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Li C, Liu Y, Liu H. Expression of c-Myc and Beclin-1 in skin of rats after burn. Exp Ther Med 2018; 16:2917-2921. [PMID: 30233665 PMCID: PMC6143901 DOI: 10.3892/etm.2018.6582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 08/01/2018] [Indexed: 11/06/2022] Open
Abstract
This study aimed to investigate the expression features of Beclin-1 and c-Myc in the skin burn of rats. A total of 48 Sprague-Dawley (SD) rats were randomly divided into the normal group (n=12), the 3-day burn group (n=12), the 5-day burn group (n=12) and the 7-day burn group (n=12). Except for the normal group, the rat models of burn were established in the other three groups, burn wounds were given routine dressing change, and rats were sacrificed at 3, 5 and 7 days after modeling to collect materials. Then, immunohistochemistry was applied to detect the expression of c-Myc and Beclin-1. The expression levels of c-Myc protein and Beclin-1 protein were measured via western blotting. The expression levels of c-Myc messenger ribonucleic acid (mRNA) and Beclin-1 mRNA were detected by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). In comparison with the normal group, three burn groups had significantly increased the expression of c-Myc and Beclin-1, and the differences were statistically significant (P<0.05). Beclin-1 expression in the 5-day burn group was obviously higher than those in the 3 and 7-day burn groups, and the differences were of statistical significance (P<0.05). The expression of c-Myc in the 7-day burn group was overtly higher than those in the 3 and 5-day burn groups, and the differences showed statistical significance (P<0.05). The expression of Beclin-1 and c-Myc in post-burn skin tissues were gradually increased, with the Beclin-1 expression level reaching the peak on the 5th day after burn, and the expression level of c-Myc was the highest on the 7th day after burn.
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Affiliation(s)
- Caihong Li
- Department of Burn and Plastic Surgery, Weifang People's Hospital, Weifang, Shandong 261000, P.R. China
| | - Yuping Liu
- Department of Burn and Plastic Surgery, Weifang People's Hospital, Weifang, Shandong 261000, P.R. China
| | - Hongjuan Liu
- Department of Burn and Plastic Surgery, Weifang People's Hospital, Weifang, Shandong 261000, P.R. China
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52
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Satpathi S, Das K, Hazra P. Silica nano-channel induced i-motif formation and stabilization at neutral and alkaline pH. Chem Commun (Camb) 2018; 54:7054-7057. [PMID: 29876546 DOI: 10.1039/c8cc02811g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Here, we have developed a new strategy to stabilize i-motif DNA in neutral and alkaline media by incorporating C-rich sequences inside silica nano-channels. Subsequently, the reversibility of this conformational transition has been achieved using a positively charged protein. Importantly, this entire conformational transition can be performed in multiple cycles, which offers an alternative way to control i-motif formation other than pH and thermal annealing.
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Affiliation(s)
- Sagar Satpathi
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune. Dr. Homi Bhabha Road, Pashan, Pune, 411008, India.
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53
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Hancock R. Crowding, Entropic Forces, and Confinement: Crucial Factors for Structures and Functions in the Cell Nucleus. BIOCHEMISTRY (MOSCOW) 2018; 83:326-337. [PMID: 29626920 DOI: 10.1134/s0006297918040041] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The view of the cell nucleus as a crowded system of colloid particles and that chromosomes are giant self-avoiding polymers is stimulating rapid advances in our understanding of its structure and activities, thanks to concepts and experimental methods from colloid, polymer, soft matter, and nano sciences and to increased computational power for simulating macromolecules and polymers. This review summarizes current understanding of some characteristics of the molecular environment in the nucleus, of how intranuclear compartments are formed, and of how the genome is highly but precisely compacted, and underlines the crucial, subtle, and sometimes unintuitive effects on structures and reactions of entropic forces caused by the high concentration of macromolecules in the nucleus.
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Affiliation(s)
- R Hancock
- Biosystems Group, Biotechnology Centre, Silesian University of Technology, Poland and Laval University Cancer Research Centre, Québec, G1R2J6, Canada.
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54
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I-motif DNA structures are formed in the nuclei of human cells. Nat Chem 2018; 10:631-637. [PMID: 29686376 DOI: 10.1038/s41557-018-0046-3] [Citation(s) in RCA: 350] [Impact Index Per Article: 58.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 03/14/2018] [Indexed: 12/25/2022]
Abstract
Human genome function is underpinned by the primary storage of genetic information in canonical B-form DNA, with a second layer of DNA structure providing regulatory control. I-motif structures are thought to form in cytosine-rich regions of the genome and to have regulatory functions; however, in vivo evidence for the existence of such structures has so far remained elusive. Here we report the generation and characterization of an antibody fragment (iMab) that recognizes i-motif structures with high selectivity and affinity, enabling the detection of i-motifs in the nuclei of human cells. We demonstrate that the in vivo formation of such structures is cell-cycle and pH dependent. Furthermore, we provide evidence that i-motif structures are formed in regulatory regions of the human genome, including promoters and telomeric regions. Our results support the notion that i-motif structures provide key regulatory roles in the genome.
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55
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Tanaka S, Yukami S, Fukushima K, Wakabayashi K, Ohya Y, Kuzuya A. Bulk pH-Responsive DNA Quadruplex Hydrogels Prepared by Liquid-Phase, Large-Scale DNA Synthesis. ACS Macro Lett 2018; 7:295-299. [PMID: 35632920 DOI: 10.1021/acsmacrolett.8b00063] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A new pH-responsive hydrogel biomaterial, that is composed of solely two popular biocompatible materials, oligodeoxynucleotides (ODN) and polyethylene glycol (PEG) have been prepared. Merely five deoxycytidine residues were elongated to the ends of linear or 4-arm PEG in ×1000 larger scale than conventional systems by using liquid-phase DNA synthesis technique, and applied them as a macromonomer for the preparation of hydrogels. The syntheses of the conjugates are simply elongating ODN onto the ends of PEG as a semisolid phase substrate using standard phosphoramidite chemistry. The resulting dC5-PEG conjugates gave quite stable and stiff hydrogels triggered by the formation of a unique DNA quadruplex, i-motif. Introduction of only one chemical linkage between two linear conjugates resulted in unexpectedly high thermal stabilities for the melting temperatures of i-motifs themselves. Nonlinearly improved rheological properties compared to the original linear conjugates were also observed, probably because of topological entanglement between macromonomers of fused circles.
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56
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Zamiri B, Mirceta M, Abu-Ghazalah R, Wold MS, Pearson CE, Macgregor RB. Stress-induced acidification may contribute to formation of unusual structures in C9orf72-repeats. Biochim Biophys Acta Gen Subj 2018; 1862:1482-1491. [PMID: 29550431 DOI: 10.1016/j.bbagen.2018.03.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 02/22/2018] [Accepted: 03/04/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND Expansion of the C9orf72 hexanucleotide repeat (GGGGCC)n·(GGCCCC)n is the most common cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Both strands of the C9orf72 repeat have been shown to form unusual DNA and RNA structures that are thought to be involved in mutagenesis and/or pathogenesis. We previously showed that the C-rich DNA strands from the C9orf72 repeat can form four-stranded quadruplexes at neutral pH. The cytosine residues become protonated under slightly acidic pH (pH 4.5-6.2), facilitating the formation of intercalated i-motif structures. METHODS Using CD spectroscopy, UV melting, and gel electrophoresis, we demonstrate a pH-induced structural transition of the C-rich DNA strand of the C9orf72 repeat at pHs reported to exist in living cells under stress, including during neurodegeneration and cancer. RESULTS We show that the repeats with lengths of 4, 6, and 8 units, form intercalated quadruplex i-motifs at low pH (pH < 5) and monomolecular hairpins and monomolecular quadruplexes under neutral-basic conditions (pH ≥ 8). Furthermore, we show that the human replication protein A (RPA) binds to the G-rich and C-rich DNA strands under acidic conditions, suggesting that it can bind to i-motif structures. CONCLUSIONS In the proper sequence context, i-motif structures can form at pH values found in some cells in vivo. GENERAL SIGNIFICANCE DNA conformational plasticity exists over broad range of solution conditions.
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Affiliation(s)
- Bita Zamiri
- Graduate Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Mila Mirceta
- Program of Genetics & Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada; Program of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A1, Canada
| | - Rashid Abu-Ghazalah
- W. Booth School of Engineering Technology Practice and Technology, McMaster University, Hamilton, Ontario L8S 0A3, Canada
| | - Marc S Wold
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Christopher E Pearson
- Program of Genetics & Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada; Program of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A1, Canada
| | - Robert B Macgregor
- Graduate Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada.
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57
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Protopopova AD, Tsvetkov VB, Varizhuk AM, Barinov NA, Podgorsky VV, Klinov DV, Pozmogova GE. The structural diversity of C-rich DNA aggregates: unusual self-assembly of beetle-like nanostructures. Phys Chem Chem Phys 2018; 20:3543-3553. [PMID: 29336444 DOI: 10.1039/c7cp05380k] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We studied the ability of oligonucleotides CnT25 (n = 2, 5, 7, 9, 12, 25) to form an intermolecular i-motif using circular dichroism, ultra-violet spectroscopy, nuclear magnetic resonance, high-resolution atomic force microscopy, high-performance liquid chromatography, and molecular dynamics simulations. The arrangement of single-stranded oligonucleotides in multimer i-motifs was very unusual: C-tracts of different oligonucleotides followed each other consecutively in order to fold into a closed intermolecular i-motif core with minimal loops (one cytidine in a loop spanning over a minor groove, three cytidines in a loop over a major groove); intact T-tracts protruded from predefined loci allowing visualization of beetle-like nanostructures by atomic force microscopy. The same structures were formed from analogous biotinylated oligonucleotides demonstrating one of the potential applications of such structures as carriers of multiple functional groups. Our findings open up possibilities for the rational design of pH-sensitive DNA aggregates and evaluation of the efficiency of their assembly.
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Affiliation(s)
- A D Protopopova
- Biophysics Department, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia.
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58
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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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59
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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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60
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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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61
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Saxena S, Joshi S, Shankaraswamy J, Tyagi S, Kukreti S. Magnesium and molecular crowding of the cosolutes stabilize the i-motif structure at physiological pH. Biopolymers 2018; 107. [PMID: 28295161 DOI: 10.1002/bip.23018] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 03/06/2017] [Accepted: 03/06/2017] [Indexed: 11/09/2022]
Abstract
Most of the important genomic regions, especially the G,C rich gene promoters, consist of sequences with potential to form G,C-tetraplexes on both the DNA strands. In this study, we used three C-rich oligonucleotides (11Py, 21Py, and HTPy), of which 11Py and 21Py are located at various transcriptional regulatory elements of the human genome while HTPy sequence is a C-rich strand of human telomere sequence. These C-rich oligonucleotides formed i-motif structures, verified by Circular Dichroism (CD), UV absorption melting experiments, and native gel electrophoresis. The CD spectra revealed that 11Py and 21Py form i-motif structures at acidic pH values of 4.5 and 5.7 in the presence of 100 mM NaCl but remain unstructured at pH 7.0. However, 21Py can form stable i-motif structure even at neutral pH in presence of 1 mM MgCl2 . UV-thermal melting studies showed stabilization of 21Py i-motif at pH 5.7 in the presence of Na+ or K+ with increasing concentration of MgCl2 or CaCl2 from 1 to 10 mM. Significant shift in the CD peak of HTPy sequence was observed as the positive peak from 286 nm shifted to 276 nm while the negative peak from 265 to 254 nm. Further, inevitable necessity of 1 mM Mg2+ to form i-motif structure at neutral pH was observed. Under similar ionic conditions and neutral pH, all the three C-rich sequences were able to form stable i-motif structures (11Py, 21Py) or altered i-motif/homoduplex structures (HTPy) in the presence of MgCl2 and cell mimicking molecular crowding conditions of 40 wt% PEG 200. It is concluded that presence of Mg2+ ions and molecular crowding agents induce and stabilize i-motif structures at physiological solution environment.
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Affiliation(s)
- Sarika Saxena
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, 201313, India
| | - Savita Joshi
- Department of Chemistry, Nucleic Acids Research laboratory, University of Delhi (North Campus), Delhi, 110007, India
| | - J Shankaraswamy
- Amity International Centre for Post Harvest Technology and Cold Chain Management, Amity University Uttar Pradesh, Noida, 201313, India
| | - Shikhar Tyagi
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, 201313, India
| | - Shrikant Kukreti
- Department of Chemistry, Nucleic Acids Research laboratory, University of Delhi (North Campus), Delhi, 110007, India
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62
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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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63
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Topological impact of noncanonical DNA structures on Klenow fragment of DNA polymerase. Proc Natl Acad Sci U S A 2017; 114:9605-9610. [PMID: 28827350 DOI: 10.1073/pnas.1704258114] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Noncanonical DNA structures that stall DNA replication can cause errors in genomic DNA. Here, we investigated how the noncanonical structures formed by sequences in genes associated with a number of diseases impacted DNA polymerization by the Klenow fragment of DNA polymerase. Replication of a DNA sequence forming an i-motif from a telomere, hypoxia-induced transcription factor, and an insulin-linked polymorphic region was effectively inhibited. On the other hand, replication of a mixed-type G-quadruplex (G4) from a telomere was less inhibited than that of the antiparallel type or parallel type. Interestingly, the i-motif was a better inhibitor of replication than were mixed-type G4s or hairpin structures, even though all had similar thermodynamic stabilities. These results indicate that both the stability and topology of structures formed in DNA templates impact the processivity of a DNA polymerase. This suggests that i-motif formation may trigger genomic instability by stalling the replication of DNA, causing intractable diseases.
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64
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Nguyen T, Fraire C, Sheardy RD. Linking pH, Temperature, and K+ Concentration for DNA i-Motif Formation. J Phys Chem B 2017; 121:7872-7877. [DOI: 10.1021/acs.jpcb.7b06317] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Tra Nguyen
- Department of Chemistry and
Biochemistry, Texas Woman’s University, Denton, Texas 76204, United States
| | - Claudette Fraire
- Department of Chemistry and
Biochemistry, Texas Woman’s University, Denton, Texas 76204, United States
| | - Richard D. Sheardy
- Department of Chemistry and
Biochemistry, Texas Woman’s University, Denton, Texas 76204, United States
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65
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Kaiser CE, Van Ert NA, Agrawal P, Chawla R, Yang D, Hurley LH. Insight into the Complexity of the i-Motif and G-Quadruplex DNA Structures Formed in the KRAS Promoter and Subsequent Drug-Induced Gene Repression. J Am Chem Soc 2017; 139:8522-8536. [PMID: 28570076 PMCID: PMC5978000 DOI: 10.1021/jacs.7b02046] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Activating KRAS mutations frequently occur in pancreatic, colorectal, and lung adenocarcinomas. While many attempts have been made to target oncogenic KRAS, no clinically useful therapies currently exist. Most efforts to target KRAS have focused on inhibiting the mutant protein; a less explored approach involves targeting KRAS at the transcriptional level. The promoter element of the KRAS gene contains a GC-rich nuclease hypersensitive site with three potential DNA secondary structure-forming regions. These are referred to as the Near-, Mid-, and Far-regions, on the basis of their proximity to the transcription start site. As a result of transcription-induced negative superhelicity, these regions can open up to form unique DNA secondary structures: G-quadruplexes on the G-rich strand and i-motifs on the C-rich strand. While the G-quadruplexes have been well characterized, the i-motifs have not been investigated as thoroughly. Here we show that the i-motif that forms in the C-rich Mid-region is the most stable and exists in a dynamic equilibrium with a hybrid i-motif/hairpin species and an unfolded hairpin species. The transcription factor heterogeneous nuclear ribonucleoprotein K (hnRNP K) was found to bind selectively to the i-motif species and to positively modulate KRAS transcription. Additionally, we identified a benzophenanthridine alkaloid that dissipates the hairpin species and destabilizes the interaction of hnRNP K with the Mid-region i-motif. This same compound stabilizes the three existing KRAS G-quadruplexes. The combined effect of the compound on the Mid-region i-motif and the G-quadruplexes leads to downregulation of KRAS gene expression. This dual i-motif/G-quadruplex-interactive compound presents a new mechanism to modulate gene expression.
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Affiliation(s)
- Christine E. Kaiser
- College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
| | - Natalie A. Van Ert
- College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
| | - Prashansa Agrawal
- College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
| | - Reena Chawla
- BIO5 Institute, University of Arizona, Tucson, Arizona 85721, United States
| | - Danzhou Yang
- College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
- University of Arizona Cancer Center, University of Arizona, Tucson, Arizona 85724, United States
- BIO5 Institute, University of Arizona, Tucson, Arizona 85721, United States
| | - Laurence H. Hurley
- College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
- University of Arizona Cancer Center, University of Arizona, Tucson, Arizona 85724, United States
- BIO5 Institute, University of Arizona, Tucson, Arizona 85721, United States
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66
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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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67
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Dolinnaya NG, Ogloblina AM, Yakubovskaya MG. Structure, Properties, and Biological Relevance of the DNA and RNA G-Quadruplexes: Overview 50 Years after Their Discovery. BIOCHEMISTRY (MOSCOW) 2017; 81:1602-1649. [PMID: 28260487 PMCID: PMC7087716 DOI: 10.1134/s0006297916130034] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
G-quadruplexes (G4s), which are known to have important roles in regulation of key biological processes in both normal and pathological cells, are the most actively studied non-canonical structures of nucleic acids. In this review, we summarize the results of studies published in recent years that change significantly scientific views on various aspects of our understanding of quadruplexes. Modern notions on the polymorphism of DNA quadruplexes, on factors affecting thermodynamics and kinetics of G4 folding–unfolding, on structural organization of multiquadruplex systems, and on conformational features of RNA G4s and hybrid DNA–RNA G4s are discussed. Here we report the data on location of G4 sequence motifs in the genomes of eukaryotes, bacteria, and viruses, characterize G4-specific small-molecule ligands and proteins, as well as the mechanisms of their interactions with quadruplexes. New information on the structure and stability of G4s in telomeric DNA and oncogene promoters is discussed as well as proof being provided on the occurrence of G-quadruplexes in cells. Prominence is given to novel experimental techniques (single molecule manipulations, optical and magnetic tweezers, original chemical approaches, G4 detection in situ, in-cell NMR spectroscopy) that facilitate breakthroughs in the investigation of the structure and functions of G-quadruplexes.
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Affiliation(s)
- N G Dolinnaya
- Lomonosov Moscow State University, Department of Chemistry, Moscow, 119991, Russia.
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68
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Shahid S, Hassan MI, Islam A, Ahmad F. Size-dependent studies of macromolecular crowding on the thermodynamic stability, structure and functional activity of proteins: in vitro and in silico approaches. Biochim Biophys Acta Gen Subj 2017; 1861:178-197. [DOI: 10.1016/j.bbagen.2016.11.014] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 11/09/2016] [Accepted: 11/10/2016] [Indexed: 11/27/2022]
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69
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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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70
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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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71
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Anti-sense DNA d(GGCCCC)n expansions in C9ORF72 form i-motifs and protonated hairpins. Sci Rep 2015; 5:17944. [PMID: 26632347 PMCID: PMC4668579 DOI: 10.1038/srep17944] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 11/09/2015] [Indexed: 12/14/2022] Open
Abstract
The G4C2 hexanucleotide repeat expansion mutation (HREM) in C9ORF72, represents the most common mutation associated with amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Three main disease mechanisms have been proposed to date: C9ORF72 haploinsufficiency, RNA toxicity, and accumulation of dipeptide repeat proteins. Pure GC content of the HREM potentially enables the formation of various non-B DNA structures such as G-quadruplexes and i-motifs. These structures are proposed to act as promoters and regulatory elements affecting replication, transcription and translation of the surrounding region. G-quadruplexes have already been shown on the G-rich sense DNA and RNA strands (G4C2)n, the structure of the anti-sense (G2C4)n strand remains unresolved. Similar C-rich sequences may, under acidic conditions, form i-motifs consisting of two parallel duplexes in a head to tail orientation held together by hemi-protonated C+-C pairs. We show that d(G2C4)n repeats do form i-motif and protonated hairpins even under near-physiological conditions. Rather than forming a DNA duplex, i-motifs persist even in the presence of the sense strand. This preferential formation of G-quadruplex and i-motif/hairpin structures over duplex DNA, may explain HREM replicational and transcriptional instability. Furthermore, i-motifs/hairpins can represent a novel pharmacological target for C9ORF72 associated ALS and FTLD.
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72
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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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73
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Garavís M, Méndez-Lago M, Gabelica V, Whitehead SL, González C, Villasante A. The structure of an endogenous Drosophila centromere reveals the prevalence of tandemly repeated sequences able to form i-motifs. Sci Rep 2015; 5:13307. [PMID: 26289671 PMCID: PMC4542561 DOI: 10.1038/srep13307] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 07/21/2015] [Indexed: 12/21/2022] Open
Abstract
Centromeres are the chromosomal loci at which spindle microtubules attach to mediate chromosome segregation during mitosis and meiosis. In most eukaryotes, centromeres are made up of highly repetitive DNA sequences (satellite DNA) interspersed with middle repetitive DNA sequences (transposable elements). Despite the efforts to establish complete genomic sequences of eukaryotic organisms, the so-called 'finished' genomes are not actually complete because the centromeres have not been assembled due to the intrinsic difficulties in constructing both physical maps and complete sequence assemblies of long stretches of tandemly repetitive DNA. Here we show the first molecular structure of an endogenous Drosophila centromere and the ability of the C-rich dodeca satellite strand to form dimeric i-motifs. The finding of i-motif structures in simple and complex centromeric satellite DNAs leads us to suggest that these centromeric sequences may have been selected not by their primary sequence but by their ability to form noncanonical secondary structures.
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Affiliation(s)
- Miguel Garavís
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Nicolás Cabrera 1, 28049 Madrid, Spain.,Instituto de Química Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
| | - María Méndez-Lago
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Valérie Gabelica
- Univ. Bordeaux, ARNA Laboratory, IECB, 2 rue Robert Escarpit, F-33600 Pessac, France.,Inserm ARNA Laboratory, 146 rue Leo Saignat, F-33000 Bordeaux, France
| | - Siobhan L Whitehead
- The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Carlos González
- Instituto de Química Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Alfredo Villasante
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Nicolás Cabrera 1, 28049 Madrid, Spain
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74
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Ding Y, Fleming AM, He L, Burrows CJ. Unfolding Kinetics of the Human Telomere i-Motif Under a 10 pN Force Imposed by the α-Hemolysin Nanopore Identify Transient Folded-State Lifetimes at Physiological pH. J Am Chem Soc 2015; 137:9053-60. [PMID: 26110559 PMCID: PMC4513840 DOI: 10.1021/jacs.5b03912] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
![]()
Cytosine
(C)-rich DNA can adopt i-motif folds under acidic conditions,
with the human telomere i-motif providing a well-studied example.
The dimensions of this i-motif are appropriate for capture in the
nanocavity of the α-hemolysin (α-HL) protein pore under
an electrophoretic force. Interrogation of the current vs time (i–t) traces when the i-motif interacts
with α-HL identified characteristic signals that were pH dependent.
These features were evaluated from pH 5.0 to 7.2, a region surrounding
the transition pH of the i-motif (6.1). When the i-motif without polynucleotide
tails was studied at pH 5.0, the folded structure entered the nanocavity
of α-HL from either the top or bottom face to yield characteristic
current patterns. Addition of a 5′ 25-mer poly-2′-deoxyadensosine
tail allowed capture of the i-motif from the unfolded terminus, and
this was used to analyze the pH dependency of unfolding. At pH values
below the transition point, only folded strands were observed, and
when the pH was increased above the transition pH, the number of folded
events decreased, while the unfolded events increased. At pH 6.8 and
7.2 4% and 2% of the strands were still folded, respectively. The
lifetimes for the folded states at pH 6.8 and 7.2 were 21 and 9 ms,
respectively, at 160 mV electrophoretic force. These lifetimes are
sufficiently long to affect enzymes operating on DNA. Furthermore,
these transient lifetimes are readily obtained using the α-HL
nanopore, a feature that is not easily achievable by other methods.
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Affiliation(s)
- Yun Ding
- Department of Chemistry, University of Utah, 315 S 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Aaron M Fleming
- Department of Chemistry, University of Utah, 315 S 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Lidong He
- Department of Chemistry, University of Utah, 315 S 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, 315 S 1400 East, Salt Lake City, Utah 84112-0850, United States
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75
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Greco ML, Folini M, Sissi C. Double stranded promoter region of BRAF undergoes to structural rearrangement in nearly physiological conditions. FEBS Lett 2015; 589:2117-23. [DOI: 10.1016/j.febslet.2015.06.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 06/10/2015] [Accepted: 06/19/2015] [Indexed: 10/23/2022]
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76
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Lannes L, Halder S, Krishnan Y, Schwalbe H. Tuning the pH Response of i-Motif DNA Oligonucleotides. Chembiochem 2015; 16:1647-56. [PMID: 26032298 DOI: 10.1002/cbic.201500182] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Indexed: 12/19/2022]
Abstract
Cytosine-rich single-stranded DNA oligonucleotides are able to adopt an i-motif conformation, a four-stranded structure, near a pH of 6. This unique pH-dependent conformational switch is reversible and hence can be controlled by changing the pH. Here, we show that the pH response range of the human telomeric i-motif can be shifted towards more basic pH values by introducing 5-methylcytidines (5-MeC) and towards more acidic pH values by introducing 5-bromocytidines (5-BrC). No thermal destabilisation was observed in these chemically modified i-motif sequences. The time required to attain the new conformation in response to sudden pH changes was slow for all investigated sequences but was found to be ten times faster in the 5-BrC derivative of the i-motif.
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Affiliation(s)
- Laurie Lannes
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt/Main (Germany)
| | - Saheli Halder
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bellary Road, Bangalore 560065 (India)
| | - Yamuna Krishnan
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bellary Road, Bangalore 560065 (India).,Department of Chemistry, University of Chicago, E305, GCIS, 929 E, 57th Street, Chicago, IL 60637 (USA)
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt/Main (Germany).
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77
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Reilly SM, Lyons DF, Wingate SE, Wright RT, Correia JJ, Jameson DM, Wadkins RM. Folding and hydrodynamics of a DNA i-motif from the c-MYC promoter determined by fluorescent cytidine analogs. Biophys J 2015; 107:1703-11. [PMID: 25296324 DOI: 10.1016/j.bpj.2014.08.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 08/05/2014] [Accepted: 08/07/2014] [Indexed: 10/24/2022] Open
Abstract
The four-stranded i-motif (iM) conformation of cytosine-rich DNA has importance to a wide variety of biochemical systems that range from their use in nanomaterials to potential roles in oncogene regulation. The iM structure is formed at slightly acidic pH, where hemiprotonation of cytosine results in a stable C-C(+) basepair. Here, we performed fundamental studies to examine iM formation from a C-rich strand from the promoter of the human c-MYC gene. We used a number of biophysical techniques to characterize both the hydrodynamic properties and folding kinetics of a folded iM. Our hydrodynamic studies using fluorescence anisotropy decay and analytical ultracentrifugation show that the iM structure has a compact size in solution and displays the rigidity of a double strand. By studying the rates of circular dichroism spectral changes and quenching of fluorescent cytidine analogs, we also established a mechanism for the folding of a random coil oligo into the iM. In the course of determining this folding pathway, we established that the fluorescent dC analogs tC° and PdC can be used to monitor individual residues of an iM structure and to determine the pKa of an iM. We established that the C-C(+) hydrogen bonding of certain bases initiates the folding of the iM structure. We also showed that substitutions in the loop regions of iMs give a distinctly different kinetic signature during folding compared with bases that are intercalated. Our data reveal that the iM passes through a distinct intermediate form between the unfolded and folded forms. Taken together, our results lay the foundation for using fluorescent dC analogs to follow structural changes during iM formation. Our technique may also be useful for examining folding and structural changes in more complex iMs.
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Affiliation(s)
- Samantha M Reilly
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi
| | - Daniel F Lyons
- Department of Biochemistry, University of Mississippi Medical Center, Jackson, Mississippi
| | - Sara E Wingate
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi
| | - Robert T Wright
- Department of Biochemistry, University of Mississippi Medical Center, Jackson, Mississippi
| | - John J Correia
- Department of Biochemistry, University of Mississippi Medical Center, Jackson, Mississippi
| | - David M Jameson
- Department of Cell and Molecular Biology, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Randy M Wadkins
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi.
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78
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Kikuta K, Piao H, Brazier J, Taniguchi Y, Onizuka K, Nagatsugi F, Sasaki S. Stabilization of the i-motif structure by the intra-strand cross-link formation. Bioorg Med Chem Lett 2015; 25:3307-10. [PMID: 26105193 DOI: 10.1016/j.bmcl.2015.05.064] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 05/19/2015] [Accepted: 05/22/2015] [Indexed: 02/06/2023]
Abstract
The i-motif structures are formed by oligonucleotides containing cytosine tracts under acidic conditions. The folding of the i-motif under physiological conditions is of great interest because of its biological role. In this study, we investigated the effect of the intra-strand cross-link on the stability of the i-motif structure. The 4-vinyl-substituted analog of thymidine (T-vinyl) was incorporated into the 5'-end of the human telomere complementary strand, which formed the intra-strand cross-link with the internal adenine. The intra-strand cross-linked i-motif displayed CD spectra similar to that of the natural i-motif at acidic pH, which was transformed into a random coil with the increasing pH. The pH midpoint for the transition from the i-motif to random coil increased from pH 6.1 for the natural one to pH 6.8 for the cross-linked one. The thermodynamic parameters were obtained by measuring the thermal melting behaviors by CD and UV, and it was determined that the intra-strand cross-linked i-motif is stabilized due to a favorable entropy effect. Thus, this study has clearly indicated the validity of the intra-strand cross-linking for stabilization of the i-motif structure.
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Affiliation(s)
- Kenji Kikuta
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Haishun Piao
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - John Brazier
- School of Pharmacy, University of Reading, Whiteknights, Reading RG6 6AD, UK
| | - Yosuke Taniguchi
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kazumitsu Onizuka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Shigeki Sasaki
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
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79
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Garavís M, Escaja N, Gabelica V, Villasante A, González C. Centromeric Alpha-Satellite DNA Adopts Dimeric i-Motif Structures Capped by AT Hoogsteen Base Pairs. Chemistry 2015; 21:9816-24. [PMID: 26013031 DOI: 10.1002/chem.201500448] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Indexed: 11/11/2022]
Abstract
Human centromeric alpha-satellite DNA is composed of tandem arrays of two types of 171 bp monomers; type A and type B. The differences between these types are concentrated in a 17 bp region of the monomer called the A/B box. Here, we have determined the solution structure of the C-rich strand of the two main variants of the human alpha-satellite A box. We show that, under acidic conditions, the C-rich strands of two A boxes self-recognize and form a head-to-tail dimeric i-motif stabilized by four intercalated hemi-protonated C:C(+) base pairs. Interestingly, the stack of C:C(+) base pairs is capped by T:T and Hoogsteen A:T base pairs. The two main variants of the A box adopt a similar three-dimensional structure, although the residues involved in the formation of the i-motif core are different in each case. Together with previous studies showing that the B box (known as the CENP-B box) also forms dimeric i-motif structures, our finding of this non-canonical structure in the A box shows that centromeric alpha satellites in all human chromosomes are able to form i-motifs, which consequently raises the possibility that these structures may play a role in the structural organization of the centromere.
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Affiliation(s)
- Miguel Garavís
- Instituto de Química Física Rocasolano, CSIC, Serrano 119, 28006 Madrid (Spain).,Centro de Biología Molecular, "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Nicolás Cabrera 1, 28049 Madrid (Spain)
| | - Núria Escaja
- Departament de Química Orgànica and IBUB, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona (Spain)
| | - Valérie Gabelica
- Univ. Bordeaux, ARNA Laboratory, IECB, 2 rue Robert Escarpit 33600 Pessac (France).,Inserm, ARNA Laboratory, 146 Rue Leo Saignat, 33000 Bordeaux (France)
| | - Alfredo Villasante
- Centro de Biología Molecular, "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Nicolás Cabrera 1, 28049 Madrid (Spain)
| | - Carlos González
- Instituto de Química Física Rocasolano, CSIC, Serrano 119, 28006 Madrid (Spain).
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80
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Reilly SM, Morgan RK, Brooks TA, Wadkins RM. Effect of interior loop length on the thermal stability and pK(a) of i-motif DNA. Biochemistry 2015; 54:1364-70. [PMID: 25619229 DOI: 10.1021/bi5014722] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The four-stranded i-motif (iM) conformation of cytosine-rich DNA is important in a wide variety of biochemical systems ranging from its use in nanomaterials to a potential role in oncogene regulation. An iM is stabilized by acidic pH that allows hemiprotonated cytidines to form a C·C(+) base pair. Fundamental studies that aim to understand how the lengths of loops connecting the protonated C·C(+) pairs affect intramolecular iM physical properties are described here. We characterized both the thermal stability and the pK(a) of intramolecular iMs with differing loop lengths, in both dilute solutions and solutions containing molecular crowding agents. Our results showed that intramolecular iMs with longer central loops form at pHs and temperatures higher than those of iMs with longer outer loops. Our studies also showed that increases in thermal stability of iMs when molecular crowding agents are present are dependent on the loop that is lengthened. However, the increase in pK(a) for iMs when molecular crowding agents are present is insensitive to loop length. Importantly, we also determined the proton activity of solutions containing high concentrations of molecular crowding agents to ascertain whether the increase in pK(a) of an iM is caused by alteration of this activity in buffered solutions. We determined that crowding agents alone increase the apparent pK(a) of a number of small molecules as well as iMs but that increases to iM pK(a) were greater than that expected from a shift in proton activity.
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Affiliation(s)
- Samantha M Reilly
- Department of Chemistry and Biochemistry, University of Mississippi , University, Mississippi 38677, United States
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81
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Huang H, Hong X, Liu F, Li N. A simple approach to study the conformational switching of i-motif DNA by fluorescence anisotropy. Analyst 2015; 140:5987-91. [DOI: 10.1039/c5an01011j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Fluorescence anisotropy is a simple, reliable and sensitive approach to study the conformational switching of the i-motif structure.
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Affiliation(s)
- Hongduan Huang
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education
- Institute of Analytical Chemistry
- College of Chemistry and Molecular Engineering
- Peking University
| | - Xinying Hong
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education
- Institute of Analytical Chemistry
- College of Chemistry and Molecular Engineering
- Peking University
| | - Feng Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education
- Institute of Analytical Chemistry
- College of Chemistry and Molecular Engineering
- Peking University
| | - Na Li
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education
- Institute of Analytical Chemistry
- College of Chemistry and Molecular Engineering
- Peking University
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Amato J, Iaccarino N, Randazzo A, Novellino E, Pagano B. Noncanonical DNA Secondary Structures as Drug Targets: the Prospect of the i-Motif. ChemMedChem 2014; 9:2026-30. [DOI: 10.1002/cmdc.201402153] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Indexed: 11/06/2022]
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83
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Day HA, Pavlou P, Waller ZAE. i-Motif DNA: structure, stability and targeting with ligands. Bioorg Med Chem 2014; 22:4407-18. [PMID: 24957878 DOI: 10.1016/j.bmc.2014.05.047] [Citation(s) in RCA: 271] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 05/09/2014] [Accepted: 05/22/2014] [Indexed: 10/25/2022]
Abstract
i-Motifs are four-stranded DNA secondary structures which can form in sequences rich in cytosine. Stabilised by acidic conditions, they are comprised of two parallel-stranded DNA duplexes held together in an antiparallel orientation by intercalated, cytosine-cytosine(+) base pairs. By virtue of their pH dependent folding, i-motif forming DNA sequences have been used extensively as pH switches for applications in nanotechnology. Initially, i-motifs were thought to be unstable at physiological pH, which precluded substantial biological investigation. However, recent advances have shown that this is not always the case and that i-motif stability is highly dependent on factors such as sequence and environmental conditions. In this review, we discuss some of the different i-motif structures investigated to date and the factors which affect their topology, stability and dynamics. Ligands which can interact with these structures are necessary to aid investigations into the potential biological functions of i-motif DNA and herein we review the existing i-motif ligands and give our perspective on the associated challenges with targeting this structure.
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Affiliation(s)
- Henry A Day
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
| | - Pavlos Pavlou
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
| | - Zoë A E Waller
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK.
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Bhavsar-Jog YP, Van Dornshuld E, Brooks TA, Tschumper GS, Wadkins RM. Epigenetic modification, dehydration, and molecular crowding effects on the thermodynamics of i-motif structure formation from C-rich DNA. Biochemistry 2014; 53:1586-94. [PMID: 24564458 PMCID: PMC3985701 DOI: 10.1021/bi401523b] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
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DNA
sequences with the potential to form secondary structures such
as i-motifs (iMs) and G-quadruplexes (G4s) are abundant in the promoters
of several oncogenes and, in some instances, are known to regulate
gene expression. Recently, iM-forming DNA strands have also been employed
as functional units in nanodevices, ranging from drug delivery systems
to nanocircuitry. To understand both the mechanism of gene regulation
by iMs and how to use them more efficiently in nanotechnological applications,
it is essential to have a thorough knowledge of factors that govern
their conformational states and stabilities. Most of the prior work
to characterize the conformational dynamics of iMs have been done
with iM-forming synthetic constructs like tandem (CCT)n repeats and in standard dilute buffer systems. Here,
we present a systematic study on the consequences of epigenetic modifications,
molecular crowding, and degree of hydration on the stabilities of
an iM-forming sequence from the promoter of the c-myc gene. Our results indicate that 5-hydroxymethylation of cytosines
destabilized the iMs against thermal and pH-dependent melting; contrarily,
5-methylcytosine modification stabilized the iMs. Under molecular
crowding conditions (PEG-300, 40% w/v), the thermal stability of iMs
increased by ∼10 °C, and the pKa was raised from 6.1 ± 0.1 to 7.0 ± 0.1. Lastly, the iM’s
stability at varying degrees of hydration in 1,2-dimethoxyethane,
2-methoxyethanol, ethylene glycol, 1,3-propanediol, and glycerol cosolvents
indicated that the iMs are stabilized by dehydration because of the
release of water molecules when folded. Our results highlight the
importance of considering the effects of epigenetic modifications,
molecular crowding, and the degree of hydration on iM structural dynamics.
For example, the incorporation of 5-methylycytosines and 5-hydroxymethlycytosines
in iMs could be useful for fine-tuning the pH- or temperature-dependent
folding/unfolding of an iM. Variations in the degree of hydration
of iMs may also provide an additional control of the folded/unfolded
state of iMs without having to change the pH of the surrounding matrix.
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Affiliation(s)
- Yogini P Bhavsar-Jog
- Department of Chemistry and Biochemistry and ‡Department of Pharmacology, University of Mississippi , University, Mississippi 38677, United States
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85
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Benabou S, Aviñó A, Eritja R, González C, Gargallo R. Fundamental aspects of the nucleic acid i-motif structures. RSC Adv 2014. [DOI: 10.1039/c4ra02129k] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The latest research on fundamental aspects of i-motif structures is reviewed with special attention to their hypothetical rolein vivo.
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Affiliation(s)
- S. Benabou
- Department of Analytical Chemistry
- University of Barcelona
- E-08028 Barcelona, Spain
| | - A. Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC)
- CIBER-BBN Networking Centre on Bioengineering
- Biomaterials and Nanomedicine
- E-08034 Barcelona, Spain
| | - R. Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC)
- CIBER-BBN Networking Centre on Bioengineering
- Biomaterials and Nanomedicine
- E-08034 Barcelona, Spain
| | - C. González
- Institute of Physical Chemistry “Rocasolano”
- CSIC
- E-28006 Madrid, Spain
| | - R. Gargallo
- Department of Analytical Chemistry
- University of Barcelona
- E-08028 Barcelona, Spain
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