Damha
- Department of Chemistry; McGill University; 801 Sherbrooke St. West Montreal QC H3A 0B8 Canada
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210
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Jun J, Han SY. Theoretical exploration of gas-phase conformers of proton-bound non-covalent heterodimers of guanine and cytosine rare tautomers: structures and energies. Theor Chem Acc 2017. [DOI: 10.1007/s00214-017-2165-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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211
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Hybrid DNA i-motif: Aminoethylprolyl-PNA (pC 5) enhance the stability of DNA (dC 5) i-motif structure. Bioorg Med Chem Lett 2017; 27:5424-5428. [PMID: 29138026 DOI: 10.1016/j.bmcl.2017.11.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 11/01/2017] [Accepted: 11/02/2017] [Indexed: 11/23/2022]
Abstract
This report describes the synthesis of C-rich sequence, cytosine pentamer, of aep-PNA and its biophysical studies for the formation of hybrid DNA:aep-PNAi-motif structure with DNA cytosine pentamer (dC5) under acidic pH conditions. Herein, the CD/UV/NMR/ESI-Mass studies strongly support the formation of stable hybrid DNA i-motif structure with aep-PNA even near acidic conditions. Hence aep-PNA C-rich sequence cytosine could be considered as potential DNA i-motif stabilizing agents in vivo conditions.
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212
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Luo C, Li Y, Guo L, Zhang F, Liu H, Zhang J, Zheng J, Zhang J, Guo S. Graphene Quantum Dots Downregulate Multiple Multidrug-Resistant Genes via Interacting with Their C-Rich Promoters. Adv Healthc Mater 2017; 6. [PMID: 28748603 DOI: 10.1002/adhm.201700328] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 06/15/2017] [Indexed: 01/04/2023]
Abstract
Multidrug resistance (MDR) is the major factor in the failure of many forms of chemotherapy, mostly due to the increased efflux of anticancer drugs that mediated by ATP-binding cassette (ABC) transporters. Therefore, inhibiting ABC transporters is one of effective methods of overcoming MDR. However, high enrichment of ABC transporters in cells and their broad substrate spectra made to circumvent MDR are almost insurmountable by a single specific ABC transporter inhibitor. Here, this study demonstrates that graphene quantum dots (GQDs) could downregulate the expressions of P-glycoprotein, multidrug resistance protein MRP1, and breast cancer resistance protein genes via interacting with C-rich regions of their promoters. This is the first example that a single reagent could suppress multiple MDR genes, suggesting that it will be possible to target multiple ABC transporters simultaneously with a single reagent. The inhibitory ability of the GQDs to these drug-resistant genes is validated further by reversing the doxorubicin resistance of MCF-7/ADR cells. Notably, GQDs have superb chemical and physical properties, unique structure, low toxicity, and high biocompatibility; hence, their capability of inhibiting multiple drug-resistant genes holds great potential in cancer therapy.
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Affiliation(s)
- Chao Luo
- State Key Laboratory of Bioreactor Engineering; Shanghai Key Laboratory of New Drug Design; School of Pharmacy; East China University of Science and Technology; 130 Meilong Rd. Shanghai 200237 P. R. China
| | - Yanfang Li
- State Key Laboratory of Bioreactor Engineering; Shanghai Key Laboratory of New Drug Design; School of Pharmacy; East China University of Science and Technology; 130 Meilong Rd. Shanghai 200237 P. R. China
| | - Lijuan Guo
- State Key Laboratory of Bioreactor Engineering; Shanghai Key Laboratory of New Drug Design; School of Pharmacy; East China University of Science and Technology; 130 Meilong Rd. Shanghai 200237 P. R. China
| | - Fangwei Zhang
- School of Electronic Information and Electrical Engineering; Shanghai Jiao Tong University; 800 Dongchuan Rd. Shanghai 200240 P. R. China
| | - Hui Liu
- State Key Laboratory of Bioreactor Engineering; Shanghai Key Laboratory of New Drug Design; School of Pharmacy; East China University of Science and Technology; 130 Meilong Rd. Shanghai 200237 P. R. China
| | - Jiali Zhang
- School of Electronic Information and Electrical Engineering; Shanghai Jiao Tong University; 800 Dongchuan Rd. Shanghai 200240 P. R. China
| | - Jing Zheng
- State Key Laboratory of Bioreactor Engineering; Shanghai Key Laboratory of New Drug Design; School of Pharmacy; East China University of Science and Technology; 130 Meilong Rd. Shanghai 200237 P. R. China
| | - Jingyan Zhang
- State Key Laboratory of Bioreactor Engineering; Shanghai Key Laboratory of New Drug Design; School of Pharmacy; East China University of Science and Technology; 130 Meilong Rd. Shanghai 200237 P. R. China
| | - Shouwu Guo
- School of Electronic Information and Electrical Engineering; Shanghai Jiao Tong University; 800 Dongchuan Rd. Shanghai 200240 P. R. China
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213
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Zhu Y, Roy HA, Cunningham NA, Strobehn SF, Gao J, Munshi MU, Berden G, Oomens J, Rodgers MT. IRMPD Action Spectroscopy, ER-CID Experiments, and Theoretical Studies of Sodium Cationized Thymidine and 5-Methyluridine: Kinetic Trapping During the ESI Desolvation Process Preserves the Solution Structure of [Thd+Na]<sup/>. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:2423-2437. [PMID: 28836109 DOI: 10.1007/s13361-017-1753-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/01/2017] [Accepted: 07/02/2017] [Indexed: 05/25/2023]
Abstract
Thymidine (dThd) is a fundamental building block of DNA nucleic acids, whereas 5-methyluridine (Thd) is a common modified nucleoside found in tRNA. In order to determine the conformations of the sodium cationized thymine nucleosides [dThd+Na]+ and [Thd+Na]+ produced by electrospray ionization, their infrared multiple photon dissociation (IRMPD) action spectra are measured. Complementary electronic structure calculations are performed to determine the stable low-energy conformations of these complexes. Geometry optimizations and frequency analyses are performed at the B3LYP/6-311+G(d,p) level of theory, whereas energies are calculated at the B3LYP/6-311+G(2d,2p) level of theory. As protonation preferentially stabilizes minor tautomers of dThd and Thd, tautomerization facilitated by Na+ binding is also considered. Comparisons of the measured IRMPD and computed IR spectra find that [dThd+Na]+ prefers tridentate (O2,O4',O5') coordination to the canonical 2,4-diketo form of dThd with thymine in a syn orientation. In contrast, [Thd+Na]+ prefers bidentate (O2,O2') coordination to the canonical 2,4-diketo tautomer of Thd with thymine in an anti orientation. Although 2,4-dihydroxy tautomers and O2 protonated thymine nucleosides coexist in the gas phase, no evidence for minor tautomers is observed for the sodium cationized species. Consistent with experimental observations, the computational results confirm that the sodium cationized thymine nucleosides exhibit a strong preference for the canonical form of the thymine nucleobase. Survival yield analyses based on energy-resolved collision-induced dissociation (ER-CID) experiments suggest that the relative stabilities of protonated and sodium cationized dThd and Thd follow the order [dThd+H]+ < [Thd+H]+ < [dThd+Na]+ < [Thd+Na]+. Graphical Abstract ᅟ.
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Affiliation(s)
- Y Zhu
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - H A Roy
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - N A Cunningham
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - S F Strobehn
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - J Gao
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7c, 6525ED, Nijmegen, The Netherlands
| | - M U Munshi
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7c, 6525ED, Nijmegen, The Netherlands
| | - G Berden
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7c, 6525ED, Nijmegen, The Netherlands
| | - J Oomens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7c, 6525ED, Nijmegen, The Netherlands
| | - M T Rodgers
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA.
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214
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Debnath M, Ghosh S, Chauhan A, Paul R, Bhattacharyya K, Dash J. Preferential targeting of i-motifs and G-quadruplexes by small molecules. Chem Sci 2017; 8:7448-7456. [PMID: 29163897 PMCID: PMC5674183 DOI: 10.1039/c7sc02693e] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 09/07/2017] [Indexed: 01/01/2023] Open
Abstract
i-Motifs and G-quadruplexes are dynamic nucleic acid secondary structures, which are believed to play key roles in gene expression. We herein report two peptidomimetic ligands (PBP1 and PBP2) that selectively target i-motifs and G-quadruplexes over double-stranded DNA. These peptidomimetics, regioisomeric with respect to the position of triazole/prolinamide motifs, have been synthesized using a modular method involving Cu(i)-catalyzed azide and alkyne cycloaddition. The para-isomer, PBP1 exhibits high selectivity for i-motifs while the meta-isomer PBP2 binds selectively to G-quadruplex structures. Interestingly, these ligands have the ability to induce G-quadruplex or i-motif structures from the unstructured single-stranded DNA conformations, as observed using single molecule Förster resonance energy transfer (smFRET) studies. The quantitative real-time polymerase chain reaction (qRT-PCR), western blot, and dual-luciferase assays indicate that PBP1 upregulates and PBP2 downregulates BCL-2 gene expression in cancer cells.
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Affiliation(s)
- Manish Debnath
- Department of Organic Chemistry , Indian Association for the Cultivation of Science , Jadavpur , Kolkata-700032 , India .
| | - Shirsendu Ghosh
- Department of Physical Chemistry , Indian Association for the Cultivation of Science , Jadavpur , Kolkata-700032 , India
| | - Ajay Chauhan
- Department of Organic Chemistry , Indian Association for the Cultivation of Science , Jadavpur , Kolkata-700032 , India .
| | - Rakesh Paul
- Department of Organic Chemistry , Indian Association for the Cultivation of Science , Jadavpur , Kolkata-700032 , India .
| | - Kankan Bhattacharyya
- Department of Physical Chemistry , Indian Association for the Cultivation of Science , Jadavpur , Kolkata-700032 , India
| | - Jyotirmayee Dash
- Department of Organic Chemistry , Indian Association for the Cultivation of Science , Jadavpur , Kolkata-700032 , India .
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215
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Mir B, Serrano I, Buitrago D, Orozco M, Escaja N, González C. Prevalent Sequences in the Human Genome Can Form Mini i-Motif Structures at Physiological pH. J Am Chem Soc 2017; 139:13985-13988. [DOI: 10.1021/jacs.7b07383] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Bartomeu Mir
- Inorganic and Organic
Chemistry Department, Organic Chemistry Section, and IBUB, University of Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
- BIOESTRAN associated unit UB-CSIC, 08028 Barcelona, Spain
| | - Israel Serrano
- Instituto de Química Física ‘Rocasolano’, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Diana Buitrago
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
- Departament de Bioquímica
i Biomedicina, Facultat de Biologia, Universitat de Barcelona, Spain
| | - Núria Escaja
- Inorganic and Organic
Chemistry Department, Organic Chemistry Section, and IBUB, University of Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
- BIOESTRAN associated unit UB-CSIC, 08028 Barcelona, Spain
| | - Carlos González
- Instituto de Química Física ‘Rocasolano’, CSIC, Serrano 119, 28006 Madrid, Spain
- BIOESTRAN associated unit UB-CSIC, 08028 Barcelona, Spain
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216
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Benabou S, Aviñó A, Lyonnais S, González C, Eritja R, De Juan A, Gargallo R. i-motif structures in long cytosine-rich sequences found upstream of the promoter region of the SMARCA4 gene. Biochimie 2017; 140:20-33. [DOI: 10.1016/j.biochi.2017.06.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 06/06/2017] [Indexed: 12/27/2022]
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217
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Fujii T, K. Thazhathveetil A, Yildirim I, Young RM, Wasielewski MR, Schatz GC, Lewis FD. Structure and Dynamics of Electron Injection and Charge Recombination in i-Motif DNA Conjugates. J Phys Chem B 2017; 121:8058-8068. [DOI: 10.1021/acs.jpcb.7b04996] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Taiga Fujii
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Arun K. Thazhathveetil
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Ilyas Yildirim
- Department
of Chemistry and Biochemistry, Florida Atlantic University, Jupiter, Florida 33458, United States
| | - Ryan M. Young
- Argonne-Northwestern Solar Energy Research (ANSER) Center and Institute for Sustainability and Energy at Northwestern, Evanston, Illinois 60208-3113, United States
| | - Michael R. Wasielewski
- Argonne-Northwestern Solar Energy Research (ANSER) Center and Institute for Sustainability and Energy at Northwestern, Evanston, Illinois 60208-3113, United States
| | - George C. Schatz
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Frederick D. Lewis
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, United States
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218
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Kshirsagar R, Khan K, Joshi MV, Hosur RV, Muniyappa K. Probing the Potential Role of Non-B DNA Structures at Yeast Meiosis-Specific DNA Double-Strand Breaks. Biophys J 2017; 112:2056-2074. [PMID: 28538144 DOI: 10.1016/j.bpj.2017.04.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 04/13/2017] [Accepted: 04/19/2017] [Indexed: 12/29/2022] Open
Abstract
A plethora of evidence suggests that different types of DNA quadruplexes are widely present in the genome of all organisms. The existence of a growing number of proteins that selectively bind and/or process these structures underscores their biological relevance. Moreover, G-quadruplex DNA has been implicated in the alignment of four sister chromatids by forming parallel guanine quadruplexes during meiosis; however, the underlying mechanism is not well defined. Here we show that a G/C-rich motif associated with a meiosis-specific DNA double-strand break (DSB) in Saccharomyces cerevisiae folds into G-quadruplex, and the C-rich sequence complementary to the G-rich sequence forms an i-motif. The presence of G-quadruplex or i-motif structures upstream of the green fluorescent protein-coding sequence markedly reduces the levels of gfp mRNA expression in S. cerevisiae cells, with a concomitant decrease in green fluorescent protein abundance, and blocks primer extension by DNA polymerase, thereby demonstrating the functional significance of these structures. Surprisingly, although S. cerevisiae Hop1, a component of synaptonemal complex axial/lateral elements, exhibits strong affinity to G-quadruplex DNA, it displays a much weaker affinity for the i-motif structure. However, the Hop1 C-terminal but not the N-terminal domain possesses strong i-motif binding activity, implying that the C-terminal domain has a distinct substrate specificity. Additionally, we found that Hop1 promotes intermolecular pairing between G/C-rich DNA segments associated with a meiosis-specific DSB site. Our results support the idea that the G/C-rich motifs associated with meiosis-specific DSBs fold into intramolecular G-quadruplex and i-motif structures, both in vitro and in vivo, thus revealing an important link between non-B form DNA structures and Hop1 in meiotic chromosome synapsis and recombination.
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Affiliation(s)
- Rucha Kshirsagar
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Krishnendu Khan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Mamata V Joshi
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Ramakrishna V Hosur
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - K Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bangalore, India.
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219
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Polyzos AA, McMurray CT. Close encounters: Moving along bumps, breaks, and bubbles on expanded trinucleotide tracts. DNA Repair (Amst) 2017; 56:144-155. [PMID: 28690053 PMCID: PMC5558859 DOI: 10.1016/j.dnarep.2017.06.017] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Expansion of simple triplet repeats (TNR) underlies more than 30 severe degenerative diseases. There is a good understanding of the major pathways generating an expansion, and the associated polymerases that operate during gap filling synthesis at these "difficult to copy" sequences. However, the mechanism by which a TNR is repaired depends on the type of lesion, the structural features imposed by the lesion, the assembled replication/repair complex, and the polymerase that encounters it. The relationships among these parameters are exceptionally complex and how they direct pathway choice is poorly understood. In this review, we consider the properties of polymerases, and how encounters with GC-rich or abnormal structures might influence polymerase choice and the success of replication and repair. Insights over the last three years have highlighted new mechanisms that provide interesting choices to consider in protecting genome stability.
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Affiliation(s)
- Aris A Polyzos
- MBIB Division, Lawrence Berkeley Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, United States
| | - Cynthia T McMurray
- MBIB Division, Lawrence Berkeley Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, United States.
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220
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Dembska A, Kierzek E, Juskowiak B. Studying the influence of stem composition in pH-sensitive molecular beacons onto their sensing properties. Anal Chim Acta 2017; 990:157-167. [PMID: 29029739 DOI: 10.1016/j.aca.2017.07.040] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Revised: 06/21/2017] [Accepted: 07/17/2017] [Indexed: 01/04/2023]
Abstract
Intracellular sensing using fluorescent molecular beacons is a potentially useful strategy for real-time, in vivo monitoring of important cellular events. This work is focused on evaluation of pyrene excimer signaling molecular beacons (MBs) for the monitoring of pH changes in vitro as well as inside living cells. The recognition element in our MB called pHSO (pH-sensitive oligonucleotide) is the loop enclosing cytosine-rich fragment that is able to form i-motif structure in a specific pH range. However, alteration of a sequence of the 6 base pairs containing stem of MB allowed the design of pHSO probes that exhibited different dynamic pH range and possessed slightly different transition midpoint between i-motif and open loop configuration. Moreover, this conformational transition was accompanied by spectral changes showing developed probes different pyrene excimer-monomer emission ratio triggered by pH changes. The potential of these MBs for intracellular pH sensing is demonstrated on the example of HeLa cells line.
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Affiliation(s)
- Anna Dembska
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland.
| | - Elzbieta Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Science, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Bernard Juskowiak
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland
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221
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Stevens AJ, Kennedy MA. Methylated Cytosine Maintains G-Quadruplex Structures during Polymerase Chain Reaction and Contributes to Allelic Dropout. Biochemistry 2017; 56:3691-3698. [DOI: 10.1021/acs.biochem.7b00480] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Aaron J. Stevens
- Department of Pathology, University of Otago, Christchurch, New Zealand
| | - Martin A. Kennedy
- Department of Pathology, University of Otago, Christchurch, New Zealand
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222
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Affiliation(s)
- Wenhu Zhou
- Xiangya
School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Runjhun Saran
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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223
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Brown RV, Wang T, Chappeta VR, Wu G, Onel B, Chawla R, Quijada H, Camp SM, Chiang ET, Lassiter QR, Lee C, Phanse S, Turnidge MA, Zhao P, Garcia JGN, Gokhale V, Yang D, Hurley LH. The Consequences of Overlapping G-Quadruplexes and i-Motifs in the Platelet-Derived Growth Factor Receptor β Core Promoter Nuclease Hypersensitive Element Can Explain the Unexpected Effects of Mutations and Provide Opportunities for Selective Targeting of Both Structures by Small Molecules To Downregulate Gene Expression. J Am Chem Soc 2017; 139:7456-7475. [PMID: 28471683 PMCID: PMC5977998 DOI: 10.1021/jacs.6b10028] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The platelet-derived growth factor receptor β (PDGFR-β) signaling pathway is a validated and important target for the treatment of certain malignant and nonmalignant pathologies. We previously identified a G-quadruplex-forming nuclease hypersensitive element (NHE) in the human PDGFR-β promoter that putatively forms four overlapping G-quadruplexes. Therefore, we further investigated the structures and biological roles of the G-quadruplexes and i-motifs in the PDGFR-β NHE with the ultimate goal of demonstrating an alternate and effective strategy for molecularly targeting the PDGFR-β pathway. Significantly, we show that the primary G-quadruplex receptor for repression of PDGFR-β is the 3'-end G-quadruplex, which has a GGA sequence at the 3'-end. Mutation studies using luciferase reporter plasmids highlight a novel set of G-quadruplex point mutations, some of which seem to provide conflicting results on effects on gene expression, prompting further investigation into the effect of these mutations on the i-motif-forming strand. Herein we characterize the formation of an equilibrium between at least two different i-motifs from the cytosine-rich (C-rich) sequence of the PDGFR-β NHE. The apparently conflicting mutation results can be rationalized if we take into account the single base point mutation made in a critical cytosine run in the PDGFR-β NHE that dramatically affects the equilibrium of i-motifs formed from this sequence. We identified a group of ellipticines that targets the G-quadruplexes in the PDGFR-β promoter, and from this series of compounds, we selected the ellipticine analog GSA1129, which selectively targets the 3'-end G-quadruplex, to shift the dynamic equilibrium in the full-length sequence to favor this structure. We also identified a benzothiophene-2-carboxamide (NSC309874) as a PDGFR-β i-motif-interactive compound. In vitro, GSA1129 and NSC309874 downregulate PDGFR-β promoter activity and transcript in the neuroblastoma cell line SK-N-SH at subcytotoxic cell concentrations. GSA1129 also inhibits PDGFR-β-driven cell proliferation and migration. With an established preclinical murine model of acute lung injury, we demonstrate that GSA1129 attenuates endotoxin-mediated acute lung inflammation. Our studies underscore the importance of considering the effects of point mutations on structure formation from the G- and C-rich sequences and provide further evidence for the involvement of both strands and associated structures in the control of gene expression.
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Affiliation(s)
- Robert V. Brown
- College of Pharmacy, University of Arizona, 1703 East Mabel Street, Tucson, Arizona 85721, United States
| | - Ting Wang
- College of Medicine, University of Arizona, 1501 North Campbell Avenue, Tucson, Arizona 85724, United States
| | | | - Guanhui Wu
- College of Pharmacy, University of Arizona, 1703 East Mabel Street, Tucson, Arizona 85721, United States
| | - Buket Onel
- College of Pharmacy, University of Arizona, 1703 East Mabel Street, Tucson, Arizona 85721, United States
| | - Reena Chawla
- BIO5 Institute, 1657 East Helen Street, Tucson, Arizona 85721, United States
| | - Hector Quijada
- College of Medicine, University of Arizona, 1501 North Campbell Avenue, Tucson, Arizona 85724, United States
| | - Sara M. Camp
- College of Medicine, University of Arizona, 1501 North Campbell Avenue, Tucson, Arizona 85724, United States
| | - Eddie T. Chiang
- College of Medicine, University of Arizona, 1501 North Campbell Avenue, Tucson, Arizona 85724, United States
| | - Quinea R. Lassiter
- College of Agriculture & Life Sciences, University of Arizona, 1117 East Lowell Street, Tucson, Arizona 85721, United States
| | - Carmen Lee
- College of Agriculture & Life Sciences, University of Arizona, 1117 East Lowell Street, Tucson, Arizona 85721, United States
- College of Science, University of Arizona, 1040 East Fourth Street, Tucson, Arizona 85721, United States
| | - Shivani Phanse
- College of Science, University of Arizona, 1040 East Fourth Street, Tucson, Arizona 85721, United States
| | - Megan A. Turnidge
- College of Science, University of Arizona, 1040 East Fourth Street, Tucson, Arizona 85721, United States
| | - Ping Zhao
- School of Chemistry and Chemical Engineering, Guangdong Pharmaceutical University, No. 280 Waihuandong Road, Education Mega Centre, Guanzhou 510006, Peoples Republic of China
| | - Joe G. N. Garcia
- College of Medicine, University of Arizona, 1501 North Campbell Avenue, Tucson, Arizona 85724, United States
| | - Vijay Gokhale
- College of Pharmacy, University of Arizona, 1703 East Mabel Street, Tucson, Arizona 85721, United States
- BIO5 Institute, 1657 East Helen Street, Tucson, Arizona 85721, United States
| | - Danzhou Yang
- College of Pharmacy, University of Arizona, 1703 East Mabel Street, Tucson, Arizona 85721, United States
- BIO5 Institute, 1657 East Helen Street, Tucson, Arizona 85721, United States
- University of Arizona Cancer Center, 1515 North Campbell Avenue, Tucson, Arizona 85724, United States
| | - Laurence H. Hurley
- College of Pharmacy, University of Arizona, 1703 East Mabel Street, Tucson, Arizona 85721, United States
- BIO5 Institute, 1657 East Helen Street, Tucson, Arizona 85721, United States
- University of Arizona Cancer Center, 1515 North Campbell Avenue, Tucson, Arizona 85724, United States
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224
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Mir B, Solés X, González C, Escaja N. The effect of the neutral cytidine protonated analogue pseudoisocytidine on the stability of i-motif structures. Sci Rep 2017; 7:2772. [PMID: 28584239 PMCID: PMC5459817 DOI: 10.1038/s41598-017-02723-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 04/05/2017] [Indexed: 01/07/2023] Open
Abstract
Incorporation of pseudoisocytidine (psC), a neutral analogue of protonated cytidine, in i-motifs has been studied by spectroscopic methods. Our results show that neutral psC:C base pairs can stabilize i-motifs at neutral pH, but the stabilization only occurs when psC:C base pairs are located at the ends of intercalated C:C+ stacks. When psC occupies central positions, the resulting i-motifs are only observed at low pH and psC:C+ or psC:psC+ hemiprotonated base pairs are formed instead of their neutral analogs. Overall, our results suggest that positively charged base pairs are necessary to stabilize this non-canonical DNA structure.
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Affiliation(s)
- B Mir
- Inorganic and Organic Chemistry Department, Organic Chemistry Section, and IBUB, University of Barcelona, Martí i Franquès 1-11, 08028, Barcelona, Spain
| | - X Solés
- Inorganic and Organic Chemistry Department, Organic Chemistry Section, and IBUB, University of Barcelona, Martí i Franquès 1-11, 08028, Barcelona, Spain
| | - C González
- Instituto de Química Física Rocasolano, CSIC, Serrano 119, 28006, Madrid, Spain. .,BIOESTRAN, associated unit UB-CSIC, Spain.
| | - N Escaja
- Inorganic and Organic Chemistry Department, Organic Chemistry Section, and IBUB, University of Barcelona, Martí i Franquès 1-11, 08028, Barcelona, Spain. .,BIOESTRAN, associated unit UB-CSIC, Spain.
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225
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Sheng Q, Neaverson JC, Mahmoud T, Stevenson CEM, Matthews SE, Waller ZAE. Identification of new DNA i-motif binding ligands through a fluorescent intercalator displacement assay. Org Biomol Chem 2017; 15:5669-5673. [PMID: 28567459 PMCID: PMC5708337 DOI: 10.1039/c7ob00710h] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
This work describes a new way to screen for i-motif binding compounds and several new families of ligands with potential for use in experiments into the structure and function of i-motif DNA.
i-Motifs are quadruplex DNA structures formed from sequences rich in cytosine and held together by intercalated, hemi-protonated cytosine–cytosine base pairs. These sequences are prevalent in gene promoter regions and may play a role in gene transcription. Targeting these structures with ligands could provide a novel way to target genetic disease but there are very few ligands which have been shown to interact with i-motif DNA. Fluorescent intercalator displacement (FID) assays are a simple way to screen ligands against DNA secondary structures. Here we characterise how thiazole orange interacts with i-motif DNA and assess its ability for use in a FID assay. Additionally, we report FID-based ligand screening using thiazole orange against the i-motif forming sequence from the human telomere to reveal new i-motif binding compounds which have the potential for further development.
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Affiliation(s)
- Qiran Sheng
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Joseph C Neaverson
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Tasnim Mahmoud
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Clare E M Stevenson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Susan E Matthews
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Zoë A E Waller
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK. and Centre for Molecular and Structural Biochemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
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226
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Aviñó A, Dellafiore M, Gargallo R, González C, Iribarren AM, Montserrat J, Eritja R. Stabilization of Telomeric I-Motif Structures by (2'S)-2'-Deoxy-2'-C-Methylcytidine Residues. Chembiochem 2017; 18:1123-1128. [PMID: 28407336 DOI: 10.1002/cbic.201700112] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Indexed: 01/12/2023]
Abstract
G-quadruplexes and i-motifs are tetraplex structures present in telomeres and the promoter regions of oncogenes. The possibility of producing nanodevices with pH-sensitive functions has triggered interest in modified oligonucleotides with improved structural properties. We synthesized C-rich oligonucleotides carrying conformationally restricted (2'S)-2'-deoxy-2'-C-methyl-cytidine units. The effect of this modified nucleoside on the stability of intramolecular i-motifs from the vertebrate telomere was investigated by UV, CD, and NMR spectroscopy. The replacement of selected positions of the C-core with C-modified residues induced the formation of stable intercalated tetraplexes at near-neutral pH. This study demonstrates the possibility of enhancing the stability of the i-motif by chemical modification.
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Affiliation(s)
- Anna Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC), Spanish Council for Scientific Research (CSIC), Jordi Girona 18-26, 08034, Barcelona, Spain.,Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN)
| | - María Dellafiore
- INGEBI (CONICET), Vuelta de Obligado 2490-(1428), Buenos Aires, Argentina
| | - Raimundo Gargallo
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Martí i Franquès, 1-11, 08028, Barcelona, Spain.,BIOESTRAN, Associated Unit UB-CSIC
| | - Carlos González
- BIOESTRAN, Associated Unit UB-CSIC.,Institute of Physical Chemistry Rocasolano (IQFR), Spanish Council for Scientific Research (CSIC), Serrano 119, 28006, Madrid, Spain
| | - Adolfo M Iribarren
- CONICET. Laboratorio de Biotransformaciones, Universidad Nacional de Quilmes, Roque Saenz Peña 352 (1876) Bernal, Prov. de Buenos Aires, Argentina
| | - Javier Montserrat
- CONICET. Universidad Nacional de General Sarmiento, J. M. Gutiérrez 1150, 1613, Los Polvorines, Buenos Aires, Argentina
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC), Spanish Council for Scientific Research (CSIC), Jordi Girona 18-26, 08034, Barcelona, Spain.,Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN)
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227
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Han Y, Diao D, Lu Z, Li X, Guo Q, Huo Y, Xu Q, Li Y, Cao S, Wang J, Wang Y, Zhao J, Li Z, He M, Luo Z, Lou X. Selection of Group-Specific Phthalic Acid Esters Binding DNA Aptamers via Rationally Designed Target Immobilization and Applications for Ultrasensitive and Highly Selective Detection of Phthalic Acid Esters. Anal Chem 2017; 89:5270-5277. [PMID: 28414217 DOI: 10.1021/acs.analchem.6b04808] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Phthalic acid esters (PAEs) are ubiquitous in the environment, and some of them are recognized as endocrine disruptors that cause concerns on ecosystem functioning and public health. Due to the diversity of PAEs in the environment, there is a vital need to detect the total concentration of PAEs in a timely and low-cost way. To fulfill this requirement, it is highly desired to obtain group-specific PAE binders that are specific to the basic PAE skeleton. In this study, for the first time we have identified the group-specific PAE-binding aptamers via rationally designed target immobilization. The two target immobilization strategies were adopted to display either the phthalic ester group or the alkyl chain, respectively, at the surface of the immobilization matrix. The former enabled the rapid enrichment of aptamers after four rounds of selection. The top 100 sequences are cytosine-rich (44.7%) and differentiate from each other by only 1-4 nucleotides at limited locations. The top two aptamers all display the nanomolar dissociation constants to both the immobilized target and the free PAEs [dibutyl phthalate (DBP), butyl benzyl phthalate (BBP), bis(2-ethylhexyl) phthalate (DEHP)]. We further demonstrate the applications of the aptamers in the development of high-throughput PAE assays and DEHP electrochemical biosensors with exceptional sensitivity [limit of detection (LOD), 10 pM] and selectivity (>105-fold). PAE aptamers targeting one of the most sought for targets thus offer the promise of convenient, low-cost detection of total PAEs. Our study also provides insights on the aptamer selection and sensor development of highly hydrophobic small molecules.
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Affiliation(s)
- Yu Han
- Department of Chemistry, Capital Normal University , Beijing, 100048, China
| | - Donglin Diao
- Department of Chemistry, Capital Normal University , Beijing, 100048, China
| | - Zhangwei Lu
- Department of Chemistry, Capital Normal University , Beijing, 100048, China
| | - Xiaoning Li
- Department of Chemistry, Capital Normal University , Beijing, 100048, China
| | - Qian Guo
- Department of Chemistry, Capital Normal University , Beijing, 100048, China
| | - Yumeng Huo
- Department of Chemistry, Capital Normal University , Beijing, 100048, China
| | - Qing Xu
- Department of Chemistry, Capital Normal University , Beijing, 100048, China
| | - Youshan Li
- Department of Chemistry, Capital Normal University , Beijing, 100048, China
| | - Shengli Cao
- Department of Chemistry, Capital Normal University , Beijing, 100048, China
| | - Jianchun Wang
- Department of Chemistry, Capital Normal University , Beijing, 100048, China
| | - Yuan Wang
- Department of Chemistry, Capital Normal University , Beijing, 100048, China
| | - Jiaxing Zhao
- Department of Chemistry, Capital Normal University , Beijing, 100048, China
| | - Zhongfeng Li
- Department of Chemistry, Capital Normal University , Beijing, 100048, China
| | - Miao He
- School of Environment, Tsinghua University , Beijing 100084, China
| | - Zhaofeng Luo
- School of Life Sciences, University of Science and Technology of China , Hefei 230027, China
| | - Xinhui Lou
- Department of Chemistry, Capital Normal University , Beijing, 100048, China
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228
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Bertrand B, Fernandez-Cestau J, Angulo J, Cominetti MMD, Waller ZAE, Searcey M, O'Connell MA, Bochmann M. Cytotoxicity of Pyrazine-Based Cyclometalated (C^N pz^C)Au(III) Carbene Complexes: Impact of the Nature of the Ancillary Ligand on the Biological Properties. Inorg Chem 2017; 56:5728-5740. [PMID: 28441013 PMCID: PMC5434479 DOI: 10.1021/acs.inorgchem.7b00339] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
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The synthesis of a series of cyclometalated gold(III) complexes
supported by pyrazine-based (C^N^C)-type pincer ligands is reported,
including the crystal structure of a cationic example. The compounds
provide a new platform for the study of antiproliferative properties
of gold(III) complexes. Seven complexes were tested: the neutral series
(C^Npz^C)AuX [X = Cl (1), 6-thioguanine (4), C≡CPh (5), SPh (6)] and
an ionic series that included the N-methyl complex
[(C^NpzMe^C)AuCl]BF4 (7) and the
N-heterocyclic carbene complexes [(C^Npz^C)AuL]+ with L = 1,3-dimethylbenzimidazol-2-ylidene (2) or
1,3,7,9-tetramethylxanthin-8-ylidene (3). Tests against
human leukemia cells identified 1, 2, 3, and 4 as particularly promising, whereas protecting
the noncoordinated N atom on the pyrazine ring by methylation (as
in 7) reduced the cytotoxicity. Complex 2 proved to be the most effective of the entire series against the
HL60 leukemia, MCF-7 breast cancer, and A549 lung cancer cell lines,
with IC50 values down to submicromolar levels, associated
with a lower toxicity toward healthy human lung fibroblast cells.
The benzimidazolylidene complex 2 accumulated more effectively
in human lung cancer cells than its caffeine-based analogue 3 and the gold(III) chloride 1. Compound 2 proved to be unaffected by glutathione under physiological
conditions for periods of up to 6 days and stabilizes the DNA G-quadruplex
and i-motif structures; the latter is the first such report for gold
compounds. We also show the first evidence of inhibition of MDM2–p53
protein–protein interactions by a gold-based compound and identified
the binding mode of the compound with MDM2 using saturation transfer
difference NMR spectroscopy combined with docking calculations. We synthesized
three new (C^Npz^C)Au(III) complexes and screened them
along with four other complexes as potential anticancer agents against
leukemia cells. We tested the cellular uptake, the interaction with
G4 and i-motif DNA structures, and the interaction with MDM2 protein.
We highlight the very different biological behaviors of the compounds
due to the different ancillary ligands.
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Affiliation(s)
- Benoît Bertrand
- School of Chemistry, University of East Anglia , Norwich NR4 7TJ, United Kingdom
| | | | - Jesus Angulo
- School of Pharmacy, University of East Anglia , Norwich NR4 7TJ, United Kingdom
| | - Marco M D Cominetti
- School of Pharmacy, University of East Anglia , Norwich NR4 7TJ, United Kingdom
| | - Zoë A E Waller
- School of Pharmacy, University of East Anglia , Norwich NR4 7TJ, United Kingdom
| | - Mark Searcey
- School of Chemistry, University of East Anglia , Norwich NR4 7TJ, United Kingdom.,School of Pharmacy, University of East Anglia , Norwich NR4 7TJ, United Kingdom
| | - Maria A O'Connell
- School of Pharmacy, University of East Anglia , Norwich NR4 7TJ, United Kingdom
| | - Manfred Bochmann
- School of Chemistry, University of East Anglia , Norwich NR4 7TJ, United Kingdom
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229
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Zhu Y, Hamlow LA, He CC, Lee JK, Gao J, Berden G, Oomens J, Rodgers MT. Gas-Phase Conformations and N-Glycosidic Bond Stabilities of Sodium Cationized 2'-Deoxyguanosine and Guanosine: Sodium Cations Preferentially Bind to the Guanine Residue. J Phys Chem B 2017; 121:4048-4060. [PMID: 28355483 DOI: 10.1021/acs.jpcb.7b02906] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
2'-Deoxyguanosine (dGuo) and guanosine (Guo) are fundamental building blocks of DNA and RNA nucleic acids. In order to understand the effects of sodium cationization on the gas-phase conformations and stabilities of dGuo and Guo, infrared multiple photon dissociation (IRMPD) action spectroscopy experiments and complementary electronic structure calculations are performed. The measured IRMPD spectra of [dGuo+Na]+ and [Guo+Na]+ are compared to calculated IR spectra predicted for the stable low-energy structures computed for these species to determine the most favorable sodium cation binding sites, identify the structures populated in the experiments, and elucidate the influence of the 2'-hydroxyl substituent on the structures and IRMPD spectral features. These results are compared with those from a previous IRMPD study of the protonated guanine nucleosides to elucidate the differences between sodium cationization and protonation on structure. Energy-resolved collision-induced dissociation (ER-CID) experiments and survival yield analyses of protonated and sodium cationized dGuo and Guo are performed to compare the effects of these cations toward activating the N-glycosidic bonds of these nucleosides. For both [dGuo+Na]+ and [Guo+Na]+, the gas-phase structures populated in the experiments are found to involve bidentate binding of the sodium cation to the O6 and N7 atoms of guanine, forming a 5-membered chelation ring, with guanine found in both anti and syn orientations and C2'-endo (2T3 or 3T2) puckering of the sugar. The ER-CID results, IRMPD yields and the computed C1'-N9 bond lengths indicate that sodium cationization activates the N-glycosidic bond less effectively than protonation for both dGuo and Guo. The 2'-hydroxyl substituent of Guo is found to impact the preferred structures very little except that it enables a 2'OH···3'OH hydrogen bond to be formed, and stabilizes the N-glycosidic bond relative to that of dGuo in both the sodium cationized and protonated complexes.
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Affiliation(s)
- Y Zhu
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
| | - L A Hamlow
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
| | - C C He
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
| | - J K Lee
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
| | - J Gao
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University , Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - G Berden
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University , Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - J Oomens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University , Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - M T Rodgers
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
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230
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Joo HN, Van Thi Nguyen T, Chae HK, Seo YJ. pH-Dependant fluorescence switching of an i-motif structure incorporating an isomeric azobenzene/pyrene fluorophore. Bioorg Med Chem Lett 2017; 27:2415-2419. [PMID: 28416130 DOI: 10.1016/j.bmcl.2017.04.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 04/01/2017] [Accepted: 04/04/2017] [Indexed: 12/28/2022]
Abstract
In this study, we synthesized an Azo-py phosphoramidite, featuring azobenzene and pyrene units, as a novel fluorescent and isomeric (trans- and cis-azobenzene units) material, which we incorporated in an i-motif DNA sequence. We then monitored the structural dynamics and changes in fluorescence as the modified DNA sequences transformed from single strands at pH 7 to i-motif quadruplex structures at pH 3. After incorporating Azo-py into the 4A loop position of an i-motif sequence, dramatic changes in fluorescence occurred as the DNA structures changed from single-strands to i-motif quadruplex structures. Interestingly, the cis form of Azo-py induced a more stable i-motif structure than did the trans form, as confirmed from circular dichroism spectra and melting temperature data. The absorption and fluorescence signals of these Azo-py-incorporated i-motif systems exhibited switchable and highly correlated signaling patterns. Such isomeric structures based on Azo-py might find potential applications in biology, where control over stable i-motif quadruplex structures might be performed with switchable fluorescence signaling.
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Affiliation(s)
- Han Na Joo
- Department of Chemistry, Chonbuk National University, Jeonju 561-756, South Korea
| | - Thuy Van Thi Nguyen
- Department of Bioactive Material Sciences, Research Center of Bioactive Materials, Chonbuk National University, Jeonju 561-756, South Korea
| | - Hyeon Kyeong Chae
- Department of Chemistry, Chonbuk National University, Jeonju 561-756, South Korea
| | - Young Jun Seo
- Department of Chemistry, Chonbuk National University, Jeonju 561-756, South Korea; Department of Bioactive Material Sciences, Research Center of Bioactive Materials, Chonbuk National University, Jeonju 561-756, South Korea.
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231
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Fleming AM, Ding Y, Rogers RA, Zhu J, Zhu J, Burton AD, Carlisle CB, Burrows CJ. 4n-1 Is a "Sweet Spot" in DNA i-Motif Folding of 2'-Deoxycytidine Homopolymers. J Am Chem Soc 2017; 139:4682-4689. [PMID: 28290680 DOI: 10.1021/jacs.6b10117] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Strands of DNA with four or more contiguous runs of 2'-deoxycytidine (dC) nucleotides have the potential to adopt i-motif folds, generally under mildly acidic conditions. Analysis of dC homo-oligonucleotide strands ranging in length from 10 to 30 nucleotides by five different pH-dependent methods identified a pattern in strand length vs stability. Beginning with dC11, which does not fold, the transition pH (pHT) increased with chain length with the addition of up to four nucleotides, after which the stability dramatically decreased, and the trend repeated this cycle up to dC27. The analysis found dCn strands of length 15, 19, 23, and 27 nucleotides (i.e., 4n-1) to have pHT values >7.2 and thermal stabilities >37 °C at pH 7.0. Model studies using thymidine nucleotides to lock in i-motif loop lengths support the conclusion that the most stable dCn i-motifs possess one nucleotide in each of the three loops and a core built of an even number of base pairs. The pattern identified from the model studies occurs with a frequency of four nucleotides at lengths of 15, 19, 23, and 27 in accordance with the results obtained for the dCn strands. This observation led us to interrogate the human genome for dCn runs. Inspection of the human genome indicates that dCn runs are enriched in critical regions of the genome (promoters, UTRs, and introns), while being depleted in coding and intergenic regions, and these findings may have biological implications. Lastly, the ability to tune i-motif stabilities by the length of the strand might be harnessed for stimulus-responsive applications in DNA scaffolds, sensors, nanotechnology, and other chemical applications.
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Affiliation(s)
- Aaron M Fleming
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Yun Ding
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - R Aaron Rogers
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Judy Zhu
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Julia Zhu
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Ashlee D Burton
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Connor B Carlisle
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
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232
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González J, Usabiaga I, Arnaiz PF, León I, Martínez R, Millán J, Fernández JA. Competition between stacked and hydrogen bonded structures of cytosine aggregates. Phys Chem Chem Phys 2017; 19:8826-8834. [DOI: 10.1039/c6cp08476a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The four bases of DNA constitute what is known as the “alphabet of life”.
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Affiliation(s)
- Jorge González
- Department of Physical Chemistry
- Faculty of Science and Technology
- University of the Basque Country (UPV/EHU)
- Leioa
- Spain
| | - Imanol Usabiaga
- Department of Physical Chemistry
- Faculty of Science and Technology
- University of the Basque Country (UPV/EHU)
- Leioa
- Spain
| | - Pedro F. Arnaiz
- Department of Physical Chemistry
- Faculty of Science and Technology
- University of the Basque Country (UPV/EHU)
- Leioa
- Spain
| | - Iker León
- Department of Physical Chemistry
- Faculty of Science and Technology
- University of the Basque Country (UPV/EHU)
- Leioa
- Spain
| | - Rodrigo Martínez
- Department of Chemistry
- Faculty of Science and Technology
- University of La Rioja
- Logroño
- Spain
| | - Judith Millán
- Department of Chemistry
- Faculty of Science and Technology
- University of La Rioja
- Logroño
- Spain
| | - José A. Fernández
- Department of Physical Chemistry
- Faculty of Science and Technology
- University of the Basque Country (UPV/EHU)
- Leioa
- Spain
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233
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Karaca Ö, Meier-Menches SM, Casini A, Kühn FE. On the binding modes of metal NHC complexes with DNA secondary structures: implications for therapy and imaging. Chem Commun (Camb) 2017; 53:8249-8260. [DOI: 10.1039/c7cc03074f] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This perspective review aims at providing an overview of the most representative examples of bioactive metal NHC complexes reacting with nucleic acidsviadifferent binding modes.
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Affiliation(s)
- Özden Karaca
- Molecular Catalysis
- Department of Chemistry
- Catalysis Research Center
- Technische Universität München
- 85747 Garching bei München
| | | | - Angela Casini
- School of Chemistry
- Cardiff University
- CF103AT Cardiff
- UK
- Institute of Advanced Studies
| | - Fritz E. Kühn
- Molecular Catalysis
- Department of Chemistry
- Catalysis Research Center
- Technische Universität München
- 85747 Garching bei München
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234
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Shimoyama A, Fujisaka A, Obika S. Evaluation of size-exclusion chromatography for the analysis of phosphorothioate oligonucleotides. J Pharm Biomed Anal 2016; 136:55-65. [PMID: 28063336 DOI: 10.1016/j.jpba.2016.12.036] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 12/24/2016] [Accepted: 12/24/2016] [Indexed: 11/17/2022]
Abstract
We evaluated size exclusion chromatography (SEC) for the detection of high-order structure of phosphorothioate oligonucleotides (PS-oligo). Because of strong interaction between PS-oligo and column packing material, peaks were broader and elution time was longer than those of the corresponding natural DNA oligonucleotides. However, single- and double-stranded structures of PS-oligo were clearly separated and discriminated, while single-stranded with high-order structures such as G-quadruplex and hairpin structure were not distinguished from each other.
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Affiliation(s)
- Atsuko Shimoyama
- Analytical Research Laboratories, Technology, Astellas Pharma Inc., 5-2-3 Tokodai, Tsukuba-Shi, Ibaraki 300-2698, Japan; Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Aki Fujisaka
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; Faculty of Pharmacy, Osaka Ohtani University, 3-11-1 Nishikiori-Kita, Tondabayashi, Osaka 584-8540, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
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235
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Wright EP, Day HA, Ibrahim AM, Kumar J, Boswell LJE, Huguin C, Stevenson CEM, Pors K, Waller ZAE. Mitoxantrone and Analogues Bind and Stabilize i-Motif Forming DNA Sequences. Sci Rep 2016; 6:39456. [PMID: 28004744 PMCID: PMC5177923 DOI: 10.1038/srep39456] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 11/23/2016] [Indexed: 11/21/2022] Open
Abstract
There are hundreds of ligands which can interact with G-quadruplex DNA, yet very few which target i-motif. To appreciate an understanding between the dynamics between these structures and how they can be affected by intervention with small molecule ligands, more i-motif binding compounds are required. Herein we describe how the drug mitoxantrone can bind, induce folding of and stabilise i-motif forming DNA sequences, even at physiological pH. Additionally, mitoxantrone was found to bind i-motif forming sequences preferentially over double helical DNA. We also describe the stabilisation properties of analogues of mitoxantrone. This offers a new family of ligands with potential for use in experiments into the structure and function of i-motif forming DNA sequences.
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Affiliation(s)
- Elisé P Wright
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Henry A Day
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Ali M Ibrahim
- Institute of Cancer Therapeutics, Faculty of Life Sciences, University of Bradford, Bradford, West Yorkshire, BD7 1DP, UK
| | - Jeethendra Kumar
- Institute of Cancer Therapeutics, Faculty of Life Sciences, University of Bradford, Bradford, West Yorkshire, BD7 1DP, UK
| | - Leo J E Boswell
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Camille Huguin
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Clare E M Stevenson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Klaus Pors
- Institute of Cancer Therapeutics, Faculty of Life Sciences, University of Bradford, Bradford, West Yorkshire, BD7 1DP, UK
| | - Zoë A E Waller
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.,Centre for Molecular and Structural Biochemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
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236
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Kosevich MV, Zobnina VG, Stepanian SG, Karachevtsev VA, Adamowicz L. The effect of protonation of cytosine and adenine on their interactions with carbon nanotubes. J Mol Graph Model 2016; 70:77-84. [DOI: 10.1016/j.jmgm.2016.09.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 09/08/2016] [Accepted: 09/20/2016] [Indexed: 01/12/2023]
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237
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Kim BG, Chalikian TV. Thermodynamic linkage analysis of pH-induced folding and unfolding transitions of i-motifs. Biophys Chem 2016; 216:19-22. [DOI: 10.1016/j.bpc.2016.06.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 06/09/2016] [Accepted: 06/09/2016] [Indexed: 10/21/2022]
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238
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Yoshida W, Yoshioka H, Bay DH, Iida K, Ikebukuro K, Nagasawa K, Karube I. Detection of DNA Methylation of G-Quadruplex and i-Motif-Forming Sequences by Measuring the Initial Elongation Efficiency of Polymerase Chain Reaction. Anal Chem 2016; 88:7101-7. [PMID: 27351368 DOI: 10.1021/acs.analchem.6b00982] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
DNA methylation has been proposed as one of the promising biomarkers for cancer diagnosis. In this study, we developed a DNA methylation detection system utilizing G-quadruplex and i-motif-forming sequences that requires neither sodium bisulfite treatment nor methylated DNA ligands. We hypothesized that G-quadruplex and i-motif structures would be stabilized by DNA methylation and arrest DNA polymerase activity during quantitative polymerase chain reaction (qPCR). The PCR products from VEGF, RET G-quadruplex, and i-motif-forming sequences were used as templates and analyzed by qPCR. Our results indicated that the initial elongation efficiency of PCR decreased with increasing DNA methylation levels in the G-quadruplex and i-motif-forming sequences. Moreover, we demonstrated that the initial elongation efficiency of PCR decreased with increased DNA methylation of the VEGF region on genomic DNA. These results indicated that DNA methylation of the G-quadruplex and i-motif-forming sequences on genomic DNA can be detected by qPCR.
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Affiliation(s)
- Wataru Yoshida
- School of Bioscience and Biotechnology, Tokyo University of Technology , 1404-1 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan
| | - Hitomi Yoshioka
- School of Bioscience and Biotechnology, Tokyo University of Technology , 1404-1 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan
| | - Daniyah Habiballah Bay
- School of Bioscience and Biotechnology, Tokyo University of Technology , 1404-1 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan.,Biology Department, Umm Al-Qura University , P.O. Box 715, Makkah, 21955, Kingdom of Saudi Arabia
| | - Keisuke Iida
- Graduate School of Science and Engineering, Saitama University , Kitaadachi-gun, Saitama, 362-0806, 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 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan
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239
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Alba JJ, Sadurní A, Gargallo R. Nucleic Acid i-Motif Structures in Analytical Chemistry. Crit Rev Anal Chem 2016; 46:443-54. [DOI: 10.1080/10408347.2016.1143347] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Joan Josep Alba
- Department of Analytical Chemistry, University of Barcelona, Barcelona, Spain
| | - Anna Sadurní
- Department of Analytical Chemistry, University of Barcelona, Barcelona, Spain
| | - Raimundo Gargallo
- Department of Analytical Chemistry, University of Barcelona, Barcelona, Spain
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240
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Dembska A. The analytical and biomedical potential of cytosine-rich oligonucleotides: A review. Anal Chim Acta 2016; 930:1-12. [PMID: 27265899 DOI: 10.1016/j.aca.2016.05.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 04/30/2016] [Accepted: 05/04/2016] [Indexed: 02/04/2023]
Abstract
Polycytosine DNA strands are often found among natural sequences, including the ends of telomeres, centromeres, and introns or in the regulatory regions of genes. A characteristic feature of oligonucleotides that are rich in cytosine (C-rich) is their ability to associate under acidic conditions to form a tetraplex i-motif consisting of two parallel stranded cytosine-hemiprotonated cytosine (C·C+) base-paired duplexes that are mutually intercalated in an antiparallel orientation. Nanotechnology has been exploiting the advantages of i-motif pH-dependent formation to fabricate nanomachines, nanoswitches, electrodes and intelligent nanosurfaces or nanomaterials. Although a few reviews regarding the structure, properties and applications of i-motifs have been published, this review focuses on recently developed biosensors (e.g., to detect pH, glucose or silver ions) and drug-delivery biomaterials. Furthermore, we have included examples of sensors based on parallel C-rich triplexes and silver nanoclusters (AgNCs) fabricated on cytosine-rich DNA strands. The potential diagnostic and therapeutic applications of this type of material are discussed.
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Affiliation(s)
- Anna Dembska
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland.
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241
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Assi HA, Harkness RW, Martin-Pintado N, Wilds CJ, Campos-Olivas R, Mittermaier AK, González C, Damha MJ. Stabilization of i-motif structures by 2'-β-fluorination of DNA. Nucleic Acids Res 2016; 44:4998-5009. [PMID: 27166371 PMCID: PMC4914123 DOI: 10.1093/nar/gkw402] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 05/02/2016] [Indexed: 01/12/2023] Open
Abstract
i-Motifs are four-stranded DNA structures consisting of two parallel DNA duplexes held together by hemi-protonated and intercalated cytosine base pairs (C:CH+). They have attracted considerable research interest for their potential role in gene regulation and their use as pH responsive switches and building blocks in macromolecular assemblies. At neutral and basic pH values, the cytosine bases deprotonate and the structure unfolds into single strands. To avoid this limitation and expand the range of environmental conditions supporting i-motif folding, we replaced the sugar in DNA by 2-deoxy-2-fluoroarabinose. We demonstrate that such a modification significantly stabilizes i-motif formation over a wide pH range, including pH 7. Nuclear magnetic resonance experiments reveal that 2-deoxy-2-fluoroarabinose adopts a C2′-endo conformation, instead of the C3′-endo conformation usually found in unmodified i-motifs. Nevertheless, this substitution does not alter the overall i-motif structure. This conformational change, together with the changes in charge distribution in the sugar caused by the electronegative fluorine atoms, leads to a number of favorable sequential and inter-strand electrostatic interactions. The availability of folded i-motifs at neutral pH will aid investigations into the biological function of i-motifs in vitro, and will expand i-motif applications in nanotechnology.
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Affiliation(s)
- Hala Abou Assi
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
| | - Robert W Harkness
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
| | | | - Christopher J Wilds
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada Department of Chemistry and Biochemistry, Concordia University, Montreal, QC H4B 1R6, Canada
| | | | | | - Carlos González
- Instituto de Química Física 'Rocasolano', CSIC, 28006 Madrid, Spain
| | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
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242
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Li J, Mo L, Lu CH, Fu T, Yang HH, Tan W. Functional nucleic acid-based hydrogels for bioanalytical and biomedical applications. Chem Soc Rev 2016; 45:1410-31. [PMID: 26758955 PMCID: PMC4775362 DOI: 10.1039/c5cs00586h] [Citation(s) in RCA: 354] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Hydrogels are crosslinked hydrophilic polymers that can absorb a large amount of water. By their hydrophilic, biocompatible and highly tunable nature, hydrogels can be tailored for applications in bioanalysis and biomedicine. Of particular interest are DNA-based hydrogels owing to the unique features of nucleic acids. Since the discovery of the DNA double helical structure, interest in DNA has expanded beyond its genetic role to applications in nanotechnology and materials science. In particular, DNA-based hydrogels present such remarkable features as stability, flexibility, precise programmability, stimuli-responsive DNA conformations, facile synthesis and modification. Moreover, functional nucleic acids (FNAs) have allowed the construction of hydrogels based on aptamers, DNAzymes, i-motif nanostructures, siRNAs and CpG oligodeoxynucleotides to provide additional molecular recognition, catalytic activities and therapeutic potential, making them key players in biological analysis and biomedical applications. To date, a variety of applications have been demonstrated with FNA-based hydrogels, including biosensing, environmental analysis, controlled drug release, cell adhesion and targeted cancer therapy. In this review, we focus on advances in the development of FNA-based hydrogels, which have fully incorporated both the unique features of FNAs and DNA-based hydrogels. We first introduce different strategies for constructing DNA-based hydrogels. Subsequently, various types of FNAs and the most recent developments of FNA-based hydrogels for bioanalytical and biomedical applications are described with some selected examples. Finally, the review provides an insight into the remaining challenges and future perspectives of FNA-based hydrogels.
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Affiliation(s)
- Juan Li
- The Key Lab of Analysis and Detection Technology for Food Safety of the MOE and Fujian Province, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350002, China. and Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Molecular Engineering and Theranostics, Hunan University, Changsha 410082, China.
| | - Liuting Mo
- Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Molecular Engineering and Theranostics, Hunan University, Changsha 410082, China.
| | - Chun-Hua Lu
- The Key Lab of Analysis and Detection Technology for Food Safety of the MOE and Fujian Province, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350002, China.
| | - Ting Fu
- Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Molecular Engineering and Theranostics, Hunan University, Changsha 410082, China. and Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, University of Florida, Gainesville, FL 32611-7200, USA
| | - Huang-Hao Yang
- The Key Lab of Analysis and Detection Technology for Food Safety of the MOE and Fujian Province, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350002, China.
| | - Weihong Tan
- Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Molecular Engineering and Theranostics, Hunan University, Changsha 410082, China. and Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, University of Florida, Gainesville, FL 32611-7200, USA
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243
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Chandrasekaran AR. Programmable DNA scaffolds for spatially-ordered protein assembly. NANOSCALE 2016; 8:4436-4446. [PMID: 26852879 DOI: 10.1039/c5nr08685j] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Ever since the notion of using DNA as a material was realized, it has been employed in the construction of complex structures that facilitate the assembly of nanoparticles or macromolecules with nanometer-scale precision. Specifically, tiles fashioned from DNA strands and DNA origami sheets have been shown to be suitable as scaffolds for immobilizing proteins with excellent control over their spatial positioning. Supramolecular assembly of proteins into periodic arrays in one or more dimensions is one of the most challenging aspects in the design of scaffolds for biomolecular investigations and macromolecular crystallization. This review provides a brief overview of how various biomolecular interactions with high degree of specificity such as streptavidin-biotin, antigen-antibody, and aptamer-protein interactions have been used to fabricate linear and multidimensional assemblies of structurally intact and functional proteins. The use of DNA-binding proteins as adaptors, polyamide recognition on DNA scaffolds and oligonucleotide linkers for protein assembly are also discussed.
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244
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Gao J, Berden G, Rodgers MT, Oomens J. Interaction of Cu(+) with cytosine and formation of i-motif-like C-M(+)-C complexes: alkali versus coinage metals. Phys Chem Chem Phys 2016; 18:7269-77. [PMID: 26894838 DOI: 10.1039/c6cp00234j] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The Watson-Crick structure of DNA is among the most well-known molecular structures of our time. However, alternative base-pairing motifs are also known to occur, often depending on base sequence, pH, or the presence of cations. Pairing of cytosine (C) bases induced by the sharing of a single proton (C-H(+)-C) may give rise to the so-called i-motif, which occurs primarily in expanded trinucleotide repeats and the telomeric region of DNA, particularly at low pH. At physiological pH, silver cations were recently found to stabilize C dimers in a C-Ag(+)-C structure analogous to the hemiprotonated C-dimer. Here we use infrared ion spectroscopy in combination with density functional theory calculations at the B3LYP/6-311G+(2df,2p) level to show that copper in the 1+ oxidation state induces an analogous formation of C-Cu(+)-C structures. In contrast to protons and these transition metal ions, alkali metal ions induce a different dimer structure, where each ligand coordinates the alkali metal ion in a bidentate fashion in which the N3 and O2 atoms of both cytosine ligands coordinate to the metal ion, sacrificing hydrogen-bonding interactions between the ligands for improved chelation of the metal cation.
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Affiliation(s)
- Juehan Gao
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525 ED Nijmegen, The Netherlands.
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245
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Abstract
Fluorescent silver nanoclusters (Ag-NCs) are in prominence as novel sensing materials due to their biocompatibility, photostability, and molecule-like optical properties. The present work is carried out on an array (17 sequences) of 16 bases long cytosine rich, single stranded DNA templates 5′-C3XiC3XiiC3XiiiC3Xiv-3′ where i, ii, iii, iv correspond to T/G/C deoxynucleobases (with default base A). Among all the oligonucleotides, a sequence C3AC3AC3TC3G (3T4G) has been identified, which grows three different near-infrared-emitting NC species with absorption/emission maxima at ~620/700 (species I), 730/800 (species II), and 830 (Species III) nm, respectively. The nature of the spectral profiles, along with relevant parameters namely absorption maximum (λabsmax), emission maximum (λemmax), anisotropy (r), lifetime (τ), circular dichroism spectral data are used to understand the microenvironments of the fluorescent NC species I, II, and III. DNA:Ag stiochiometric, pH and solvent dependent studies proved that i-motif scaffolds with different folding topologies are associated with the growth of these three species and a certain concentration of silver and H+ favor the growth of species III. Size exclusion chromatographic measurements provided similar indications that a folded, more compact, classic i-motif template is associated with the formation of the longer NIR (~830 nm) absorbing species. This study provides a more definitive approach to design and obtain a targeted DNA templated Ag-NC with required emission properties for biophysical and cellular applications.
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Affiliation(s)
- Bidisha Sengupta
- Department of Chemistry, Tougaloo College, 500 West County Line Road, Tougaloo, MS 39174, USA; (C.C.); (K.C.); (A.S.)
- Correspondence: ; Tel.: +1-601-977-7779; Fax: +1-601-977-7898
| | - Christa Corley
- Department of Chemistry, Tougaloo College, 500 West County Line Road, Tougaloo, MS 39174, USA; (C.C.); (K.C.); (A.S.)
| | - Keith Cobb
- Department of Chemistry, Tougaloo College, 500 West County Line Road, Tougaloo, MS 39174, USA; (C.C.); (K.C.); (A.S.)
| | - Anthony Saracino
- Department of Chemistry, Tougaloo College, 500 West County Line Road, Tougaloo, MS 39174, USA; (C.C.); (K.C.); (A.S.)
| | - Steffen Jockusch
- Department of Chemistry, Columbia University, 3000 Broadway, New York, NY 10027, USA;
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246
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Kaushik M, Kaushik S, Roy K, Singh A, Mahendru S, Kumar M, Chaudhary S, Ahmed S, Kukreti S. A bouquet of DNA structures: Emerging diversity. Biochem Biophys Rep 2016; 5:388-395. [PMID: 28955846 PMCID: PMC5600441 DOI: 10.1016/j.bbrep.2016.01.013] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 12/28/2015] [Accepted: 01/22/2016] [Indexed: 11/29/2022] Open
Abstract
Structural polymorphism of DNA has constantly been evolving from the time of illustration of the double helical model of DNA by Watson and Crick. A variety of non-canonical DNA structures have constantly been documented across the globe. DNA attracted worldwide attention as a carrier of genetic information. In addition to the classical Watson–Crick duplex, DNA can actually adopt diverse structures during its active participation in cellular processes like replication, transcription, recombination and repair. Structures like hairpin, cruciform, triplex, G-triplex, quadruplex, i-motif and other alternative non-canonical DNA structures have been studied at length and have also shown their in vivo occurrence. This review mainly focuses on non-canonical structures adopted by DNA oligonucleotides which have certain prerequisites for their formation in terms of sequence, its length, number and orientation of strands along with varied solution conditions. This conformational polymorphism of DNA might be the basis of different functional properties of a specific set of DNA sequences, further giving some insights for various extremely complicated biological phenomena. Many of these structures have already shown their linkages with diseases like cancer and genetic disorders, hence making them an extremely striking target for structure-specific drug designing and therapeutic applications. DNA can adopt diverse range of structures other than classical Watson–Crick duplex. Discussion of alternate structures like hairpin, cruciform, triplex, quadruplex etc. This review gives some insights for the biological relevance of DNA structures.
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Affiliation(s)
- Mahima Kaushik
- Cluster Innovation Centre, University of Delhi, Delhi, India.,Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Shikha Kaushik
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Kapil Roy
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Anju Singh
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Swati Mahendru
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Mohan Kumar
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Swati Chaudhary
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Saami Ahmed
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Shrikant Kukreti
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
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247
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Chang T, Gong H, Ding P, Liu X, Li W, Bing T, Cao Z, Shangguan D. Activity Enhancement of G-Quadruplex/Hemin DNAzyme by Flanking d(CCC). Chemistry 2016; 22:4015-21. [PMID: 26813684 DOI: 10.1002/chem.201504797] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Indexed: 12/17/2022]
Abstract
G-quadruplex (G4)/hemin DNAzymes have been extensively applied in bioanalysis and molecular devices. However, their catalytic activity is still much lower than that of proteinous enzymes. The G4/hemin DNAzyme activity is correlated with the G4 conformations and the solution conditions. However, little is known about the effect of the flanking sequences on the activity, though they are important parts of G4s. Here, we report sequences containing d(CCC), flanked on both ends of the G4-core sequences remarkably enhance their DNAzyme activity. By using circular dichroism and UV-visible spectroscopy, the d(CCC) flanking sequences were demonstrated to improve the hemin binding affinity to G4s instead of increasing the parallel G4 formation, which might explain the enhanced DNAzyme activity. Meanwhile, the increased hemin binding ability promoted the degradation of hemin within the DNAzyme by H2O2. Furthermore, the DNAzyme with d(CCC) flanking sequences showed strong tolerance to pH value changes, which makes it more suitable for applications requiring wide pH conditions. The results highlight the influence of the flanking sequences on the DNAzyme activity and provide insightful information for the design of highly active DNAzymes.
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Affiliation(s)
- Tianjun Chang
- Institute of Resources and Environment, Henan Polytechnic University, Jiaozuo, 454000, P.R. China
| | - Hongmei Gong
- Institute of Resources and Environment, Henan Polytechnic University, Jiaozuo, 454000, P.R. China
| | - Pi Ding
- Institute of Resources and Environment, Henan Polytechnic University, Jiaozuo, 454000, P.R. China
| | - Xiangjun Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P.R. China
| | - Weiguo Li
- Institute of Resources and Environment, Henan Polytechnic University, Jiaozuo, 454000, P.R. China
| | - Tao Bing
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P.R. China
| | - Zehui Cao
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P.R. China
| | - Dihua Shangguan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P.R. China.
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248
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Bedrat A, Lacroix L, Mergny JL. Re-evaluation of G-quadruplex propensity with G4Hunter. Nucleic Acids Res 2016; 44:1746-59. [PMID: 26792894 PMCID: PMC4770238 DOI: 10.1093/nar/gkw006] [Citation(s) in RCA: 423] [Impact Index Per Article: 52.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 01/03/2016] [Indexed: 01/01/2023] Open
Abstract
Critical evidence for the biological relevance of G-quadruplexes (G4) has recently been obtained in seminal studies performed in a variety of organisms. Four-stranded G-quadruplex DNA structures are promising drug targets as these non-canonical structures appear to be involved in a number of key biological processes. Given the growing interest for G4, accurate tools to predict G-quadruplex propensity of a given DNA or RNA sequence are needed. Several algorithms such as Quadparser predict quadruplex forming propensity. However, a number of studies have established that sequences that are not detected by these tools do form G4 structures (false negatives) and that other sequences predicted to form G4 structures do not (false positives). Here we report development and testing of a radically different algorithm, G4Hunter that takes into account G-richness and G-skewness of a given sequence and gives a quadruplex propensity score as output. To validate this model, we tested it on a large dataset of 392 published sequences and experimentally evaluated quadruplex forming potential of 209 sequences using a combination of biophysical methods to assess quadruplex formation in vitro. We experimentally validated the G4Hunter algorithm on a short complete genome, that of the human mitochondria (16.6 kb), because of its relatively high GC content and GC skewness as well as the biological relevance of these quadruplexes near instability hotspots. We then applied the algorithm to genomes of a number of species, including humans, allowing us to conclude that the number of sequences capable of forming stable quadruplexes (at least in vitro) in the human genome is significantly higher, by a factor of 2–10, than previously thought.
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Affiliation(s)
- Amina Bedrat
- Université de Bordeaux, ARNA Laboratory, F-33000 Bordeaux, France Inserm U1212, CNRS UMR 5320, IECB, F-33600 Pessac, France
| | - Laurent Lacroix
- CNRS-Université de Toulouse UMR5099, F-31000 Toulouse, France
| | - Jean-Louis Mergny
- Université de Bordeaux, ARNA Laboratory, F-33000 Bordeaux, France Inserm U1212, CNRS UMR 5320, IECB, F-33600 Pessac, France
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249
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G-Quadruplexes Involving Both Strands of Genomic DNA Are Highly Abundant and Colocalize with Functional Sites in the Human Genome. PLoS One 2016; 11:e0146174. [PMID: 26727593 PMCID: PMC4699641 DOI: 10.1371/journal.pone.0146174] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 12/13/2015] [Indexed: 11/20/2022] Open
Abstract
The G-quadruplex is a non-canonical DNA structure biologically significant in DNA replication, transcription and telomere stability. To date, only G4s with all guanines originating from the same strand of DNA have been considered in the context of the human nuclear genome. Here, I discuss interstrand topological configurations of G-quadruplex DNA, consisting of guanines from both strands of genomic DNA; an algorithm is presented for predicting such structures. I have identified over 550,000 non-overlapping interstrand G-quadruplex forming sequences in the human genome—significantly more than intrastrand configurations. Functional analysis of interstrand G-quadruplex sites shows strong association with transcription initiation, the results are consistent with the XPB and XPD transcriptional helicases binding only to G-quadruplex DNA with interstrand topology. Interstrand quadruplexes are also enriched in origin of replication sites. Several topology classes of interstrand quadruplex-forming sequences are possible, and different topologies are enriched in different types of structural elements. The list of interstrand quadruplex forming sequences, and the computer program used for their prediction are available at the web address http://moment.utmb.edu/allquads.
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250
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Xu L, Hong S, Sun N, Wang K, Zhou L, Ji L, Pei R. Berberine as a novel light-up i-motif fluorescence ligand and its application in designing molecular logic systems. Chem Commun (Camb) 2016; 52:179-82. [DOI: 10.1039/c5cc08242k] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Berberine is reported as a light-up fluorescence ligand for i-motif structures, which enables the development of label-free DNA-based logic gates.
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Affiliation(s)
- Lijun Xu
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou, 215123
| | - Shanni Hong
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou, 215123
| | - Na Sun
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou, 215123
| | - Kewei Wang
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou, 215123
| | - Lu Zhou
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou, 215123
| | - Liya Ji
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou, 215123
| | - Renjun Pei
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou, 215123
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