1
|
Mezzina L, Nicosia A, Barone L, Vento F, Mineo PG. Water-Soluble Star Polymer as a Potential Photoactivated Nanotool for Lysozyme Degradation. Polymers (Basel) 2024; 16:301. [PMID: 38276709 PMCID: PMC10819795 DOI: 10.3390/polym16020301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
The development of nanotools for chemical sensing and macromolecular modifications is a new challenge in the biomedical field, with emphasis on artificial peptidases designed to cleave peptide bonds at specific sites. In this landscape, metal porphyrins are attractive due to their ability to form stable complexes with amino acids and to generate reactive oxygen species when irradiated by light of appropriate wavelengths. The issues of hydrophobic behavior and aggregation in aqueous environments of porphyrins can be solved by using its PEGylated derivatives. This work proposes the design of an artificial photo-protease agent based on a PEGylated mercury porphyrin, able to form a stable complex with l-Tryptophan, an amino acid present also in the lysozyme structure (a well-known protein model). The sensing and photodegradation features of PEGylated mercury porphyrin were exploited to detect and degrade both l-Trp and lysozyme using ROS, generated under green (532 nm) and red (650 nm) light lasers. The obtained system (Star3600_Hg) and its behavior as a photo-protease agent were studied by means of several spectroscopies (UV-Vis, fluorescence and circular dichroism), and MALDI-TOF mass spectrometry, showing the cleavage of lysozyme and the appearance of several short-chain residues. The approach of this study paves the way for potential applications in theranostics and targeted bio-medical therapies.
Collapse
Affiliation(s)
- Lidia Mezzina
- Department of Chemical Sciences and INSTM UdR of Catania, University of Catania, V.le A. Doria 6, I-95125 Catania, Italy; (L.M.); (L.B.); (F.V.)
| | - Angelo Nicosia
- Department of Chemical Sciences and INSTM UdR of Catania, University of Catania, V.le A. Doria 6, I-95125 Catania, Italy; (L.M.); (L.B.); (F.V.)
| | - Laura Barone
- Department of Chemical Sciences and INSTM UdR of Catania, University of Catania, V.le A. Doria 6, I-95125 Catania, Italy; (L.M.); (L.B.); (F.V.)
| | - Fabiana Vento
- Department of Chemical Sciences and INSTM UdR of Catania, University of Catania, V.le A. Doria 6, I-95125 Catania, Italy; (L.M.); (L.B.); (F.V.)
| | - Placido Giuseppe Mineo
- Department of Chemical Sciences and INSTM UdR of Catania, University of Catania, V.le A. Doria 6, I-95125 Catania, Italy; (L.M.); (L.B.); (F.V.)
- Institute for Chemical and Physical Processes, National Research Council (IPCF-CNR), Viale F. Stagno d’Alcontres 37, I-98158 Messina, Italy
- Institute of Polymers, Composites and Biomaterials, National Research Council (IPCB-CNR), Via P. Gaifami 18, I-95126 Catania, Italy
| |
Collapse
|
2
|
D'Urso A. Chiroptical Properties of Z-DNA Using Ionic Porphyrins and Metalloporphyrins. Methods Mol Biol 2023; 2651:131-141. [PMID: 36892764 DOI: 10.1007/978-1-0716-3084-6_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
The non-covalent interaction of achiral porphyrins with nucleic acids has been extensively studied, and various macrocycles have been indeed utilized as reporters of different sequences of DNA bases. Nevertheless, few studies have been published on the capability of these macrocycles to discriminate among the various nucleic acid conformations. Circular dichroism spectroscopy allowed to characterize the binding of several cationic and anionic mesoporphyrins and metallo derivatives with Z-DNA, in order to exploit the functionality of these systems as probes, storing system, and logic gate.
Collapse
Affiliation(s)
- Alessandro D'Urso
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Catania, Italy.
| |
Collapse
|
3
|
Li L, Zhang Y, Ma W, Chen H, Liu M, An R, Cheng B, Liang X. Nonalternating purine pyrimidine sequences can form stable left-handed DNA duplex by strong topological constraint. Nucleic Acids Res 2021; 50:684-696. [PMID: 34967416 PMCID: PMC8789069 DOI: 10.1093/nar/gkab1283] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/01/2021] [Accepted: 12/16/2021] [Indexed: 11/14/2022] Open
Abstract
In vivo, left-handed DNA duplex (usually refers to Z-DNA) is mainly formed in the region of DNA with alternating purine pyrimidine (APP) sequence and plays significant biological roles. It is well known that d(CG)n sequence can form Z-DNA most easily under negative supercoil conditions, but its essence has not been well clarified. The study on sequence dependence of Z-DNA stability is very difficult without modification or inducers. Here, by the strong topological constraint caused by hybridization of two complementary short circular ssDNAs, left-handed duplex part was generated for various sequences, and their characteristics were investigated by using gel-shift after binding to specific proteins, CD and Tm analysis, and restriction enzyme cleavage. Under the strong topological constraint, non-APP sequences can also form left-handed DNA duplex as stable as that of APP sequences. As compared with non-APP sequences, the thermal stability difference for APP sequences between Z-form and B-form is smaller, which may be the reason that Z-DNA forms preferentially for APP ones. This result can help us to understand why nature selected APP sequences to regulate gene expression by transient Z-DNA formation, as well as why polymer with chirality can usually form both duplexes with left- or right-handed helix.
Collapse
Affiliation(s)
- Lin Li
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Yaping Zhang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Wanzhi Ma
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Hui Chen
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Mengqin Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Ran An
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, China
| | - Bingxiao Cheng
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, China
| |
Collapse
|
4
|
Osadchuk I, Aav R, Borovkov V, Clot E. Chirogenesis in Zinc Porphyrins: Theoretical Evaluation of Electronic Transitions, Controlling Structural Factors and Axial Ligation. Chemphyschem 2021; 22:1817-1833. [PMID: 34213815 PMCID: PMC8457158 DOI: 10.1002/cphc.202100345] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/24/2021] [Indexed: 12/15/2022]
Abstract
In the present work, sixteen different zinc porphyrins (possessing different meso substituents) with and without a chiral guest were modelled using DFT and TD-DFT approaches in order to understand the influence of various controlling factors on electronic circular dichroism (ECD) spectra. Two major aspects are influenced by these factors: excitation energy of the electronic transitions and their intensity. In the case of excitation energy, the influence increases in the following order: orientation of the peripheral substituents
Collapse
Affiliation(s)
- Irina Osadchuk
- Department of Chemistry and BiotechnologySchool of ScienceTallinn University of Technology AddressAkadeemia tee 1512618TallinnEstonia
- ICGMUniv MontpellierCNRS, ENSCMMontpellierFrance
| | - Riina Aav
- Department of Chemistry and BiotechnologySchool of ScienceTallinn University of Technology AddressAkadeemia tee 1512618TallinnEstonia
| | - Victor Borovkov
- Department of Chemistry and BiotechnologySchool of ScienceTallinn University of Technology AddressAkadeemia tee 1512618TallinnEstonia
| | - Eric Clot
- ICGMUniv MontpellierCNRS, ENSCMMontpellierFrance
| |
Collapse
|
5
|
Interactions of porphyrins with DNA: A review focusing recent advances in chemical modifications on porphyrins as artificial nucleases. J Inorg Biochem 2021; 219:111434. [PMID: 33819802 DOI: 10.1016/j.jinorgbio.2021.111434] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 03/18/2021] [Accepted: 03/18/2021] [Indexed: 12/14/2022]
Abstract
The advance of porphyrins as artificial nucleases along the years have developed a class of compounds having potential therapeutic applications. Being an extrovert of chemistry, a variety of chemical modifications have been done on porphyrin macrocycle in order to improve the spectroscopic properties and to adapt as artificial receptors that can recognize molecules. The last twenty years has witnessed broad research in the arena of porphyrin- DNA interactions and their evolution from simple to more complex entities. In this review, we summarize the recent advances in the porphyrin-based structural modifications, with a specific emphasis on various effects of porphyrin on DNA cleavage potency. We particularly detailed the nuclease activity of cationic and anionic porphyrins, porphyrin dimers and conjugates as well as heme proteins till the third generation porphyrins as artificial nucleases.
Collapse
|
6
|
Norvaiša K, Kielmann M, Senge MO. Porphyrins as Colorimetric and Photometric Biosensors in Modern Bioanalytical Systems. Chembiochem 2020; 21:1793-1807. [PMID: 32187831 PMCID: PMC7383976 DOI: 10.1002/cbic.202000067] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 03/04/2020] [Indexed: 12/18/2022]
Abstract
Advances in porphyrin chemistry have provided novel materials and exciting technologies for bioanalysis such as colorimetric sensor array (CSA), photo-electrochemical (PEC) biosensing, and nanocomposites as peroxidase mimetics for glucose detection. This review highlights selected recent advances in the construction of supramolecular assemblies based on the porphyrin macrocycle that provide recognition of various biologically important entities through the unique porphyrin properties associated with colorimetry, spectrophotometry, and photo-electrochemistry.
Collapse
Affiliation(s)
- Karolis Norvaiša
- School of Chemistry, SFI Tetrapyrrole LaboratoryTrinity Biomedical Sciences Institute152–160 Pearse Street, Trinity College Dublin The University of DublinDublin2Ireland
| | - Marc Kielmann
- School of Chemistry, SFI Tetrapyrrole LaboratoryTrinity Biomedical Sciences Institute152–160 Pearse Street, Trinity College Dublin The University of DublinDublin2Ireland
| | - Mathias O. Senge
- School of Chemistry, SFI Tetrapyrrole LaboratoryTrinity Biomedical Sciences Institute152–160 Pearse Street, Trinity College Dublin The University of DublinDublin2Ireland
- Institute for Advanced Study (TUM-IAS)Lichtenberg-Strasse 2a85748GarchingGermany
| |
Collapse
|
7
|
Gangemi CMA, D'Urso A, Tomaselli GA, Berova N, Purrello R. A novel porphyrin-based molecular probe ZnTCPPSpm4 with catalytic, stabilizing and chiroptical diagnostic power towards DNA B-Z transition. J Inorg Biochem 2017; 173:141-143. [PMID: 28525806 DOI: 10.1016/j.jinorgbio.2017.05.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 05/09/2017] [Accepted: 05/10/2017] [Indexed: 12/01/2022]
Abstract
In this work we have designed a new zinc(II) porphyrin with four spermines conjugate in the meso positions, meso-tetrakis-(4-carboxysperminephenyl)porphyrin, ZnTCPPSpm4) with the aim of acting as a chiroptical probe for the Z-form of DNA, a high energy transient conformation of DNA. In addition to monitor by Electronic Circular Dichroism chiroptical response the formation of Z-DNA in the presence of micromolar concentration of spermine, this porphyrin based molecular probe is also able to catalyze and stabilize this important DNA structure. The ZnTCPPSpm4 conjugate represents a perfect example of single molecule, which possesses all these three properties at the same time. The increased stability of Z-DNA in the presence of this derivative opens possibility for further studies on the mechanism of B- to Z-DNA transition, and on the design of new probes with improved efficiency.
Collapse
Affiliation(s)
- Chiara M A Gangemi
- Dipartimento di Scienze Chimiche, Università di Catania, V.le Andrea Doria 6, 95125, Catania, Italy; Department of Chemistry, Columbia University, 3000, Broadway, NY, 10027, USA
| | - Alessandro D'Urso
- Dipartimento di Scienze Chimiche, Università di Catania, V.le Andrea Doria 6, 95125, Catania, Italy
| | - Gaetano A Tomaselli
- Dipartimento di Scienze Chimiche, Università di Catania, V.le Andrea Doria 6, 95125, Catania, Italy
| | - Nina Berova
- Department of Chemistry, Columbia University, 3000, Broadway, NY, 10027, USA.
| | - Roberto Purrello
- Dipartimento di Scienze Chimiche, Università di Catania, V.le Andrea Doria 6, 95125, Catania, Italy.
| |
Collapse
|
8
|
Abstract
![]()
DNA is well-known as bearer of the genetic code.
Since its structure
elucidation nearly seven decades ago by Watson, Crick, Wilkins, and
Franklin, much has been learned about its detailed structure, function,
and genetic coding. The development of automated solid-phase synthesis,
and with it the availability of synthetic DNA with any desired sequence
in lengths of up to hundreds of bases in the best case, has contributed
much to the advancement of the field of DNA research. In addition,
classic organic synthesis has allowed introduction of a very large
number of modifications in the DNA in a sequence specific manner,
which have initially been targeted at altering the biological function
of DNA. However, in recent years DNA has become a very attractive
scaffold in supramolecular chemistry, where DNA is taken out of its
biological role and serves as both stick and glue molecule to assemble
novel functional structures with nanometer precision. The attachment
of functionalities to DNA has led to the creation of supramolecular
systems with applications in light harvesting, energy and electron
transfer, sensing, and catalysis. Functional DNA is clearly having
a significant impact in the field of bioinspired nanosystems. Of particular interest is the use of porphyrins in supramolecular
chemistry and bionanotechnology, because they are excellent functional
groups due to their electronic properties that can be tailored through
chemical modifications of the aromatic core or through insertion of
almost any metal of the periodic table into the central cavity. The
porphyrins can be attached either to the nucleobase, to the phosphate
group, or to the ribose moiety. Additionally, noncovalent templating
through Watson–Crick base pairing forms an alternative and
attractive approach. With this, the combination of two seemingly simple
molecules gives rise to a highly complex system with unprecedented
possibilities for modulation of function, and with it applications,
particularly when combined with other functional groups. Here, an
overview is given on the developments of using porphyrin modified
DNA for the construction of functional assemblies. Strategies for
the synthesis and characterization are presented alongside selected
applications where the porphyrin modification has proven to be particularly
useful and superior to other modifiers but also has revealed its limitations.
We also discuss implications on properties and behavior of the porphyrin–DNA,
where similar issues could arise when using other hydrophobic and
bulky substituents on DNA. This includes particularly problems regarding
synthesis of the building blocks, DNA synthesis, yields, solubility,
and intermolecular interactions.
Collapse
Affiliation(s)
- Eugen Stulz
- School of Chemistry & Institute for Life Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, U.K
| |
Collapse
|
9
|
Kawara K, Tsuji G, Taniguchi Y, Sasaki S. Synchronized Chiral Induction between [5]Helicene-Spermine Ligand andB-ZDNA Transition. Chemistry 2017; 23:1763-1769. [DOI: 10.1002/chem.201605276] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Indexed: 12/25/2022]
Affiliation(s)
- Kensuke Kawara
- Graduate School of Pharmaceutical Sciences; Kyushu University; 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
| | - Genichiro Tsuji
- Graduate School of Pharmaceutical Sciences; Kyushu University; 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
| | - Yosuke Taniguchi
- Graduate School of Pharmaceutical Sciences; Kyushu University; 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
| | - Shigeki Sasaki
- Graduate School of Pharmaceutical Sciences; Kyushu University; 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
| |
Collapse
|
10
|
|
11
|
Pietropaolo A, D'urso A, Purrello R, Berova N. Effect of Different Z-Inducers on the Stabilization of Z Portion in BZ-DNA Sequence: Correlation Between Experimental and Simulation Data. Chirality 2015; 27:773-8. [PMID: 26365889 DOI: 10.1002/chir.22502] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 07/24/2015] [Accepted: 07/25/2015] [Indexed: 12/28/2022]
Abstract
In this study we show the outstanding agreement between simulation and experimental data concerning the efficient stabilization effect by NaCl of Z conformation. We demonstrate by circular dichroism (CD) experiments that Na(+) not only is able to induce a B to Z form transition in a short (GC)3 alternated portion of a sequence having 17 basis, but also is the best stabilizer in comparison with other Z inducers used (spermine and NiCl2). This result was confirmed by free energy calculations.
Collapse
Affiliation(s)
| | - Alessandro D'urso
- Department of Chemical Science, University of Catania, Catania, Italy
| | - Roberto Purrello
- Department of Chemical Science, University of Catania, Catania, Italy
| | - Nina Berova
- Department of Chemistry, Columbia University, New York, NY, USA
| |
Collapse
|
12
|
Choi JK, Reed A, Balaz M. Chiroptical properties, binding affinity, and photostability of a conjugated zinc porphyrin dimer complexed with left-handed Z-DNA and right-handed B-DNA. Dalton Trans 2014; 43:563-7. [PMID: 24129690 DOI: 10.1039/c3dt52210e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have studied the UV-vis absorption and chiroptical properties, binding affinity and photostability of a conjugated positively charged butadiyne-linked Zn(ii) porphyrin dimer bound to DNA sequence poly(dG-dC)2. Right-handed B-DNA, spermine-induced Z-DNA and Co(iii)-induced Z-DNA have been explored. Resonance light scattering (RLS) spectra showed formation of porphyrin aggregates in the presence of all DNA forms with the largest aggregates formed with B-DNA. The porphyrin dimer gave rise to induced bisignate circular dichroism (CD) signals in the presence of the left-handed Z-DNA conformations. On the other hand, the dimer stayed nearly chiroptically silent when complexed with the B-form of poly(dG-dC)2. Our results indicated that the conjugated Zn(ii) porphyrin dimer can be used as a sensor for the chiroptical detection of Z-DNA in the visible (400-500 nm) and near-infrared region of the electromagnetic spectrum (700-800 nm). The helicity of DNA had little effect on the dimer binding affinities. The photostability of the porphyrin dimer complexed with any form of DNA was higher than that of the free molecule. The porphyrin dimer bound to Z-DNA exhibited slower photobleaching than the B-DNA dimer complex.
Collapse
Affiliation(s)
- Jung Kyu Choi
- Department of Chemistry, University of Wyoming, Laramie, WY 82071, USA.
| | | | | |
Collapse
|
13
|
Sasaki H, Sasaki S. B-Z transition of (dA-T)(n) duplexes induced by a spermine porphyrin-conjugate via an intermediate DNA conformation. Chem Commun (Camb) 2014; 49:9024-6. [PMID: 23979223 DOI: 10.1039/c3cc45213a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The spermine conjugate of the cationic porphyrin ligand (1) selectively induced the B-Z transition of the [(dA-T)n]2 sequence at low salt concentrations. The [(dG-C)n]2 sequence was not transformed into the Z-form. The B-Z transition was induced via an intermediate DNA conformation, which was formed by the external binding and formation of an assembly of 1 onto B-DNA.
Collapse
Affiliation(s)
- Hideaki Sasaki
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
| | | |
Collapse
|
14
|
Abstract
In this review, free-base and metalloporphyrins, functionalized on meso-positions by quaternary pyridinium units, also referred to as cationic porphyrins, are presented. The article consists of five parts. In the first part free-base porphyrins are described, especially taking account on generation of singlet oxygen; next parts concern metalloporphyrins. The second and third parts deal with zinc and manganese porphyrins, respectively; in the fourth part copper, palladium, and platinum porphyrins are presented. In the fifth part, describing porphyrins with various metal ions an attention is paid to porphyrin metal-organic frameworks (MOFs) and metal-organic materials (MOMs) in which metalloporphyrins are immobilized; syntheses and characterization of obtained products are shown.
Collapse
Affiliation(s)
- Beata Girek
- Institute of Chemistry, Environmental Protection and Biotechnology, Jan Dlugosz University in Czestochowa, Armii Krajowej 13/15, 42-200 Czestochowa, Poland
| | - Wanda Sliwa
- Institute of Chemistry, Environmental Protection and Biotechnology, Jan Dlugosz University in Czestochowa, Armii Krajowej 13/15, 42-200 Czestochowa, Poland
| |
Collapse
|
15
|
Choi JK, D'Urso A, Balaz M. Chiroptical properties of anionic and cationic porphyrins and metalloporphyrins in complex with left-handed Z-DNA and right-handed B-DNA. J Inorg Biochem 2013; 127:1-6. [PMID: 23831582 DOI: 10.1016/j.jinorgbio.2013.05.018] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 05/28/2013] [Accepted: 05/29/2013] [Indexed: 11/24/2022]
Abstract
We report the chiroptical signature and binding interactions of cationic (meso-tetrakis(4-N-methylptridyl)porphyrin, 2HT4) and anionic (meso-tetrakis(4-sulfonatophenyl)porphyrin, 2HTPPS) porphyrins and their zinc(II) and nickel(II) derivatives (ZnT4, ZnTPPS, NiT4, and NiTPPS) with right-handed B-form and two forms of left-handed Z-form of alternating guanine-cytosine polydeoxynucleotide poly(dG-dC)2. NiTPPS is able to spectroscopically discriminate between spermine-induced Z-DNA and Co(III)-induced Z-DNA via new induced circular dichroism signal in the visible region of the electromagnetic spectrum.
Collapse
Affiliation(s)
- Jung Kyu Choi
- University of Wyoming, Department of Chemistry, Laramie, WY 82071, USA
| | | | | |
Collapse
|
16
|
D'Urso A, Nardis S, Pomarico G, Fragalà ME, Paolesse R, Purrello R. Interaction of tricationic corroles with single/double helix of homopolymeric nucleic acids and DNA. J Am Chem Soc 2013; 135:8632-8. [PMID: 23692291 DOI: 10.1021/ja4023539] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In this manuscript a multitechnique approach is proposed to characterize the interaction between new tri-N-methylpyridyl corrole (TMPC) and its germanium(IV) derivative (GeTMPC), with single- and double-stranded nucleic acid homopolymers and calf thymus DNA. The specificity of each spectroscopic technique has been exploited to analyze the different aspects of corrole binding. Noteworthy, this approach allows us to distinguish between H aggregation of TMPC in the presence of polyriboadenilic acid (poly(rA)) and J aggregates in the presence of polyribocytidinic acid (poly(rC)) as well as to identify the formation of GeTMPC dimers in the presence of single-stranded poly(rA) and pseudointercalation with single-stranded poly(rC).
Collapse
Affiliation(s)
- Alessandro D'Urso
- Department of Chemical Science, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | | | | | | | | | | |
Collapse
|
17
|
Recent Advancements in Chiral Porphyrin Self-Assembly. TOPICS IN HETEROCYCLIC CHEMISTRY 2013. [DOI: 10.1007/7081_2013_110] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
18
|
Gong L, Jang YJ, Kim J, Kim SK. Z-Form DNA Specific Binding Geometry of Zn(II) meso-Tetrakis(N-methylpyridinium-4-yl)porphyrin Probed by Linear Dichroism Spectroscopy. J Phys Chem B 2012; 116:9619-26. [DOI: 10.1021/jp3041346] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lindan Gong
- Department of Chemistry, Yeungnam University Dae-dong, Gyeongsan
City, Gyeong-buk, 712-749, Republic of Korea
| | - Yoon Jung Jang
- Department of Chemistry, Yeungnam University Dae-dong, Gyeongsan
City, Gyeong-buk, 712-749, Republic of Korea
| | - Jinheung Kim
- Department of Chemistry
and Nano Science, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Seog K. Kim
- Department of Chemistry, Yeungnam University Dae-dong, Gyeongsan
City, Gyeong-buk, 712-749, Republic of Korea
| |
Collapse
|
19
|
Santoro AM, Lo Giudice MC, D’Urso A, Lauceri R, Purrello R, Milardi D. Cationic Porphyrins Are Reversible Proteasome Inhibitors. J Am Chem Soc 2012; 134:10451-7. [DOI: 10.1021/ja300781u] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Anna Maria Santoro
- IBB-CNR, Istituto di Biostrutture e Bioimmagini, UOS di Catania c/o Dipartimento
di Scienze Chimiche Viale A. Doria 6 - 95125 Catania
| | - Maria Cristina Lo Giudice
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A.
Doria 6 - 95125 Catania
| | - Alessandro D’Urso
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A.
Doria 6 - 95125 Catania
| | - Rosaria Lauceri
- IBB-CNR, Istituto di Biostrutture e Bioimmagini, UOS di Catania c/o Dipartimento
di Scienze Chimiche Viale A. Doria 6 - 95125 Catania
| | - Roberto Purrello
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A.
Doria 6 - 95125 Catania
| | - Danilo Milardi
- IBB-CNR, Istituto di Biostrutture e Bioimmagini, UOS di Catania c/o Dipartimento
di Scienze Chimiche Viale A. Doria 6 - 95125 Catania
| |
Collapse
|
20
|
Holmes AE, Choi JK, Francis J, D'Urso A, Balaz M. Sulfonated Ni(II)porphyrin improves the detection of Z-DNA in condensed and non-condensed BZB DNA sequences. J Inorg Biochem 2012; 110:18-20. [PMID: 22459169 DOI: 10.1016/j.jinorgbio.2012.02.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Revised: 01/31/2012] [Accepted: 02/01/2012] [Indexed: 11/26/2022]
Abstract
We report a very selective and sensitive spectroscopic detection of Z-DNA embedded in B-DNA in condensed as well as non-condensed DNA using anionic Ni(II) meso-tetrakis(4-sulphonatophenyl)porphyrin, NiTPPS. A combination of micromolar concentrations of Ni(II) and spermine(4+) allowed us to prepare left-handed Z-DNA in short oligonucleotides without DNA condensation. A strong induced circular dichroism (ICD) signal was observed in the visible absorption region when NiTPPS was added to BZ DNA (Z-DNA fragment located at the end of a B-DNA tract with one B/Z DNA junction) and BZB DNA (Z-DNA sequence embedded in B-DNA having two B/Z DNA junctions). Almost no ICD signal was detected when NiTPPS was added to B-DNA. NiTPPS showed different binding modes with condensed and non-condensed Z-DNAs and allowed the distinction between condensed Z-DNA (positive bisignate CD couplet) and non-condensed Z-DNA (negative bisignate CD couplet).
Collapse
Affiliation(s)
- Andrea E Holmes
- Department of Chemistry, Doane College, 1014 Boswell Ave, Crete, NE 68333, USA
| | | | | | | | | |
Collapse
|
21
|
|
22
|
Choi JK, D’Urso A, Trauernicht M, Shabbir-Hussain M, Holmes AE, Balaz M. 3,3'-diethylthiatricarbocyanine iodide: a highly sensitive chiroptical reporter of DNA helicity and sequence. Int J Mol Sci 2011; 12:8052-62. [PMID: 22174649 PMCID: PMC3233455 DOI: 10.3390/ijms12118052] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Revised: 11/02/2011] [Accepted: 11/07/2011] [Indexed: 11/16/2022] Open
Abstract
Using UV-vis absorption and circular dichroism (CD) spectroscopies, we explored the binding interactions of 3,3′-diethylthiatricarbocyanine iodide (Cy7) with polynucleotides of different sequences and helicity. CD showed to be a very diagnostic tool giving different spectroscopic chiroptical signatures for all explored DNA sequences upon Cy7 binding. Cy7 was able to spectroscopically discriminate between the right handed B-DNA of poly(dG-dC)2 and its left handed Z-DNA counterpart induced by spermine or Co(III)hexamine via nearly opposite induced circular dichroic signal.
Collapse
Affiliation(s)
- Jung Kyu Choi
- Department of Chemistry, University of Wyoming, Laramie, WY 82071, USA; E-Mails: (J.K.C.); (A.D.); (M.S.-H.)
| | - Alessandro D’Urso
- Department of Chemistry, University of Wyoming, Laramie, WY 82071, USA; E-Mails: (J.K.C.); (A.D.); (M.S.-H.)
- Doane College, 1014 Boswell, Crete, NE 68333, USA; E-Mails: (M.T.); (A.E.H.)
| | - Mitch Trauernicht
- Doane College, 1014 Boswell, Crete, NE 68333, USA; E-Mails: (M.T.); (A.E.H.)
| | - Murtaza Shabbir-Hussain
- Department of Chemistry, University of Wyoming, Laramie, WY 82071, USA; E-Mails: (J.K.C.); (A.D.); (M.S.-H.)
| | - Andrea E. Holmes
- Doane College, 1014 Boswell, Crete, NE 68333, USA; E-Mails: (M.T.); (A.E.H.)
| | - Milan Balaz
- Department of Chemistry, University of Wyoming, Laramie, WY 82071, USA; E-Mails: (J.K.C.); (A.D.); (M.S.-H.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-307-766-4330; Fax: +1-307-766-2807
| |
Collapse
|