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Panczyk T, Nieszporek K, Wolski P. Stability and Existence of Noncanonical I-motif DNA Structures in Computer Simulations Based on Atomistic and Coarse-Grained Force Fields. Molecules 2022; 27:molecules27154915. [PMID: 35956863 PMCID: PMC9370271 DOI: 10.3390/molecules27154915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/13/2022] [Accepted: 07/26/2022] [Indexed: 11/24/2022] Open
Abstract
Cytosine-rich DNA sequences are able to fold into noncanonical structures, in which semi-protonated cytosine pairs develop extra hydrogen bonds, and these bonds are responsible for the overall stability of a structure called the i-motif. The i-motif can be formed in many regions of the genome, but the most representative is the telomeric region in which the CCCTAA sequences are repeated thousands of times. The ability to reverse folding/unfolding in response to pH change makes the above sequence and i-motif very promising components of nanomachines, extended DNA structures, and drug carriers. Molecular dynamics analysis of such structures is highly beneficial due to direct insights into the microscopic structure of the considered systems. We show that Amber force fields for DNA predict the stability of the i-motif over a long timescale; however, these force fields are not able to predict folding of the cytosine-rich sequences into the i-motif. The reason is the kinetic partitioning of the folding process, which makes the transitions between various intermediates too time-consuming in atomistic force field representation. Application of coarse-grained force fields usually highly accelerates complex structural transitions. We, however, found that three of the most popular coarse-grained force fields for DNA (oxDNA, 3SPN, and Martini) were not able to predict the stability of the i-motif structure. Obviously, they were not able to accelerate the folding of unfolded states into an i-motif. This observation must be strongly highlighted, and the need to develop suitable extensions of coarse-grained force fields for DNA is pointed out. However, it will take a great deal of effort to successfully solve these problems.
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Affiliation(s)
- Tomasz Panczyk
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, ul. Niezapominajek 8, 30239 Cracow, Poland;
- Correspondence:
| | - Krzysztof Nieszporek
- Department of Theoretical Chemistry, Institute of Chemical Sciences, Faculty of Chemistry, Maria Curie-Sklodowska University in Lublin pl. Maria Curie-Sklodowska 3, 20031 Lublin, Poland;
| | - Pawel Wolski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, ul. Niezapominajek 8, 30239 Cracow, Poland;
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2
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CpG Methylation Altered the Stability and Structure of the i-Motifs Located in the CpG Islands. Int J Mol Sci 2022; 23:ijms23126467. [PMID: 35742916 PMCID: PMC9223787 DOI: 10.3390/ijms23126467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/04/2022] [Accepted: 06/07/2022] [Indexed: 11/25/2022] Open
Abstract
Cytosine methylation within the 5′-C-phosphate-G-3′ sequence of nucleotides (called CpG methylation) is a well-known epigenetic modification of genomic DNA that plays an important role in gene expression and development. CpG methylation is likely to be altered in the CpG islands. CpG islands are rich in cytosine, forming a structure called the i-motif via cytosine-cytosine hydrogen bonding. However, little is known about the effect of CpG methylation on the i-motif. In this study, The CpG methylation-induced structural changes on the i-motif was examined by thermal stability, circular dichroism (CD) spectroscopy, and native-polyacrylamide gel electrophoresis (Native-PAGE) evaluation of five i-motif-forming DNAs from four cancer-related genes (VEGF, C-KIT, BCL2, and HRAS). This research shows that CpG methylation increased the transitional pH of several i-motif-forming DNAs and their thermal stability. When examining the effect of CpG methylation on the i-motif in the presence of opposite G4-forming DNAs, CpG methylation influenced the proportion of G4 and i-motif formation. This study showed that CpG methylation altered the stability and structure of the i-motif in CpG islands.
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Pant P, Aggarwal L. Assessing the DNA structural integrity via selective annihilation of Watson-Crick hydrogen bonds: Insights from molecular dynamics simulations. Biophys Chem 2022; 282:106758. [DOI: 10.1016/j.bpc.2021.106758] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/09/2021] [Accepted: 12/30/2021] [Indexed: 01/17/2023]
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Han X, Xu X, Wu Z, Wu Z, Qi X. Synchronous conjugation of i-motif DNA and therapeutic siRNA on the vertexes of tetrahedral DNA nanocages for efficient gene silence. Acta Pharm Sin B 2021; 11:3286-3296. [PMID: 34729316 PMCID: PMC8546665 DOI: 10.1016/j.apsb.2021.02.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 11/09/2020] [Accepted: 12/12/2021] [Indexed: 12/24/2022] Open
Abstract
The functionality of DNA biomacromolecules has been widely excavated, as therapeutic drugs, carriers, and functionalized modification derivatives. In this study, we developed a series of DNA tetrahedron nanocages (Td), via synchronous conjugating different numbers of i-(X) and therapeutic siRNA on four vertexes of tetrahedral DNA nanocage (aX-Td@bsiRNA, a+b = 4). This i-motif-conjugated Td exhibited good endosomal escape behaviours in A549 tumor cells, and the escape efficiency was affected by the number of i-motif. Furthermore, the downregulating mRNA and protein expression level of epidermal growth factor receptor (EGFR) caused by this siRNA embedded Td were verified in A549 cells. The tumor growth inhibition efficiency of the 2X-Td@2siRNA treated group in tumor-bearing mice was significantly higher than that of non-i-motif-conjugated Td@2siRNA (3.14-fold) and free siRNA (3.63-fold). These results demonstrate a general strategy for endowing DNA nanostructures with endosomal escape behaviours to achieve effective in vivo gene delivery and therapy.
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Mondal M, Yang L, Cai Z, Patra P, Gao YQ. A perspective on the molecular simulation of DNA from structural and functional aspects. Chem Sci 2021; 12:5390-5409. [PMID: 34168783 PMCID: PMC8179617 DOI: 10.1039/d0sc05329e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
As genetic material, DNA not only carries genetic information by sequence, but also affects biological functions ranging from base modification to replication, transcription and gene regulation through its structural and dynamic properties and variations. The motion and structural properties of DNA involved in related biological processes are also multi-scale, ranging from single base flipping to local DNA deformation, TF binding, G-quadruplex and i-motif formation, TAD establishment, compartmentalization and even chromosome territory formation, just to name a few. The sequence-dependent physical properties of DNA play vital role in all these events, and thus it is interesting to examine how simple sequence information affects DNA and the formation of the chromatin structure in these different hierarchical orders. Accordingly, molecular simulations can provide atomistic details of interactions and conformational dynamics involved in different biological processes of DNA, including those inaccessible by current experimental methods. In this perspective, which is mainly based on our recent studies, we provide a brief overview of the atomistic simulations on how the hierarchical structure and dynamics of DNA can be influenced by its sequences, base modifications, environmental factors and protein binding in the context of the protein-DNA interactions, gene regulation and structural organization of chromatin. We try to connect the DNA sequence, the hierarchical structures of DNA and gene regulation.
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Affiliation(s)
- Manas Mondal
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory 518055 Shenzhen China
| | - Lijiang Yang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University 100871 Beijing China
| | - Zhicheng Cai
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University 100871 Beijing China.,Biomedical Pioneering Innovation Center, Peking University 100871 Beijing China
| | - Piya Patra
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory 518055 Shenzhen China .,Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University 100871 Beijing China
| | - Yi Qin Gao
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory 518055 Shenzhen China .,Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University 100871 Beijing China.,Biomedical Pioneering Innovation Center, Peking University 100871 Beijing China.,Beijing Advanced Innovation Center for Genomics, Peking University 100871 Beijing China
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Zhang X, Zhang Y, Zhang W. Dynamic topology of double-stranded telomeric DNA studied by single-molecule manipulation in vitro. Nucleic Acids Res 2020; 48:6458-6470. [PMID: 32496520 PMCID: PMC7337930 DOI: 10.1093/nar/gkaa479] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 05/17/2020] [Accepted: 05/27/2020] [Indexed: 12/18/2022] Open
Abstract
The dynamic topological structure of telomeric DNA is closely related to its biological function; however, no such structural information on full-length telomeric DNA has been reported due to difficulties synthesizing long double-stranded telomeric DNA. Herein, we developed an EM-PCR and TA cloning-based approach to synthesize long-chain double-stranded tandem repeats of telomeric DNA. Using mechanical manipulation assays based on single-molecule atomic force microscopy, we found that mechanical force can trigger the melting of double-stranded telomeric DNA and the formation of higher-order structures (G-quadruplexes or i-motifs). Our results show that only when both the G-strand and C-strand of double-stranded telomeric DNA form higher-order structures (G-quadruplexes or i-motifs) at the same time (e.g. in the presence of 100 mM KCl under pH 4.7), that the higher-order structure(s) can remain after the external force is removed. The presence of monovalent K+, single-wall carbon nanotubes (SWCNTs), acidic conditions, or short G-rich fragments (∼30 nt) can shift the transition from dsDNA to higher-order structures. Our results provide a new way to regulate the topology of telomeric DNA.
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Affiliation(s)
- Xiaonong Zhang
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130012, People's Republic of China
| | - Yingqi Zhang
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130012, People's Republic of China
| | - Wenke Zhang
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130012, People's Republic of China
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Rogers RA, Meyer MR, Stewart KM, Eyring GM, Fleming AM, Burrows CJ. Hysteresis in poly-2'-deoxycytidine i-motif folding is impacted by the method of analysis as well as loop and stem lengths. Biopolymers 2020; 112:e23389. [PMID: 33098582 DOI: 10.1002/bip.23389] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 06/06/2020] [Accepted: 06/11/2020] [Indexed: 02/06/2023]
Abstract
In DNA, i-motif (iM) folds occur under slightly acidic conditions when sequences rich in 2'-deoxycytidine (dC) nucleotides adopt consecutive dC self base pairs. The pH stability of an iM is defined by the midpoint in the pH transition (pHT ) between the folded and unfolded states. Two different experiments to determine pHT values via circular dichroism (CD) spectroscopy were performed on poly-dC iMs of length 15, 19, or 23 nucleotides. These experiments demonstrate two points: (1) pHT values were dependent on the titration experiment performed, and (2) pH-induced denaturing or annealing processes produced isothermal hysteresis in the pHT values. These results in tandem with model iMs with judicious mutations of dC to thymidine to favor particular folds found the hysteresis was maximal for the shorter poly-dC iMs and those with an even number of base pairs, while the hysteresis was minimal for longer poly-dC iMs and those with an odd number of base pairs. Experiments to follow the iM folding via thermal changes identified thermal hysteresis between the denaturing and annealing cycles. Similar trends were found to those observed in the CD experiments. The results demonstrate that the method of iM analysis can impact the pHT parameter measured, and hysteresis was observed in the pHT and Tm values.
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Affiliation(s)
- R Aaron Rogers
- Department of Chemistry, University of Utah, Salt Lake City, Utah, U.S.A
| | - Madeline R Meyer
- Department of Chemistry, University of Utah, Salt Lake City, Utah, U.S.A
| | - Kayla M Stewart
- Department of Chemistry, University of Utah, Salt Lake City, Utah, U.S.A
| | - Gabriela M Eyring
- Department of Chemistry, University of Utah, Salt Lake City, Utah, U.S.A
| | - Aaron M Fleming
- Department of Chemistry, University of Utah, Salt Lake City, Utah, U.S.A
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, Salt Lake City, Utah, U.S.A
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Navarro A, Benabou S, Eritja R, Gargallo R. Influence of pH and a porphyrin ligand on the stability of a G-quadruplex structure within a duplex segment near the promoter region of the SMARCA4 gene. Int J Biol Macromol 2020; 159:383-393. [PMID: 32416304 DOI: 10.1016/j.ijbiomac.2020.05.062] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/06/2020] [Accepted: 05/09/2020] [Indexed: 12/20/2022]
Abstract
In a previous work, the formation of G-quadruplex structures in a 44-nucleotide long sequence found near the promoter region of the SMARCA4 gene was reported. The central 25 nucleotides were able to fold into an antiparallel G-quadruplex structure, the stability of which was pH-dependent. In the present work, the effect of the presence of lateral nucleotides and the complementary cytosine-rich strand on the stability of this G-quadruplex has been characterized. Moreover, the role of the model ligand TMPyP4 has been studied. Spectroscopic and separation techniques, as well as multivariate data analysis methods, have been used with these purposes. The results have shown that stability of the G-quadruplex as a function of pH or temperature is greatly reduced in the presence of the lateral nucleotides. The influence of the complementary strand does not prevent the formation of the G-quadruplex. Moreover, attempts to modulate the equilibria by an external ligand led us to determine the influence of the TMPyP4 porphyrin on these complex equilibria. This study could eventually help to understand the regulation of SMARCA4 expression.
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Affiliation(s)
- Alba Navarro
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Spain
| | - Sanae Benabou
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Spain; Université de Bordeaux, CNRS, Inserm, Laboratoire Acides Nucléiques: Régulations Naturelle et Artificielle (ARNA, U1212, UMR5320), IECB, 2 rue Robert Escarpit, 33600 Pessac, France
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona, Spain
| | - Raimundo Gargallo
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Spain.
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Chaudhary S, Kaushik M, Ahmed S, Kukreti S. Exploring potential of i-motif DNA formed in the promoter region of GRIN1 gene for nanotechnological applications. RESULTS IN CHEMISTRY 2020. [DOI: 10.1016/j.rechem.2020.100086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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11
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Wolski P, Wojton P, Nieszporek K, Panczyk T. Interaction of Human Telomeric i-Motif DNA with Single-Walled Carbon Nanotubes: Insights from Molecular Dynamics Simulations. J Phys Chem B 2019; 123:10343-10353. [PMID: 31735024 DOI: 10.1021/acs.jpcb.9b07292] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This work deals with molecular dynamics simulations of human telomeric i-motif DNA interacting with functionalized single-walled carbon nanotubes. We study two kinds of i-motifs differing by the protonation state of cytosines, i.e., unprotonated ones representative to neutral pH and with half of the cytosines protonated and representative to acidic conditions. These i-motifs interact with two kinds of carbon nanotubes differing mainly in chirality (diameter), i.e., (10, 0) and (20, 0). Additionally, these nanotubes were on-tip functionalized by amino groups or by guanine- containing residues. We found that protonated i-motif adsorbs strongly, although not specifically, on the nanotube surfaces with its 3' and 5' ends directed toward the surface and that adsorption does not affect the i-motif shape and hydrogen bonds existing between C:C+ pairs. The functional groups on the nanotube tips have minimal effect either on position of i-motif or on its binding strength. Unprotonated i-motif, in turn, deteriorates significantly during interaction with the nanotubes and its binding strength is rather high as well. We found that (10, 0) nanotubes destroy the i-motif shape faster than (20, 0). Moreover the i-motif either tries to wrap the nanotube or migrates to its tip and becomes immobilized due to interaction with guanine residue localized on the nanotube tip and attempts to incorporate its 3' end into the nanotube interior. No hydrogen bonds exist within the unprotonated i-motif prior to and after adsorption on the nanotube. Thus, carbon nanotubes do not improve the stability of unprotonated i-motif due to simple adsorption or just physical interactions. We hypothesize that the stabilizing effect of carbon nanotubes reported in the literature is due to proton transfer from the functional group in the nanotube to cytosines and subsequent formation of C:C+ pairs.
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Affiliation(s)
- Pawel Wolski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences , ul. Niezapominajek 8 , 30239 Cracow , Poland
| | - Patrycja Wojton
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences , ul. Niezapominajek 8 , 30239 Cracow , Poland
| | - Krzysztof Nieszporek
- Department of Chemistry , Maria Curie-Sklodowska University , pl. M. Curie-Sklodowskiej 3 , 20031 Lublin , Poland
| | - Tomasz Panczyk
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences , ul. Niezapominajek 8 , 30239 Cracow , Poland
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12
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Mondal M, Bhattacharyya D, Gao YQ. Structural properties and influence of solvent on the stability of telomeric four-stranded i-motif DNA. Phys Chem Chem Phys 2019; 21:21549-21560. [PMID: 31536074 DOI: 10.1039/c9cp03253c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Repetitive cytosine rich i-motif forming sequences are abundant in the telomere, centromere and promoters of several oncogenes and in some instances are known to regulate transcription and gene expression. The in vivo existence of i-motif structures demands further insight into the factors affecting their formation and stability and development of better understanding of their gene regulatory functions. Most prior studies characterizing the conformational dynamics of i-motifs are based on i-motif forming synthetic constructs. Here, we present a systematic study on the stability and structural properties of biologically relevant i-motifs of telomeric and centromeric repeat fragments. Our results based on molecular dynamics simulations and quantum chemical calculations indicate that along with base pairing interactions within the i-motif core the overall folded conformation is associated with the stable C-HO sugar "zippers" in the narrow grooves and structured water molecules along the wide grooves. The stacked geometry of the hemi-protonated cytosine pairs within the i-motif core is mainly governed by the repulsive base stacking interaction. The loop sequence can affect the structural dynamics of the i-motif by altering the loop motion and backbone conformation. Overall this study provides microscopic insight into the i-motif structure that will be helpful to understand the structural aspect of mechanisms of gene regulation by i-motif DNA.
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Affiliation(s)
- Manas Mondal
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China.
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Panczyk T, Wojton P, Wolski P. Mechanism of unfolding and relative stabilities of G-quadruplex and I-motif noncanonical DNA structures analyzed in biased molecular dynamics simulations. Biophys Chem 2019; 250:106173. [DOI: 10.1016/j.bpc.2019.106173] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 04/12/2019] [Accepted: 04/12/2019] [Indexed: 12/01/2022]
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Wolski P, Nieszporek K, Panczyk T. G-Quadruplex and I-Motif Structures within the Telomeric DNA Duplex. A Molecular Dynamics Analysis of Protonation States as Factors Affecting Their Stability. J Phys Chem B 2018; 123:468-479. [DOI: 10.1021/acs.jpcb.8b11547] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pawel Wolski
- Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, ul. Niezapominajek 8, 30239 Cracow, Poland
| | - Krzysztof Nieszporek
- Department of Chemistry, Maria Curie-Sklodowska University, pl. M. Curie-Sklodowskiej 3, 20031 Lublin, Poland
| | - Tomasz Panczyk
- Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, ul. Niezapominajek 8, 30239 Cracow, Poland
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