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Amato J, D'Aria F, Marzano S, Iaccarino N, Randazzo A, Giancola C, Pagano B. On the thermodynamics of folding of an i-motif DNA in solution under favorable conditions. Phys Chem Chem Phys 2021; 23:15030-15037. [PMID: 34151914 DOI: 10.1039/d1cp01779a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Under slightly acidic conditions, cytosine-rich DNA sequences can form non-canonical secondary structures called i-motifs, which occur as four stretches of cytosine repeats form hemi-protonated C·C+ base pairs. The growing interest in the i-motif structures as important components in functional DNA-based nanotechnology or as potential targets of anticancer drugs, increases the need for a deep understanding of the energetics of their structural transitions. Here, a combination of spectroscopic and calorimetric techniques is used to unravel the thermodynamics of folding of an i-motif DNA under favorable conditions. The results give new insights into the energetic aspects of i-motifs and show that thermodynamic and thermal stability are related but not identical properties of such DNA structures.
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Affiliation(s)
- Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Naples, I-80131, Italy.
| | - Federica D'Aria
- Department of Pharmacy, University of Naples Federico II, Naples, I-80131, Italy.
| | - Simona Marzano
- Department of Pharmacy, University of Naples Federico II, Naples, I-80131, Italy.
| | - Nunzia Iaccarino
- Department of Pharmacy, University of Naples Federico II, Naples, I-80131, Italy.
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, Naples, I-80131, Italy.
| | - Concetta Giancola
- Department of Pharmacy, University of Naples Federico II, Naples, I-80131, Italy.
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Naples, I-80131, Italy.
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2
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Školáková P, Renčiuk D, Palacký J, Krafčík D, Dvořáková Z, Kejnovská I, Bednářová K, Vorlíčková M. Systematic investigation of sequence requirements for DNA i-motif formation. Nucleic Acids Res 2019; 47:2177-2189. [PMID: 30715498 PMCID: PMC6412112 DOI: 10.1093/nar/gkz046] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 01/16/2019] [Accepted: 01/18/2019] [Indexed: 12/13/2022] Open
Abstract
The formation of intercalated motifs (iMs) - secondary DNA structures based on hemiprotonated C.C+ pairs in suitable cytosine-rich DNA sequences, is reflected by typical changes in CD and UV absorption spectra. By means of spectroscopic methods, electrophoresis, chemical modifications and other procedures, we characterized iM formation and stability in sequences with different cytosine block lengths interrupted by various numbers and types of nucleotides. Particular attention was paid to the formation of iMs at pH conditions close to neutral. We identified the optimal conditions and minimal requirements for iM formation in DNA sequences, and addressed gaps and inaccurate data interpretations in existing studies to specify principles of iM formation and modes of their folding.
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Affiliation(s)
- Petra Školáková
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Daniel Renčiuk
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Jan Palacký
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Daniel Krafčík
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 735/5, 625 00 Brno, Czech Republic
| | - Zuzana Dvořáková
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Iva Kejnovská
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Klára Bednářová
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Michaela Vorlíčková
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
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Rogers RA, Fleming AM, Burrows CJ. Unusual Isothermal Hysteresis in DNA i-Motif pH Transitions: A Study of the RAD17 Promoter Sequence. Biophys J 2019; 114:1804-1815. [PMID: 29694860 DOI: 10.1016/j.bpj.2018.03.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/07/2018] [Accepted: 03/14/2018] [Indexed: 11/15/2022] Open
Abstract
We have interrogated the isothermal folding behavior of the DNA i-motif of the human telomere, dC19, and a high-stability i-motif-forming sequence in the promoter of the human DNA repair gene RAD17 using human physiological solution and temperature conditions. We developed a circular-dichroism-spectroscopy-based pH titration method that is followed by analysis of titration curves in the derivative domain and found that the observed pH-dependent folding behavior can be significantly different and, in some cases, multiphasic, with a dependence on how rapidly i-motif folding is induced. Interestingly, the human telomere sequence exhibits unusual isothermal hysteresis in which the unfolding process always occurs at a higher pH than the folding process. For the RAD17 i-motif, rapid folding by injection into a low-pH solution results in triphasic unfolding behavior that is completely diminished when samples are slowly folded in a stepwise manner via pH titration. Chemical footprinting of the RAD17 sequence and pH titrations of dT-substituted mutants of the RAD17 sequence were used to develop a model of RAD17 folding and unfolding. These results may provide valuable information pertinent to i-motif use in sensors and materials, as well as insight into the potential biological activity of i-motif-forming sequences under stepwise or instantaneous changes in pH.
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Affiliation(s)
- R Aaron Rogers
- Department of Chemistry, University of Utah, Salt Lake City, Utah
| | - Aaron M Fleming
- Department of Chemistry, University of Utah, Salt Lake City, Utah
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Cambón A, Villar-Alvarez E, Alatorre-Meda M, Pardo A, Hiram B, Barbosa S, Taboada P, Mosquera V. Characterization of the complexation phenomenon and biological activity in vitro of polyplexes based on Tetronic T901 and DNA. J Colloid Interface Sci 2018; 519:58-70. [PMID: 29482097 DOI: 10.1016/j.jcis.2018.02.051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 02/15/2018] [Accepted: 02/16/2018] [Indexed: 12/31/2022]
Abstract
The complexation process and underlying mechanisms that rule the interaction of DNA with the cationic block copolymer Tetronic T901 to form polyplexes and their potential transfection efficiency have been studied under different solution conditions. We noted that T901 favors the formation of self-assembled structures with partially condensed DNA at smaller polymer concentrations than other Pluronic™/Tetronic™-type copolymers previously analysed. The observed polyplexes display sizes from the nano- to the micro- range as derived from DLS, electronic and optical microscopies. Also, copolymer micelles are observed at concentrations below the copolymer critical micellar concentration (cmc) induced by the presence of DNA. The complexation process is dependent on solution conditions, with electrostatic and ionic interactions being more important at acidic pH thanks to the predominant diprotonated form of the block copolymer which is less aggregation-prone, whilst dispersive forces are increasingly enhanced under basic conditions or when rising the solution temperature. Whatever the case, the complexation is mainly governed by entropic contributions, as denoted from ITC data. In vitro transfection experiments after complexing T901 with a pDNA encoding the expression of green fluorescein protein, GFP, show a relative successful fluorescence of transfected HeLa cells, which confirms the uptake, internalization and release of the genetic material within the cells at suitable [N]/[P] ratios with relatively low cytotoxicity. Despite the observed successful outcomes, the obtained transfection efficacies are slightly lower than those obtained with Lipofectamine2000, so further optimization of the polyplex formation conditions is envisaged in future studies.
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Affiliation(s)
- Adriana Cambón
- Colloids and Polymers Physics Group, Department of Particle Physics, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Eva Villar-Alvarez
- Colloids and Polymers Physics Group, Department of Particle Physics, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Manuel Alatorre-Meda
- CONACyT-Instituto Tecnológico de Tijuana, Centro de Graduados e Investigación en Química, Blvd. Alberto Limón Padilla S/N, 22510 Tijuana, B.C., Mexico
| | - Alberto Pardo
- Colloids and Polymers Physics Group, Department of Particle Physics, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Baltazar Hiram
- Colloids and Polymers Physics Group, Department of Particle Physics, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain; Departamento de Física, Universidad de Sonora, Rosales y Transversal, 83000 Hermosillo, Sonora, Mexico
| | - Silvia Barbosa
- Colloids and Polymers Physics Group, Department of Particle Physics, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Pablo Taboada
- Colloids and Polymers Physics Group, Department of Particle Physics, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain.
| | - Víctor Mosquera
- Colloids and Polymers Physics Group, Department of Particle Physics, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
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Gao Y, Wu S, Ye X. The effects of monovalent metal ions on the conformation of human telomere DNA using analytical ultracentrifugation. SOFT MATTER 2016; 12:5959-5967. [PMID: 27329676 DOI: 10.1039/c6sm01010e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A human telomere DNA segment (HT-DNA) can fold into a G-quadruplex in the presence of some monovalent cations. These cations can interact with the phosphate groups of the DNA segment and/or with the O6 oxygen atom of guanines, which are called non-specific interactions and specific interactions, respectively. However, until now how these two interactions affect the structure of HT-DNA has not been well understood. In this study, a combination of analytical ultracentrifugation (AUC) and circular dichroism (CD) was used to explore the effects of these two interactions on the structure of a 22-mer single-stranded DNA with a sequence of 5'-AGGG(TTAGGG)3-3'. The results showed that the standard sedimentation coefficient (s20,w) of HT-DNA starts to increase when the concentration of potassium ions (CK(+)) is higher than 10.0 µM due to the formation of a G-quadruplex through specific interactions. Whereas, for a control DNA, a higher CK(+) value of 1.0 mM was needed for increasing s20,w due to non-specific interactions. Moreover, potassium ions could promote the formation of the G-quadruplex much more easily than lithium, sodium and cesium ions, presumably due to its appropriate size in the dehydrated state and easier dehydration. The molar mass of DNA at different cation concentrations was nearly a constant and close to the theoretical value of the molar mass of monomeric HT-DNA, indicating that what we observed is the structural change of individual DNA chains.
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Affiliation(s)
- Yating Gao
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China.
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Wang X, Ye X, Zhang G. Investigation of pH-induced conformational change and hydration of poly(methacrylic acid) by analytical ultracentrifugation. SOFT MATTER 2015; 11:5381-5388. [PMID: 26059391 DOI: 10.1039/c5sm00806a] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Analytical ultracentrifugation was performed on poly(methacrylic acid) (PMAA) with a series of weight average molar masses (Mw) in aqueous solutions as a function of pH. The scales of the sedimentation coefficient (s) and the diffusion coefficient (D) to Mw at infinite dilutions were obtained at different pH values, indicating that PMAA chains adopt a collapsed structure at low pH values, and stretch at pH higher than 5.2. Our results show that the sedimentation coefficient exhibits a minimum at pH ∼ 6.0, presumably due to the effect of the conformational change and the hydration state of PMAA chains. When pH increases from 6.0 to 8.5, PMAA chains with high molar mass shrink a little bit, presumably because the sodium ions act as a bridging agent between nonadjacent carboxylate groups. Furthermore, the weight average molar mass of PMAA at pH 8.5 increases by one fold than that at pH 4.0, indicating the condensation of sodium ions and the increase in the number of hydration water molecules around carboxylate groups at high pH values.
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Affiliation(s)
- Xiaoyan Wang
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China.
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Cao Z, Wu S, Zhang G. Dynamics of single polyelectrolyte chains in salt-free dilute solutions investigated by analytical ultracentrifugation. Phys Chem Chem Phys 2015; 17:15896-902. [PMID: 26018174 DOI: 10.1039/c5cp02111a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The dynamics of polyelectrolytes in salt-free solution is an unsolved problem. We have investigated the sedimentation and diffusion of xanthan and poly(N-methyl 4-vinyl pyridine iodide) (P4VPI) in salt-free dilute solutions by analytical ultracentrifugation (AUC) using sedimentation velocity (SV) as a function of polyelectrolyte concentration (Cp). Our study reveals two concentration regimes distinguished in either polyanion (xanthan) or polycation (P4VPI) dilute aqueous solution. When Cp is below the Debye concentration (Cd) at which the chain separation (d) is close to the debye length (lD), the interchain electrostatic repulsion is negligible, and the reciprocal apparent sedimentation coefficient (1/s), apparent diffusion coefficient (D) or reciprocal apparent molecular weight (1/Mw) is linearly related to Cp. In the range Cp > Cd with d < lD, the interchain electrostatic repulsion is present, and the dynamics of polyelectrolytes becomes complex. The real sedimentation coefficient (s0), the diffusion coefficient (D0) and the molecular weight (Mw,0) of the single polyelectrolyte chain in salt-free dilute solution can be obtained by extrapolating the concentration to zero. The present study reveals that the complex dynamics of polyelectrolytes in salt-free dilute solutions arises due to the interchain electrostatic repulsion.
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Affiliation(s)
- Zhonglin Cao
- Hefei National Laboratory for Physical Sciences at Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, 230026, China
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8
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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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Mata G, Luedtke NW. Fluorescent Probe for Proton-Coupled DNA Folding Revealing Slow Exchange of i-Motif and Duplex Structures. J Am Chem Soc 2015; 137:699-707. [DOI: 10.1021/ja508741u] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Guillaume Mata
- Department of Chemistry, University of Zürich, Winterthurerstrasse
190, CH-8057 Zürich, Switzerland
| | - Nathan W. Luedtke
- Department of Chemistry, University of Zürich, Winterthurerstrasse
190, CH-8057 Zürich, Switzerland
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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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