1
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Mir B, Serrano-Chacón I, Medina P, Macaluso V, Terrazas M, Gandioso A, Garavís M, Orozco M, Escaja N, González C. Site-specific incorporation of a fluorescent nucleobase analog enhances i-motif stability and allows monitoring of i-motif folding inside cells. Nucleic Acids Res 2024; 52:3375-3389. [PMID: 38366792 PMCID: PMC11014255 DOI: 10.1093/nar/gkae106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 01/17/2024] [Accepted: 02/09/2024] [Indexed: 02/18/2024] Open
Abstract
The i-motif is an intriguing non-canonical DNA structure, whose role in the cell is still controversial. Development of methods to study i-motif formation under physiological conditions in living cells is necessary to study its potential biological functions. The cytosine analog 1,3-diaza-2-oxophenoxazine (tCO) is a fluorescent nucleobase able to form either hemiprotonated base pairs with cytosine residues, or neutral base pairs with guanines. We show here that when tCO is incorporated in the proximity of a G:C:G:C minor groove tetrad, it induces a strong thermal and pH stabilization, resulting in i-motifs with Tm of 39ºC at neutral pH. The structural determination by NMR methods reveals that the enhanced stability is due to a large stacking interaction between the guanines of the tetrad with the tCO nucleobase, which forms a tCO:C+ in the folded structure at unusually-high pHs, leading to an increased quenching in its fluorescence at neutral conditions. This quenching is much lower when tCO is base-paired to guanines and totally disappears when the oligonucleotide is unfolded. By taking profit of this property, we have been able to monitor i-motif folding in cells.
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Affiliation(s)
- Bartomeu Mir
- Instituto de Química Física ‘Blas Cabrera’. CSIC. Serrano 119. 28006 Madrid. Spain
- Inorganic and Organic Chemistry Department. Organic Chemistry Section and IBUB. University of Barcelona, Martí i Franquès 1-11, 08028 Barcelona. Spain
| | - Israel Serrano-Chacón
- Instituto de Química Física ‘Blas Cabrera’. CSIC. Serrano 119. 28006 Madrid. Spain
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology (BIST). 08028 Barcelona. Spain
| | - Pedro Medina
- 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. 08028 Barcelona. Spain
| | - Veronica Macaluso
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology (BIST). 08028 Barcelona. Spain
| | - Montserrat Terrazas
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology (BIST). 08028 Barcelona. Spain
- Inorganic and Organic Chemistry Department. Organic Chemistry Section and IBUB. University of Barcelona, Martí i Franquès 1-11, 08028 Barcelona. Spain
| | - Albert Gandioso
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology (BIST). 08028 Barcelona. Spain
| | - Miguel Garavís
- Instituto de Química Física ‘Blas Cabrera’. CSIC. Serrano 119. 28006 Madrid. 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. 08028 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
| | - Carlos González
- Instituto de Química Física ‘Blas Cabrera’. CSIC. Serrano 119. 28006 Madrid. Spain
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2
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Boissieras J, Granzhan A. Potentiometric titrations to study ligand interactions with DNA i-motifs. Methods Enzymol 2023; 695:233-254. [PMID: 38521587 DOI: 10.1016/bs.mie.2023.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2024]
Abstract
i-Motifs are non-canonical secondary structures of DNA formed by mutual intercalation of hemi-protonated cytosine-cytosine base pairs, most typically in slightly acidic conditions (pH<7.0). These structures are well-studied in vitro and have recently been suggested to exist in cells. Despite nearly a decade of active research, the quest for small-molecule ligands that could selectively bind to and stabilize i-motifs continues, and no reference, bona fide i-motif ligand is currently available. This is, at least in part, due to the lack of robust methods to assess the interaction of ligands with i-motifs, since many techniques well-established for studies of other secondary structures (such as CD-, UV-, and FRET-melting) may generate artifacts when applied to i-motifs. Here, we describe an implementation of automated, potentiometric (pH) titrations as a robust isothermal method to assess the impact of ligands or cosolutes on thermodynamic stability of i-motifs. This approach is validated through the use of a cosolute previously known to stabilize i-motifs (PEG2000) and three small-molecule ligands that are able to stabilize, destabilize, or have no effect on the stability of i-motifs, respectively.
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Affiliation(s)
- Joseph Boissieras
- CMBC, CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, Orsay, France; CMBC, CNRS UMR9187, INSERM U1196, Université Paris Saclay, Orsay, France
| | - Anton Granzhan
- CMBC, CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, Orsay, France; CMBC, CNRS UMR9187, INSERM U1196, Université Paris Saclay, Orsay, France.
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3
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Karimi A, Wang K, Basran K, Copp W, Luedtke NW. A Bright and Ionizable Cytosine Mimic for i-Motif Structures. Bioconjug Chem 2023. [PMID: 37196003 DOI: 10.1021/acs.bioconjchem.3c00055] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
A new fluorescent cytosine analog "tsC" containing a trans-stilbene moiety was synthesized and incorporated into hemiprotonated base pairs that comprise i-motif structures. Unlike previously reported fluorescent base analogs, tsC mimics the acid-base properties of cytosine (pKa ≈ 4.3) while exhibiting bright (ε × Φ ≈ 1000 cm-1 M-1) and red-shifted fluorescence (λem = 440 → 490 nm) upon its protonation in the water-excluded interface of tsC+:C base pairs. Ratiometric analyses of tsC emission wavelengths facilitate real-time tracking of reversible conversions between single-stranded, double-stranded, and i-motif structures derived from the human telomeric repeat sequence. Comparisons between local changes in tsC protonation with global structure changes according to circular dichroism suggest partial formation of hemiprotonated base pairs in the absence of global i-motif structures at pH = 6.0. In addition to providing a highly fluorescent and ionizable cytosine analog, these results suggest that hemiprotonated C+:C base pairs can form in partially folded single-stranded DNA in the absence of global i-motif structures.
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Affiliation(s)
- Ashkan Karimi
- Department of Chemistry, McGill University, Montreal, Quebec H3A-0B8, Canada
- Centre de recherche en biologie structural, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Kaixiang Wang
- Department of Chemistry, McGill University, Montreal, Quebec H3A-0B8, Canada
| | - Kaleena Basran
- Department of Chemistry, McGill University, Montreal, Quebec H3A-0B8, Canada
| | - William Copp
- Department of Chemistry, McGill University, Montreal, Quebec H3A-0B8, Canada
| | - Nathan W Luedtke
- Department of Chemistry, McGill University, Montreal, Quebec H3A-0B8, Canada
- Centre de recherche en biologie structural, McGill University, Montreal, Quebec H3G 0B1, Canada
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec H3A-1A3, Canada
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4
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Luo X, Zhang J, Gao Y, Pan W, Yang Y, Li X, Chen L, Wang C, Wang Y. Emerging roles of i-motif in gene expression and disease treatment. Front Pharmacol 2023; 14:1136251. [PMID: 37021044 PMCID: PMC10067743 DOI: 10.3389/fphar.2023.1136251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 02/27/2023] [Indexed: 03/22/2023] Open
Abstract
As non-canonical nucleic acid secondary structures consisting of cytosine-rich nucleic acids, i-motifs can form under certain conditions. Several i-motif sequences have been identified in the human genome and play important roles in biological regulatory functions. Due to their physicochemical properties, these i-motif structures have attracted attention and are new targets for drug development. Herein, we reviewed the characteristics and mechanisms of i-motifs located in gene promoters (including c-myc, Bcl-2, VEGF, and telomeres), summarized various small molecule ligands that interact with them, and the possible binding modes between ligands and i-motifs, and described their effects on gene expression. Furthermore, we discussed diseases closely associated with i-motifs. Among these, cancer is closely associated with i-motifs since i-motifs can form in some regions of most oncogenes. Finally, we introduced recent advances in the applications of i-motifs in multiple areas.
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Affiliation(s)
| | | | | | | | | | | | | | - Chang Wang
- *Correspondence: Chang Wang, ; Yuqing Wang,
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5
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Li X, Dai X, Pan Y, Sun Y, Yang B, Chen K, Wang Y, Xu JF, Dong Y, Yang YR, Yan LT, Liu D. Studies on the Synergistic Effect of Tandem Semi-Stable Complementary Domains on Sequence-Defined DNA Block Copolymers. J Am Chem Soc 2022; 144:21267-21277. [DOI: 10.1021/jacs.2c08930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Xin Li
- Engineering Research Center of Advanced Rare Earth Materials (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Xiaobin Dai
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Yufan Pan
- Engineering Research Center of Advanced Rare Earth Materials (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yawei Sun
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering, China University of Petroleum (Huadong), Qingdao 258000, China
| | - Bo Yang
- Engineering Research Center of Advanced Rare Earth Materials (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Kun Chen
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - You Wang
- Engineering Research Center of Advanced Rare Earth Materials (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Jiang-Fei Xu
- Key Lab of Organic Optoelectronics & Molecular Engineering, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yuanchen Dong
- CAS Key Laboratory of Colloid Interface and Chemical Thermodynamics, Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Yuhe Renee Yang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Li-Tang Yan
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Dongsheng Liu
- Engineering Research Center of Advanced Rare Earth Materials (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
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6
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Yang T, Xu Q, Chen J, Jia PK, Xie BB, Wang D, Zhou X, Shao Y. Selectively Identifying Exposed-over-Unexposed C-C + Pairs in Human Telomeric i-Motif Structures with Length-Dependent Polymorphism. Anal Chem 2022; 94:14994-15001. [PMID: 36263663 DOI: 10.1021/acs.analchem.2c02875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The i-motif structure (iM) has attracted much attention, because of its in vivo bioactivity and wide in vitro applications such as DNA-based switches. Herein, the length-dependent folding of cytosine-rich repeats of the human telomeric 5'-(CCCTAA)n-1CCC-3' (iM-n, where n = 2-8) was fully explored. We found that iM-4, iM-5, and iM-8 mainly form the intramolecular monomer iM structures, while a tetramolecular structure populates only for iM-3. However, iM-6 and iM-7 have the potential to fold as well into the dimeric iM structures besides the monomer ones. The natural hypericin (Hyp) was used as the polymorphism-selective probe to recognize the iM structures. Interestingly, only iM-3, iM-6, and iM-7 can efficiently switch on the Hyp fluorescence by specifically binding with the outmost C-C+ base pairs that are exposed directly to solution. However, other iM structures that fold in a way with a coverage of the outmost C-C+ pairs by loop sequences are totally unavailable for the Hyp binding. Theoretical modeling indicates that adaptive π-π and cation-π interactions contribute to the Hyp recognition toward the exposed C-C+ pairs. This specific iM recognition can be boosted by a photocatalytic DNAzyme construct. Our work provides a reliable fluorescence method to selectively explore the polymorphism of iM structures.
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Affiliation(s)
- Tong Yang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, People's Republic of China
| | - Qiuda Xu
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, People's Republic of China
| | - Jiahui Chen
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, People's Republic of China
| | - Pei-Ke Jia
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, 1108 Gengwen Road, Hangzhou 311231, Zhejiang, People's Republic of China
| | - Bin-Bin Xie
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, 1108 Gengwen Road, Hangzhou 311231, Zhejiang, People's Republic of China
| | - Dandan Wang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, People's Republic of China
| | - Xiaoshun Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, People's Republic of China
| | - Yong Shao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, People's Republic of China
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7
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Mondal M, Gao YQ. Microscopic Insight into pH-Dependent Conformational Dynamics and Noncanonical Base Pairing in Telomeric i-Motif DNA. J Phys Chem Lett 2022; 13:5109-5115. [PMID: 35657602 DOI: 10.1021/acs.jpclett.2c00640] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Gene regulatory functions of noncanonical i-motif DNA are associated with dynamic i-motif formation in the cellular environment and pH variation. With atomistic simulations, we show the dramatic influence of solvent pH on the conformational dynamics of biologically relevant telomeric i-motif DNA coupled with protonation of cytosine bases in different conformations. We rationalized the pH-dependent dynamics and conformational variability of the i-motif in terms of base pairing and specific loop motions. The human telomeric i-motif is found to acquire various metastable folded conformations at pH values near the pKa of cytosine with the formation of a noncanonical C:C W:W trans base pair along with the hemiprotonated C:C+ pairs in the i-motif core. pH-dependent dynamics and the local solvent structure of i-motif DNA imply that the presence of a cosolvent or molecular crowding can promote i-motif formation in vivo by changing the conformational fluctuations and hydration state of the structure.
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Affiliation(s)
- Manas Mondal
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, 518107 Shenzhen, China
| | - Yi Qin Gao
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, 518107 Shenzhen, China
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, 100871 Beijing, China
- Biomedical Pioneering Innovation Center, Peking University, 100871 Beijing, China
- Beijing Advanced Innovation Center for Genomics, Peking University, 100871 Beijing, China
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8
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Mohanty BK, Karam JA, Howley BV, Dalton AC, Grelet S, Dincman T, Streitfeld WS, Yoon JH, Balakrishnan L, Chazin WJ, Long DT, Howe PH. Heterogeneous nuclear ribonucleoprotein E1 binds polycytosine DNA and monitors genome integrity. Life Sci Alliance 2021; 4:4/9/e202000995. [PMID: 34272328 PMCID: PMC8321654 DOI: 10.26508/lsa.202000995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 11/24/2022] Open
Abstract
hnRNP E1 binds polycytosine tracts of DNA and monitors genome integrity. Heterogeneous nuclear ribonucleoprotein E1 (hnRNP E1) is a tumor suppressor protein that binds site- and structure-specifically to RNA sequences to regulate mRNA stability, facilitate alternative splicing, and suppress protein translation on several metastasis-associated mRNAs. Here, we show that hnRNP E1 binds polycytosine-rich DNA tracts present throughout the genome, including those at promoters of several oncogenes and telomeres and monitors genome integrity. It binds DNA in a site- and structure-specific manner. hnRNP E1-knockdown cells displayed increased DNA damage signals including γ-H2AX at its binding sites and also showed increased mutations. UV and hydroxyurea treatment of hnRNP E1-knockdown cells exacerbated the basal DNA damage signals with increased cell cycle arrest, activation of checkpoint proteins, and monoubiquitination of proliferating cell nuclear antigen despite no changes in deubiquitinating enzymes. DNA damage caused by genotoxin treatment localized to hnRNP E1 binding sites. Our work suggests that hnRNP E1 facilitates functions of DNA integrity proteins at polycytosine tracts and monitors DNA integrity at these sites.
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Affiliation(s)
- Bidyut K Mohanty
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Joseph Aq Karam
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Breege V Howley
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Annamarie C Dalton
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Simon Grelet
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA.,Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA
| | - Toros Dincman
- Division of Hematology and Oncology, Department of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - William S Streitfeld
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Je-Hyun Yoon
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Lata Balakrishnan
- Department of Biology, School of Science, Indiana University Purdue University Indianapolis, Indianapolis, IN, USA
| | - Walter J Chazin
- Departments of Biochemistry and Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - David T Long
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Philip H Howe
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA .,Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA
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9
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Minasyan AS, Chakravarthy S, Vardelly S, Joseph M, Nesterov EE, Nesterova IV. Rational design of guiding elements to control folding topology in i-motifs with multiple quadruplexes. NANOSCALE 2021; 13:8875-8883. [PMID: 33949568 PMCID: PMC8210535 DOI: 10.1039/d1nr00611h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Nucleic acids are versatile scaffolds that accommodate a wide range of precisely defined operational characteristics. Rational design of sensing, molecular computing, nanotechnology, and other nucleic acid devices requires precise control over folding conformations in these macromolecules. Here, we report a new approach that empowers well-defined conformational transitions in DNA molecular devices. Specifically, we develop tools for precise folding of multiple DNA quadruplexes (i-motifs) within the same oligonucleotide strand. To accomplish this task, we modify a DNA strand with kinetic control elements (hairpins and double stranded stems) that fold on a much faster timescale and consequently guide quadruplexes toward the targeted folding topology. To demonstrate that such guiding elements indeed facilitate formation of the targeted folding topology, we thoroughly characterize the folding/unfolding transitions through a combination of thermodynamic techniques, size exclusion chromatography (SEC) and small-angle X-ray scattering (SAXS). Furthermore, we extend SAXS capabilities to produce a direct insight on the shape and dimensions of the folded quadruplexes by computing their electron density maps from solution scattering data.
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Affiliation(s)
- Alexander S Minasyan
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA.
| | | | - Suchitra Vardelly
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA.
| | - Mark Joseph
- Department of Natural Science, University of Maryland Eastern Shore, Princess Anne, MD 21853, USA
| | - Evgueni E Nesterov
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA.
| | - Irina V Nesterova
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA.
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10
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Turaev AV, Isaakova EA, Severov VV, Bogomazova AN, Zatsepin TS, Sardushkin MV, Aralov AV, Lagarkova MA, Pozmogova GE, Varizhuk AM. Genomic DNA i-motifs as fast sensors responsive to near-physiological pH microchanges. Biosens Bioelectron 2020; 175:112864. [PMID: 33309217 DOI: 10.1016/j.bios.2020.112864] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 11/11/2020] [Accepted: 11/24/2020] [Indexed: 02/06/2023]
Abstract
We report the design of robust sensors for measuring intracellular pH, based on the native DNA i-motifs (iMs) found in neurodegeneration- or carcinogenesis-related genes. Those iMs appear to be genomic regulatory elements and might modulate transcription in response to pH stimuli. Given their intrinsic sensitivity to minor pH changes within the physiological range, such noncanonical DNA structures can be used as sensor core elements without additional modules other than fluorescent labels or quenchers. We focused on several iMs that exhibited fast folding/unfolding kinetics. Using stopped-flow techniques and FRET-melting/annealing assays, we confirmed that the rates of temperature-driven iM-ssDNA transitions correlate with the rates of the pH-driven transitions. Thus, we propose FRET-based hysteresis analysis as an express method for selecting sensors with desired kinetic characteristics. For the leading fast-response sensor, we optimized the labelling scheme and performed intracellular calibration. Unlike the commonly used small-molecule pH indicators, that sensor was transferred efficiently to cell nuclei. Considering its favourable kinetic characteristics, the sensor can be used for monitoring proton dynamics in the nucleus. These results argue that the 'genome-inspired' design is a productive approach to the development of biocompatible molecular tools.
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Affiliation(s)
- Anton V Turaev
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia
| | - Ekaterina A Isaakova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia
| | - Vjacheslav V Severov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia
| | - Alexandra N Bogomazova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia
| | - Timofei S Zatsepin
- Skolkovo Institute of Science and Technology, Moscow Oblast, 143026, Russia
| | - Makar V Sardushkin
- Mendeleev University of Chemical Technology of Russia, Moscow, 125047, Russia
| | - Andrey V Aralov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - Maria A Lagarkova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia
| | - Galina E Pozmogova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia
| | - Anna M Varizhuk
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia; Engelhardt Institute of Molecular Biology, Moscow, 119991, Russia.
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11
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Kuang G, Zhang M, Kang S, Hu D, Li X, Wei Z, Gong X, An LK, Huang ZS, Shu B, Li D. Syntheses and Evaluation of New Bisacridine Derivatives for Dual Binding of G-Quadruplex and i-Motif in Regulating Oncogene c-myc Expression. J Med Chem 2020; 63:9136-9153. [PMID: 32787078 DOI: 10.1021/acs.jmedchem.9b01917] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The c-myc oncogene is an important regulator for cell growth and differentiation, and its aberrant overexpression is closely related to the occurrence and development of various cancers. Thus, the suppression of c-myc transcription and expression has been investigated for cancer treatment. In this study, various new bisacridine derivatives were synthesized and evaluated for their binding with c-myc promoter G-quadruplex and i-motif. We found that a9 could bind to and stabilize both G-quadruplex and i-motif, resulting in the downregulation of c-myc gene transcription. a9 could inhibit cancer cell proliferation and induce SiHa cell apoptosis and cycle arrest. a9 exhibited tumor growth inhibition activity in a SiHa xenograft tumor model, which might be related to its binding with c-myc promoter G-quadruplex and i-motif. Our results suggested that a9 as a dual G-quadruplex/i-motif binder could be effective in both oncogene replication and transcription and become a promising lead compound for further development with improved potency and selectivity.
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Affiliation(s)
- Guotao Kuang
- School of Pharmaceutical Sciences, Sun Yat-sen University, 132 Waihuan East Road, Guangzhou 510006, P. R. China
| | - Meiling Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, 132 Waihuan East Road, Guangzhou 510006, P. R. China
| | - Shuangshuang Kang
- School of Pharmaceutical Sciences, Sun Yat-sen University, 132 Waihuan East Road, Guangzhou 510006, P. R. China
| | - Dexuan Hu
- School of Pharmaceutical Sciences, Sun Yat-sen University, 132 Waihuan East Road, Guangzhou 510006, P. R. China
| | - Xiaoya Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, 132 Waihuan East Road, Guangzhou 510006, P. R. China
| | - Zuzhuang Wei
- School of Pharmaceutical Sciences, Sun Yat-sen University, 132 Waihuan East Road, Guangzhou 510006, P. R. China
| | - Xue Gong
- School of Pharmaceutical Sciences, Sun Yat-sen University, 132 Waihuan East Road, Guangzhou 510006, P. R. China
| | - Lin-Kun An
- School of Pharmaceutical Sciences, Sun Yat-sen University, 132 Waihuan East Road, Guangzhou 510006, P. R. China
| | - Zhi-Shu Huang
- School of Pharmaceutical Sciences, Sun Yat-sen University, 132 Waihuan East Road, Guangzhou 510006, P. R. China
| | - Bing Shu
- School of Pharmaceutical Sciences, Sun Yat-sen University, 132 Waihuan East Road, Guangzhou 510006, P. R. China.,School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, P. R. China
| | - Ding Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, 132 Waihuan East Road, Guangzhou 510006, P. R. China
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12
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Paul S, Hossain SS, Samanta A. Insights into the Folding Pathway of a c-MYC-Promoter-Based i-Motif DNA in Crowded Environments at the Single-Molecule Level. J Phys Chem B 2020; 124:763-770. [DOI: 10.1021/acs.jpcb.9b10633] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Sneha Paul
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | - Sk Saddam Hossain
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | - Anunay Samanta
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
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13
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Megalathan A, Cox BD, Wilkerson PD, Kaur A, Sapkota K, Reiner JE, Dhakal S. Single-molecule analysis of i-motif within self-assembled DNA duplexes and nanocircles. Nucleic Acids Res 2019; 47:7199-7212. [PMID: 31287873 PMCID: PMC6698746 DOI: 10.1093/nar/gkz565] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 06/13/2019] [Accepted: 07/04/2019] [Indexed: 12/20/2022] Open
Abstract
The cytosine (C)-rich sequences that can fold into tetraplex structures known as i-motif are prevalent in genomic DNA. Recent studies of i-motif-forming sequences have shown increasing evidence of their roles in gene regulation. However, most of these studies have been performed in short single-stranded oligonucleotides, far from the intracellular environment. In cells, i-motif-forming sequences are flanked by DNA duplexes and packed in the genome. Therefore, exploring the conformational dynamics and kinetics of i-motif under such topologically constrained environments is highly relevant in predicting their biological roles. Using single-molecule fluorescence analysis of self-assembled DNA duplexes and nanocircles, we show that the topological environments play a key role on i-motif stability and dynamics. While the human telomere sequence (C3TAA)3C3 assumes i-motif structure at pH 5.5 regardless of topological constraint, it undergoes conformational dynamics among unfolded, partially folded and fully folded states at pH 6.5. The lifetimes of i-motif and the partially folded state at pH 6.5 were determined to be 6 ± 2 and 31 ± 11 s, respectively. Consistent with the partially folded state observed in fluorescence analysis, interrogation of current versus time traces obtained from nanopore analysis at pH 6.5 shows long-lived shallow blockades with a mean lifetime of 25 ± 6 s. Such lifetimes are sufficient for the i-motif and partially folded states to interact with proteins to modulate cellular processes.
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Affiliation(s)
- Anoja Megalathan
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284, USA
| | - Bobby D Cox
- Department of Physics, Virginia Commonwealth University, 701 West Grace Street, Richmond, VA 23284, USA
| | - Peter D Wilkerson
- Department of Physics, Virginia Commonwealth University, 701 West Grace Street, Richmond, VA 23284, USA
| | - Anisa Kaur
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284, USA
| | - Kumar Sapkota
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284, USA
| | - Joseph E Reiner
- Department of Physics, Virginia Commonwealth University, 701 West Grace Street, Richmond, VA 23284, USA
| | - Soma Dhakal
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284, USA
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14
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Molnar M, Liddell SC, Wadkins RM. Effects of Polyamine Binding on the Stability of DNA i-Motif Structures. ACS OMEGA 2019; 4:8967-8973. [PMID: 31459985 PMCID: PMC6648627 DOI: 10.1021/acsomega.9b00784] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 05/13/2019] [Indexed: 05/12/2023]
Abstract
B-form DNA can adopt alternative structures under conditions such as superhelical duress. Alternative DNA structures are favored when there is asymmetric distribution of guanosine and cytosine on complimentary DNA strands. A guanosine-rich strand can form a four-stranded structure known as a quadruplex (G4). The complimentary cytosine-rich strand can utilize intercalating cytosine-cytosine base pairing to form a four-stranded structure known as the i-motif (iM). Both secondary structures are energetically uphill from double-strand DNA (dsDNA), meaning that additional factors are needed for their formation. Most iMs require slightly acidic conditions for structure stabilization. However, crowding agents such as polyethylene glycols and dextrans can shift the pK a of the iM to near-physiological pH ≈ 7. Nucleic acids have long been known to be bound and stabilized by polyamines such as putrescine, spermidine, and spermine. Polyamines have very high concentrations in cells (0.1-30 mM), and their binding to DNA is driven by electrostatic interactions. Polyamines typically bind in the minor groove of DNA. However, because of the unusual structure of iMs, it was unknown whether polyamines might also bind and stabilize iMs. The study described here was undertaken to analyze polyamine-iM interactions. The thermal stability and pH dependence of iM structures were determined in the presence of polyamines. In contrast to dsDNA, our results suggest that polyamines have considerably weaker interactions with iMs, as demonstrated by the minimal change in iM pH dependence and thermal stability. Our results suggest that polyamines are unlikely to provide a significant source of iM stabilization in vivo.
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Affiliation(s)
- Michael
M. Molnar
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | - Shelby C. Liddell
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | - Randy M. Wadkins
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
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15
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Tsvetkov VB, Zatsepin TS, Turaev AV, Farzan VM, Pozmogova GE, Aralov AV, Varizhuk AM. DNA i-Motifs With Guanidino- i-Clamp Residues: The Counterplay Between Kinetics and Thermodynamics and Implications for the Design of pH Sensors. Comput Struct Biotechnol J 2019; 17:527-536. [PMID: 31049164 PMCID: PMC6479070 DOI: 10.1016/j.csbj.2019.04.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/08/2019] [Accepted: 04/10/2019] [Indexed: 11/12/2022] Open
Abstract
I-motif structures, adopted by cytosine-rich DNA strands, have attracted considerable interest as possible regulatory elements in genomes. Applied science exploits the advantages of i-motif stabilization under acidic conditions: i-motif-based pH sensors and other biocompatible nanodevices are being developed. Two key characteristics of i-motifs as core elements of nanodevices, i.e., their stability under physiological conditions and folding/unfolding rates, still need to be improved. We have previously reported a phenoxazine derivative (i-clamp) that enhances the thermal stability of the i-motif and shifts the pH transition point closer to physiological values. Here, we performed i-clamp guanidinylation to further explore the prospects of clamp-like modifications in i-motif fine-tuning. Based on molecular modeling data, we concluded that clamp guanidinylation facilitated interstrand interactions in an i-motif core and ultimately stabilized the i-motif structure. We tested the effects of guanidino-i-clamp insertions on the thermal stabilities of genomic and model i-motifs. We also investigated the folding/unfolding kinetics of native and modified i-motifs under moderate, physiologically relevant pH alterations. We demonstrated fast folding/unfolding of native genomic and model i-motifs in response to pH stimuli. This finding supports the concept of i-motifs as possible genomic regulatory elements and encourages the future design of rapid-response pH probes based on such structures. Incorporation of guanidino-i-clamp residues at/near the 5′-terminus of i-motifs dramatically decreased the apparent unfolding rates and increased the thermal stabilities of the structures. This counterplay between the effects of modifications on i-motif stability and their effects on kinetics should be taken into account in the design of pH sensors.
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Affiliation(s)
- Vladimir B Tsvetkov
- Research and Clinical Center for Physical Chemical Medicine, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia.,I.M. Sechenov First Moscow State Medical University, Trubetskaya Str. 8-2, 119991 Moscow, Russia.,Research Institute of Influenza, Professora Popova str., 15/17, Sankt-Peterburg 197376, Russia
| | - Timofei S Zatsepin
- Skolkovo Institute of Science and Technology, Skolkovo, 143026 Moscow, Russia.,Lomonosov Moscow State University, Department of Chemistry, Leninskie Gory Str. 1-3, 119992 Moscow, Russia
| | - Anton V Turaev
- Research and Clinical Center for Physical Chemical Medicine, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia.,Moscow Institute of Physics and Technology, Institutsky lane 9, Dolgoprudny 141700, Russia
| | - Valentina M Farzan
- Skolkovo Institute of Science and Technology, Skolkovo, 143026 Moscow, Russia
| | - Galina E Pozmogova
- Research and Clinical Center for Physical Chemical Medicine, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia.,Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky prospect, 33, build. 2, Moscow 119071, Russia
| | - Andrey V Aralov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya str. 16/10, Moscow 117997, Russia
| | - Anna M Varizhuk
- Research and Clinical Center for Physical Chemical Medicine, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia.,Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, Moscow 119991, Russia
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16
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Bielecka P, Dembska A, Juskowiak B. Monitoring of pH Using an i-Motif-Forming Sequence Containing a Fluorescent Cytosine Analogue, tC. Molecules 2019; 24:molecules24050952. [PMID: 30857134 PMCID: PMC6429216 DOI: 10.3390/molecules24050952] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 02/26/2019] [Accepted: 03/05/2019] [Indexed: 01/31/2023] Open
Abstract
The i-motif is a four-stranded DNA structure formed from the cytosine (C)-rich ssDNA sequence, which is stabilized in slightly acidic pH. Additionally, labeling of a cytosine-rich sequence with a fluorescent molecule may constitute a way to construct a pH-sensitive biosensor. In this paper, we report tC-modified fluorescent probes that contain RET-related sequence C4GC4GC4GC4A. Results of the UV absorption melting experiments, circular dichroism (CD) spectra, and steady-state fluorescence measurements of tC-modified i-motifs are presented and discussed here. Efficient fluorescence quenching of tC fluorophore occurred upon lowering the pH from 8.0 to 5.5. Furthermore, we present and discuss fluorescence spectra of systems containing tC-modified i-motifs and complementary G-rich sequences in the ratios 1:1, 1:2, and 1:3 in response to pH changes. The fluorescence anisotropy was proposed for the study of conformational switching of the i-motif structure for tC-probes in the presence and absence of a complementary sequence. The possibility of using of the sensor for monitoring pH changes was demonstrated.
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Affiliation(s)
- Patrycja Bielecka
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland.
| | - Anna Dembska
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland.
| | - Bernard Juskowiak
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland.
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17
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Morgan RK, Molnar MM, Batra H, Summerford B, Wadkins RM, Brooks TA. Effects of 5-Hydroxymethylcytosine Epigenetic Modification on the Stability and Molecular Recognition of VEGF i-Motif and G-Quadruplex Structures. J Nucleic Acids 2018; 2018:9281286. [PMID: 29862069 PMCID: PMC5976936 DOI: 10.1155/2018/9281286] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 03/31/2018] [Accepted: 04/03/2018] [Indexed: 12/14/2022] Open
Abstract
Promoters often contain asymmetric G- and C-rich strands, in which the cytosines are prone to epigenetic modification via methylation (5-mC) and 5-hydroxymethylation (5-hmC). These sequences can also form four-stranded G-quadruplex (G4) or i-motif (iM) secondary structures. Although the requisite sequences for epigenetic modulation and iM/G4 formation are similar and can overlap, they are unlikely to coexist. Despite 5-hmC being an oxidization product of 5-mC, the two modified bases cluster at distinct loci. This study focuses on the intersection of G4/iM formation and 5-hmC modification using the vascular endothelial growth factor (VEGF) gene promoter's CpG sites and examines whether incorporation of 5-hmC into iM/G4 structures had any physicochemical effect on formation, stability, or recognition by nucleolin or the cationic porphyrin, TMPyP4. No marked changes were found in the formation or stability of iM and G4 structures; however, changes in recognition by nucleolin or TMPyP4 occurred with 5-hmC modification wherein protein and compound binding to 5-hmC modified G4s was notably reduced. G4/iM structures in the VEGF promoter are promising therapeutic targets for antiangiogenic therapy, and this work contributes to a comprehensive understanding of their governing principles related to potential transcriptional control and targeting.
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Affiliation(s)
- Rhianna K. Morgan
- School of Pharmacy, Department of BioMolecular Sciences, Division of Pharmacology, University of Mississippi, University, MS 38677, USA
| | - Michael M. Molnar
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, USA
| | - Harshul Batra
- School of Pharmacy, Department of BioMolecular Sciences, Division of Pharmacology, University of Mississippi, University, MS 38677, USA
| | - Bethany Summerford
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, USA
| | - Randy M. Wadkins
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, USA
| | - Tracy A. Brooks
- School of Pharmacy, Department of BioMolecular Sciences, Division of Pharmacology, University of Mississippi, University, MS 38677, USA
- School of Pharmacy and Pharmaceutical Sciences, Department of Pharmaceutical Sciences, Binghamton University, Binghamton, NY 13902, USA
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18
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Tsvetkov VB, Zatsepin TS, Belyaev ES, Kostyukevich YI, Shpakovski GV, Podgorsky VV, Pozmogova GE, Varizhuk AM, Aralov AV. i-Clamp phenoxazine for the fine tuning of DNA i-motif stability. Nucleic Acids Res 2018; 46:2751-2764. [PMID: 29474573 PMCID: PMC5888743 DOI: 10.1093/nar/gky121] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 02/01/2018] [Accepted: 02/13/2018] [Indexed: 12/13/2022] Open
Abstract
Non-canonical DNA structures are widely used for regulation of gene expression, in DNA nanotechnology and for the development of new DNA-based sensors. I-motifs (iMs) are two intercalated parallel duplexes that are held together by hemiprotonated C-C base pairs. Previously, iMs were used as an accurate sensor for intracellular pH measurements. However, iM stability is moderate, which in turn limits its in vivo applications. Here, we report the rational design of a new substituted phenoxazine 2'-deoxynucleotide (i-clamp) for iM stabilization. This residue contains a C8-aminopropyl tether that interacts with the phosphate group within the neighboring chain without compromising base pairing. We studied the influence of i-clamp on pH-dependent stability for intra- and intermolecular iM structures and found the optimal positions for modification. Two i-clamps on opposite strands provide thermal stabilization up to 10-11°C at a pH of 5.8. Thus, we developed a new modification that shows significant iM-stabilizing effect both at strongly and mildly acidic pH and increases iM transition pH values. i-Clamp can be used for tuning iM-based pH probes or assembling extra stable iM structures for various applications.
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Affiliation(s)
- Vladimir B Tsvetkov
- Biophysics Department, Research and Clinical Center for Physical Chemical Medicine, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia
- Department of Molecular Virology, FSBI Research Institute of Influenza, Ministry of Health of Russian Federation, prof. Popov str. 15/17, Saint-Petersburg, 197376, Russia
- Polyelectrolytes and Biomedical Polymers Laboratory, A.V. Topchiev Institute of Petrochemical Synthesis, RAS, Leninsky prospect str. 29, Moscow 119991, Russia
| | - Timofei S Zatsepin
- Center for Translational Biomedicine, Skolkovo Institute of Science and Technology, 3 Nobel street, Skolkovo, Moscow 143026, Russia
- Chemistry Department, Lomonosov Moscow State University, Leninskie gory str. 1–3, Moscow 119992, Russia
| | - Evgeny S Belyaev
- Frumkin Institute of Physical Chemistry and Electrochemistry of the Russian Academy of Science, Leninsky prospect str. 31, Moscow 119071 Russia
| | - Yury I Kostyukevich
- Center for Translational Biomedicine, Skolkovo Institute of Science and Technology, 3 Nobel street, Skolkovo, Moscow 143026, Russia
| | - George V Shpakovski
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya str. 16/10, Moscow 117997, Russia
| | - Victor V Podgorsky
- Biophysics Department, Research and Clinical Center for Physical Chemical Medicine, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia
| | - Galina E Pozmogova
- Biophysics Department, Research and Clinical Center for Physical Chemical Medicine, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia
| | - Anna M Varizhuk
- Biophysics Department, Research and Clinical Center for Physical Chemical Medicine, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, Moscow 119991, Russia
| | - Andrey V Aralov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya str. 16/10, Moscow 117997, Russia
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19
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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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20
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Füchtbauer AF, Preus S, Börjesson K, McPhee SA, Lilley DMJ, Wilhelmsson LM. Fluorescent RNA cytosine analogue - an internal probe for detailed structure and dynamics investigations. Sci Rep 2017; 7:2393. [PMID: 28539582 PMCID: PMC5443824 DOI: 10.1038/s41598-017-02453-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 04/10/2017] [Indexed: 12/22/2022] Open
Abstract
The bright fluorescent cytosine analogue tCO stands out among fluorescent bases due to its virtually unquenched fluorescence emission in duplex DNA. However, like most reported base analogues, it has not been thoroughly characterized in RNA. We here report on the first synthesis and RNA-incorporation of tCO, and characterize its base-mimicking and fluorescence properties in RNA. As in DNA, we find a high quantum yield inside RNA duplexes (<ΦF> = 0.22) that is virtually unaffected by the neighbouring bases (ΦF = 0.20-0.25), resulting in an average brightness of 1900 M-1 cm-1. The average fluorescence lifetime in RNA duplexes is 4.3 ns and generally two lifetimes are required to fit the exponential decays. Fluorescence properties in ssRNA are defined by a small increase in average quantum yield (<ΦF > = 0.24) compared to dsRNA, with a broader distribution (ΦF = 0.17-0.34) and slightly shorter average lifetimes. Using circular dichroism, we find that the tCO-modified RNA duplexes form regular A-form helices and in UV-melting experiments the stability of the duplexes is only slightly higher than that of the corresponding natural RNA (<ΔT m> = + 2.3 °C). These properties make tCO a highly interesting fluorescent RNA base analogue for detailed FRET-based structural measurements, as a bright internal label in microscopy, and for fluorescence anisotropy measurements of RNA dynamics.
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Affiliation(s)
- Anders Foller Füchtbauer
- Chemistry and Chemical Engineering/Chemistry and Biochemistry, Chalmers University of Technology, Gothenburg, SE-41296, Sweden
| | - Søren Preus
- Department of Chemistry, University of Copenhagen, Copenhagen, DK-2100, Denmark
| | - Karl Börjesson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, SE-41296, Sweden
| | - Scott A McPhee
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - L Marcus Wilhelmsson
- Chemistry and Chemical Engineering/Chemistry and Biochemistry, Chalmers University of Technology, Gothenburg, SE-41296, Sweden.
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21
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Sutherland C, Cui Y, Mao H, Hurley LH. A Mechanosensor Mechanism Controls the G-Quadruplex/i-Motif Molecular Switch in the MYC Promoter NHE III1. J Am Chem Soc 2016; 138:14138-14151. [DOI: 10.1021/jacs.6b09196] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Caleb Sutherland
- University of Arizona Cancer Center, 1515 North Campbell Avenue, Tucson, Arizona 85724, United States
| | - Yunxi Cui
- Department
of Chemistry and Biochemistry and School of Biomedical Sciences, Kent State University, Kent, Ohio 44242, United States
| | - Hanbin Mao
- Department
of Chemistry and Biochemistry and School of Biomedical Sciences, Kent State University, Kent, Ohio 44242, United States
| | - Laurence H. Hurley
- University of Arizona Cancer Center, 1515 North Campbell Avenue, Tucson, Arizona 85724, United States
- University of Arizona, College of Pharmacy, 1703 East Mabel Street, Tucson, Arizona 85721, United States
- BIO5 Institute, 1657 East
Helen Street, Tucson, Arizona 85721, United States
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22
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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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23
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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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24
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McConnell EM, Bolzon R, Mezin P, Frahm G, Johnston M, DeRosa MC. pHAST (pH-Driven Aptamer Switch for Thrombin) Catch-and-Release of Target Protein. Bioconjug Chem 2016; 27:1493-9. [PMID: 27115292 DOI: 10.1021/acs.bioconjchem.6b00124] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A pH-driven DNA nanomachine based on the human α-thrombin binding aptamer was designed for the specific catch-and-release of human α-thrombin at neutral and acidic pH, respectively. In neutral conditions, the thrombin aptamer component of the nanomachine is exposed and exists in the G-quadruplex conformation required to bind to the target protein. At slightly acidic pH, the polyadenine tail of the nanomachine becomes partially protonated and A+(anti)•G(syn) mispairing results in a conformational change, causing the target protein to be released. Förster resonance energy transfer (FRET) was used to monitor conformational switching over multiple pH cycles. Electrophoretic mobility shift assay (EMSA) and fluorescence anisotropy were used to show pH dependent protein binding and release by the nanomachine. This approach could be applied generally to existing G-rich aptamers to develop novel biosensors, theranostics, and nanoswitches.
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Affiliation(s)
- E M McConnell
- Chemistry Department, Carleton University 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - R Bolzon
- Chemistry Department, Carleton University 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - P Mezin
- Chemistry Department, Carleton University 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - G Frahm
- Centre for Biologics Evaluation, Health Canada , 251 Sir Frederick Banting, Ottawa, Ontario K1A 0K9, Canada
| | - M Johnston
- Centre for Biologics Evaluation, Health Canada , 251 Sir Frederick Banting, Ottawa, Ontario K1A 0K9, Canada
| | - M C DeRosa
- Chemistry Department, Carleton University 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
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Bielecka P, Juskowiak B. Fluorescent Sensor for PH Monitoring Based on an i-Motif---Switching Aptamer Containing a Tricyclic Cytosine Analogue (tC). Molecules 2015; 20:18511-25. [PMID: 26473815 PMCID: PMC6332284 DOI: 10.3390/molecules201018511] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 09/24/2015] [Accepted: 10/06/2015] [Indexed: 12/16/2022] Open
Abstract
There are cytosine-rich regions in the genome that bind protons with high specificity. Thus protonated C-rich sequence may undergo folding to tetraplex structures called i-motifs. Therefore, one can regard such specific C-rich oligonucleotides as aptamers that recognize protons and undergo conformational transitions. Proper labeling of the aptamer with a fluorescent tag constitutes a platform to construct a pH-sensitive aptasensor. Since the hemiprotonated C-C⁺ base pairs are responsible for the folded tetraplex structure of i-motif, we decided to substitute one of cytosines in an aptamer sequence with its fluorescent analogue, 1,3-diaza-2-oxophenothiazine (tC). In this paper we report on three tC-modified fluorescent probes that contain RET related sequences as a proton recognizing aptamer. Results of the circular dichroism (CD), UV absorption melting experiments, and steady-state fluorescence measurements of these tC-modified i-motif probes are presented and discussed. The pH-induced i-motif formation by the probes resulted in fluorescence quenching of tC fluorophore. Efficiency of quenching was related to the pH variations. Suitability of the sensor for monitoring pH changes was also demonstrated.
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Affiliation(s)
- Patrycja Bielecka
- Laboratory of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b 61-614 Poznan, Poland.
| | - Bernard Juskowiak
- Laboratory of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b 61-614 Poznan, Poland.
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Nesterova IV, Briscoe JR, Nesterov EE. Rational Control of Folding Cooperativity in DNA Quadruplexes. J Am Chem Soc 2015; 137:11234-7. [PMID: 26305404 DOI: 10.1021/jacs.5b06645] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Availability of basic tools for engineering molecular systems with precisely defined properties is crucial toward progress in development of new responsive materials. Among such materials are systems capable of generating an ultrasensitive response (i.e., large relative changes in output in response to small changes in input). Herein, we focus on a rational design of DNA quadruplex based structures as ultrasensitive response elements. In particular, we demonstrate how addition of allosteric guiding elements can be engineered into H(+)-responsive i-motif structure to yield maximized response sensitivity.
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Affiliation(s)
- Irina V Nesterova
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - James R Briscoe
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Evgueni E Nesterov
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
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