1
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Jurković M, Radić Stojković M, Božinović K, Nestić D, Majhen D, Delgado-Pinar E, Inclán M, García-España E, Piantanida I. Novel Tripodal Polyamine Tris-Pyrene: DNA/RNA Binding and Photodynamic Antiproliferative Activity. Pharmaceutics 2023; 15:2197. [PMID: 37765167 PMCID: PMC10536304 DOI: 10.3390/pharmaceutics15092197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 09/29/2023] Open
Abstract
A novel tri-pyrene polyamine (TAL3PYR) bearing net five positive charges at biorelevant conditions revealed strong intramolecular interactions in aqueous medium between pyrenes, characterised by pronounced excimer fluorescence. A novel compound revealed strong binding to ds-DNA and ds-RNA, along with pronounced thermal stabilisation of DNA/RNA and extensive changes in DNA/RNA structure, as evidenced by circular dichroism. New dye caused pronounced ds-DNA or ds-RNA condensation, which was attributed to a combination of electrostatic interactions between 5+ charge of dye and negatively charged polynucleotide backbone, accompanied by aromatic and hydrophobic interactions of pyrenes within polynucleotide grooves. New dye also showed intriguing antiproliferative activity, strongly enhanced upon photo-induced activation of pyrenes, and is thus a promising lead compound for theranostic applications on ds-RNA or ds-DNA targets, applicable as a new strategy in cancer and gene therapy.
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Affiliation(s)
- Marta Jurković
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (M.J.); (M.R.S.)
| | - Marijana Radić Stojković
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (M.J.); (M.R.S.)
| | - Ksenija Božinović
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (K.B.); (D.N.); (D.M.)
| | - Davor Nestić
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (K.B.); (D.N.); (D.M.)
| | - Dragomira Majhen
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (K.B.); (D.N.); (D.M.)
| | - Estefanía Delgado-Pinar
- Department of Inorganic Chemistry, Institute for Molecular Science, University of Valencia, Catedratico Jose Beltran 2, 46980 Paterna, Spain; (E.D.-P.); (M.I.)
| | - Mario Inclán
- Department of Inorganic Chemistry, Institute for Molecular Science, University of Valencia, Catedratico Jose Beltran 2, 46980 Paterna, Spain; (E.D.-P.); (M.I.)
- Escuela Superior de Ingeniería, Ciencia y Tecnología, Universidad Internacional de Valencia (VIU), 46002 Valencia, Spain
| | - Enrique García-España
- Department of Inorganic Chemistry, Institute for Molecular Science, University of Valencia, Catedratico Jose Beltran 2, 46980 Paterna, Spain; (E.D.-P.); (M.I.)
| | - Ivo Piantanida
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (M.J.); (M.R.S.)
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2
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Gupta S, Aggarwal S, Munde M. New Insights into the Role of Ligand-Binding Modes in GC-DNA Condensation through Thermodynamic and Spectroscopic Studies. ACS OMEGA 2023; 8:4554-4565. [PMID: 36777612 PMCID: PMC9909821 DOI: 10.1021/acsomega.2c01557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 09/20/2022] [Indexed: 06/18/2023]
Abstract
In biological systems, the unprompted assembly of DNA molecules by cationic ligands into condensed structures is ubiquitous. The ability of ligands to provoke DNA packaging is crucial to the molecular organization and functional control of DNA, yet their underlined physical roles have remained elusive. Here, we have examined the DNA condensation mechanism of four cationic ligands, including their primary DNA-binding modes through extensive biophysical studies. We observed contrasting changes for these ligands binding to poly[dGdC]:poly[dGdC] (GC-DNA) and poly[dAdT]:poly[dAdT] (AT-DNA). Based on a CD spectroscopic study, it was confirmed that only GC-DNA undergoes B- to Ψ-type DNA transformation in the presence of ligands. In the fluorescence displacement assay (FDA), the ability of ligands to displace GC-DNA-bound EtBr follows the order: protamine21+ > cohex3+ > Ni2+ > spermine4+, which indicates that there is no direct correlation between the ligand charge and its ability to displace the drug from the DNA, indicating that GC-DNA condensation is not just influenced by electrostatic interaction but ligand-specific interactions may also have played a crucial role. Furthermore, the detailed ITC-binding studies suggested that DNA-ligand interactions are generally driven by unfavorable enthalpy and favorable entropy. The correlations from various studies insinuate that cationic ligands show major groove binding as one of the preferred binding modes during GC-DNA condensation.
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Affiliation(s)
- Sakshi Gupta
- School
of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
- Department
of Applied Science, The NorthCap University, Sector 23-A, Gurgaon, Haryana 122017, India
| | - Soumya Aggarwal
- School
of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Manoj Munde
- School
of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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3
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Vasiliu T, Mocci F, Laaksonen A, Engelbrecht LDV, Perepelytsya S. Caging Polycations: Effect of Increasing Confinement on the Modes of Interaction of Spermidine3+ With DNA Double Helices. Front Chem 2022; 10:836994. [PMID: 35281557 PMCID: PMC8915389 DOI: 10.3389/fchem.2022.836994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/04/2022] [Indexed: 11/23/2022] Open
Abstract
Polyamines have important roles in the modulation of the cellular function and are ubiquitous in cells. The polyamines putrescine2+, spermidine3+, and spermine4+ represent the most abundant organic counterions of the negatively charged DNA in the cellular nucleus. These polyamines are known to stabilize the DNA structure and, depending on their concentration and additional salt composition, to induce DNA aggregation, which is often referred to as condensation. However, the modes of interactions of these elongated polycations with DNA and how they promote condensation are still not clear. In the present work, atomistic molecular dynamics (MD) computer simulations of two DNA fragments surrounded by spermidine3+ (Spd3+) cations were performed to study the structuring of Spd3+ “caged” between DNA molecules. Microsecond time scale simulations, in which the parallel DNA fragments were constrained at three different separations, but allowed to rotate axially and move naturally, provided information on the conformations and relative orientations of surrounding Spm3+ cations as a function of DNA-DNA separation. Novel geometric criteria allowed for the classification of DNA-Spd3+ interaction modes, with special attention given to Spd3+ conformational changes in the space between the two DNA molecules (caged Spd3+). This work shows how changes in the accessible space, or confinement, around DNA affect DNA-Spd3+ interactions, information fundamental to understanding the interactions between DNA and its counterions in environments where DNA is compacted, e.g. in the cellular nucleus.
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Affiliation(s)
- Tudor Vasiliu
- Centre of Advanced Research in Bionanoconjugates and Biopolymers “Petru Poni” Institute of Macromolecular Chemistry, Iasi, Romania
| | - Francesca Mocci
- Dipartimento di Scienze Chimiche e Geologiche, Cagliari University, Cagliari, Italy
- *Correspondence: Francesca Mocci, ; Aatto Laaksonen, ; Sergiy Perepelytsya,
| | - Aatto Laaksonen
- Centre of Advanced Research in Bionanoconjugates and Biopolymers “Petru Poni” Institute of Macromolecular Chemistry, Iasi, Romania
- Dipartimento di Scienze Chimiche e Geologiche, Cagliari University, Cagliari, Italy
- Division of Energy Science, Energy Engineering, Luleå University of Technology, Luleå, Sweden
- Division of Physical Chemistry, Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
- State Key Laboratory of Materials-Oriented and Chemical Engineering, Nanjing Tech University, Nanjing, China
- *Correspondence: Francesca Mocci, ; Aatto Laaksonen, ; Sergiy Perepelytsya,
| | | | - Sergiy Perepelytsya
- Bogolyubov Institute for Theoretical Physics of the NAS of Ukraine, Kyiv, Ukraine
- *Correspondence: Francesca Mocci, ; Aatto Laaksonen, ; Sergiy Perepelytsya,
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4
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Perepelytsya S, Uličný J, Laaksonen A, Mocci F. Pattern preferences of DNA nucleotide motifs by polyamines putrescine2+, spermidine3+ and spermine4. Nucleic Acids Res 2020; 47:6084-6097. [PMID: 31114917 PMCID: PMC6614828 DOI: 10.1093/nar/gkz434] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 04/10/2019] [Accepted: 05/08/2019] [Indexed: 12/25/2022] Open
Abstract
The interactions of natural polyamines (putrescine2+, spermidine3+ and spermine4+) with DNA double helix are studied to characterize their nucleotide sequence pattern preference. Atomistic Molecular Dynamics simulations have been carried out for three systems consisting of the same DNA fragment d(CGCGAATTCGCGAATTCGCG) with different polyamines. The results show that polyamine molecules are localized with well-recognized patterns along the double helix with different residence times. We observed a clear hierarchy in the residence times of the polyamines, with the longest residence time (ca 100ns) in the minor groove. The analysis of the sequence dependence shows that polyamine molecules prefer the A-tract regions of the minor groove - in its narrowest part. The preferable localization of putrescine2+, spermidine3+ and spermine4+ in the minor groove with A-tract motifs is correlated with modulation of the groove width by a specific nucleotide sequences. We did develop a theoretical model pointing to the electrostatic interactions as the main driving force in this phenomenon, making it even more prominent for polyamines with higher charges. The results of the study explain the specificity of polyamine interactions with A-tract region of the DNA double helix which is also observed in experiments.
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Affiliation(s)
- Sergiy Perepelytsya
- Bogolyubov Institute for Theoretical Physics of the National Academy of Sciences of Ukraine, 03143 Kyiv, Ukraine.,Department of Theoretical and Mathematical Physics, Kyiv Academic University, 03142 Kyiv, Ukraine
| | - Jozef Uličný
- Department of Biophysics, Institute of Physics, P. J. Šafárik University, 041 54 Košice, Slovakia
| | - Aatto Laaksonen
- State Key Laboratory of Materials-Oriented and Chemical Engineering, Nanjing Tech University, 210009 Nanjing, China.,Division of Physical Chemistry, Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, 10691 Stockholm, Sweden.,Centre of Advanced Research in Bionanoconjugates and Biopolymers, Petru Poni Institute of Macromolecular Chemistry, Iasi, 700487, Romania
| | - Francesca Mocci
- Centre of Advanced Research in Bionanoconjugates and Biopolymers, Petru Poni Institute of Macromolecular Chemistry, Iasi, 700487, Romania.,Department of Chemical and Geological Sciences, University of Cagliari, I-09042 Monserrato, Italy
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5
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Rocha RO, Wilson RA. Essential, deadly, enigmatic: Polyamine metabolism and roles in fungal cells. FUNGAL BIOL REV 2019. [DOI: 10.1016/j.fbr.2018.07.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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6
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Specific and highly efficient condensation of GC and IC DNA by polyaza pyridinophane derivatives. Int J Biol Macromol 2018; 109:143-151. [PMID: 29247733 DOI: 10.1016/j.ijbiomac.2017.11.156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 11/24/2017] [Accepted: 11/25/2017] [Indexed: 11/23/2022]
Abstract
Two bis-polyaza pyridinophane derivatives and their monomeric reference compounds revealed strong interactions with ds-DNA and RNA. The bis-derivatives show a specific condensation of GC- and IC-DNA, which is almost two orders of magnitude more efficient than the well-known condensation agent spermine. The type of condensed DNA was identified as ψ-DNA, characterized by the exceptionally strong CD signals. At variance to the almost silent AT(U) polynucleotides, these strong CD signals allow the determination of GC-condensates at nanomolar nucleobase concentrations. Detailed thermodynamic characterisation by ITC reveals significant differences between the DNA binding of the bis-derivative compounds (enthalpy driven) and that of spermine and of their monomeric counterparts (entropy driven). Atomic force microscopy confirmed GC-DNA compaction by the bis-derivatives and the formation of toroid- and rod-like structures responsible for the ψ-type pattern in the CD spectra.
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7
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Kiss E, Mirzahosseini A, Hubert Á, Ambrus A, Őrfi L, Horváth P. DNA binding of sunitinib: Spectroscopic evidence via circular dichroism and nuclear magnetic resonance. J Pharm Biomed Anal 2017; 150:355-361. [PMID: 29287262 DOI: 10.1016/j.jpba.2017.12.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 11/30/2017] [Accepted: 12/02/2017] [Indexed: 10/18/2022]
Abstract
Sunitinib is a non-selective tyrosine kinase inhibitor, but in its chemical structure there can be discovered certain features, which suggest the ability to bind to DNA. These elements are the planar aromatic system and the tertiary amine function, which is protonated at the pH of the organism. In this study, the binding of the drug sunitinib to DNA was investigated using circular dichroism (CD), 1H NMR and UV spectroscopies, along with CD melting. For these studies DNA was isolated from calf thymus (CT), salmon fish sperm (SS), and chicken erythrocyte (CE), however for our purposes an artificially constructed and highly purified plasmid DNA (pUC18) preparation proved to be the most suitable. DNA binding of the drug was confirmed by shifts in the characteristic CD bands of the DNA, the appearance of an induced CD (ICD) signal in the upper absorption region of sunitinib (300 nm-500 nm), and the evidence from CD melting studies and the NMR. Based on the CD and NMR measurements, it can be assumed that sunitinib has a multiple-step binding mechanism.
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Affiliation(s)
- Eszter Kiss
- Department of Pharmaceutical Chemistry, Semmelweis University, 1092 Budapest, Hőgyes Endre utca. 9, Hungary.
| | - Arash Mirzahosseini
- Department of Pharmaceutical Chemistry, Semmelweis University, 1092 Budapest, Hőgyes Endre utca. 9, Hungary.
| | - Ágnes Hubert
- Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, 1094 Budapest, Tűzoltó utca 37-47, Hungary.
| | - Attila Ambrus
- Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, 1094 Budapest, Tűzoltó utca 37-47, Hungary.
| | - László Őrfi
- Department of Pharmaceutical Chemistry, Semmelweis University, 1092 Budapest, Hőgyes Endre utca. 9, Hungary.
| | - Péter Horváth
- Department of Pharmaceutical Chemistry, Semmelweis University, 1092 Budapest, Hőgyes Endre utca. 9, Hungary.
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8
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Arias-Gonzalez JR. Single-molecule portrait of DNA and RNA double helices. Integr Biol (Camb) 2015; 6:904-25. [PMID: 25174412 DOI: 10.1039/c4ib00163j] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The composition and geometry of the genetic information carriers were described as double-stranded right helices sixty years ago. The flexibility of their sugar-phosphate backbones and the chemistry of their nucleotide subunits, which give rise to the RNA and DNA polymers, were soon reported to generate two main structural duplex states with biological relevance: the so-called A and B forms. Double-stranded (ds) RNA adopts the former whereas dsDNA is stable in the latter. The presence of flexural and torsional stresses in combination with environmental conditions in the cell or in the event of specific sequences in the genome can, however, stabilize other conformations. Single-molecule manipulation, besides affording the investigation of the elastic response of these polymers, can test the stability of their structural states and transition models. This approach is uniquely suited to understanding the basic features of protein binding molecules, the dynamics of molecular motors and to shedding more light on the biological relevance of the information blocks of life. Here, we provide a comprehensive single-molecule analysis of DNA and RNA double helices in the context of their structural polymorphism to set a rigorous interpretation of their material response both inside and outside the cell. From early knowledge of static structures to current dynamic investigations, we review their phase transitions and mechanochemical behaviour and harness this fundamental knowledge not only through biological sciences, but also for Nanotechnology and Nanomedicine.
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Affiliation(s)
- J Ricardo Arias-Gonzalez
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia), Calle Faraday no. 9, Cantoblanco, 28049 Madrid, Spain.
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9
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Abstract
Recent progress with techniques for monitoring RNA structure in cells such as ‘DMS-Seq’ and ‘Structure-Seq’ suggests that a new era of RNA structure-function exploration is on the horizon. This will also include systematic investigation of the factors required for the structural integrity of RNA. In this context, much evidence accumulated over 50 years suggests that polyamines play important roles as modulators of RNA structure. Here, we summarize and discuss recent literature relating to the roles of these small endogenous molecules in RNA function. We have included studies directed at understanding the binding interactions of polyamines with polynucleotides, tRNA, rRNA, mRNA and ribozymes using chemical, biochemical and spectroscopic tools. In brief, polyamines bind RNA in a sequence-selective fashion and induce changes in RNA structure in context-dependent manners. In some cases the functional consequences of these interactions have been observed in cells. Most notably, polyamine-mediated effects on RNA are frequently distinct from those of divalent cations (i.e. Mg2+) confirming their roles as independent molecular entities which help drive RNA-mediated processes.
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Affiliation(s)
- Helen L Lightfoot
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, CH-8093, Zürich, Switzerland
| | - Jonathan Hall
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, CH-8093, Zürich, Switzerland
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10
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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.
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Affiliation(s)
- Hideaki Sasaki
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
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11
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Abe Y, Nakagawa O, Yamaguchi R, Sasaki S. Synthesis and binding properties of new selective ligands for the nucleobase opposite the AP site. Bioorg Med Chem 2012; 20:3470-9. [PMID: 22560836 DOI: 10.1016/j.bmc.2012.04.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Revised: 04/03/2012] [Accepted: 04/04/2012] [Indexed: 01/27/2023]
Abstract
DNA is continuously damaged by endogenous and exogenous factors such as oxidative stress or DNA alkylating agents. These damaged nucleobases are removed by DNA N-glycosylase and form apurinic/apyrimidinic sites (AP sites) as intermediates in the base excision repair (BER) pathway. AP sites are also representative DNA damages formed by spontaneous hydrolysis. The AP sites block DNA polymerase and a mismatch nucleobase is inserted opposite the AP sites by polymerization to cause acute toxicities and mutations. Thus, AP site specific compounds have attracted much attention for therapeutic and diagnostic purposes. In this study, we have developed nucleobase-polyamine conjugates as the AP site binding ligand by expecting that the nucleobase part would play a role in the specific recognition of the nucleobase opposite the AP site by the Watson-Crick base pair formation and that the polyamine part should contribute to the access of the ligand to the AP site by a non-specific interaction to the DNA phosphate backbone. The nucleobase conjugated with 3,3'-diaminodipropylamine (A-ligand, G-ligand, C-ligand, T-ligand and U-ligand) showed a specific stabilization of the duplex containing the AP site depending on the complementary combination with the nucleobase opposite the AP site; that is A-ligand to T, G-ligand to C, C-ligand to G, T- and U-ligand to A. The thermodynamic binding parameters clearly indicated that the specific stabilization is due to specific binding of the ligands to the complementary AP site. These results have suggested that the complementary base pairs of the Watson-Crick type are formed at the AP site.
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Affiliation(s)
- Yukiko Abe
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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12
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Xu L, Anchordoquy T. Drug delivery trends in clinical trials and translational medicine: challenges and opportunities in the delivery of nucleic acid-based therapeutics. J Pharm Sci 2011; 100:38-52. [PMID: 20575003 DOI: 10.1002/jps.22243] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The ability to deliver nucleic acids (e.g., plasmid DNA, antisense oligonucleotides, siRNA) offers the potential to develop potent vaccines and novel therapeutics. However, nucleic acid-based therapeutics are still in their early stages as a new category of biologics. The efficacy of nucleic acids requires that these molecules be delivered to the interior of the target cell, which greatly complicates delivery strategies and compromises efficiency. Due to the safety concerns of viral vectors, synthetic vectors such as liposomes and polymers are preferred for the delivery of nucleic acid-based therapeutics. Yet, delivery efficiencies of synthetic vectors in the clinic are still too low to obtain therapeutic levels of gene expression. In this review, we focus on some key issues in the field of nucleic acid delivery such as PEGylation, encapsulation and targeted delivery and provide some perspectives for consideration in the development of improved synthetic vectors.
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Affiliation(s)
- Long Xu
- Department of Pharmaceutical Sciences, University of Colorado, 12700 East Nineteenth Avenue, Aurora, Colorado 80045, USA
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Doi I, Tsuji G, Kawakami K, Nakagawa O, Taniguchi Y, Sasaki S. The Spermine–Bisaryl Conjugate as a Potent Inducer of B‐ to Z‐DNA Transition. Chemistry 2010; 16:11993-9. [DOI: 10.1002/chem.201000947] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Issei Doi
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3‐1‐1 Maidashi, Higashi‐ku, Fukuoka, 812‐8582 (Japan), Fax: (+81) 92‐642‐6615
| | - Genichiro Tsuji
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3‐1‐1 Maidashi, Higashi‐ku, Fukuoka, 812‐8582 (Japan), Fax: (+81) 92‐642‐6615
| | - Kyoko Kawakami
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3‐1‐1 Maidashi, Higashi‐ku, Fukuoka, 812‐8582 (Japan), Fax: (+81) 92‐642‐6615
| | - Osamu Nakagawa
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3‐1‐1 Maidashi, Higashi‐ku, Fukuoka, 812‐8582 (Japan), Fax: (+81) 92‐642‐6615
| | - Yosuke Taniguchi
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3‐1‐1 Maidashi, Higashi‐ku, Fukuoka, 812‐8582 (Japan), Fax: (+81) 92‐642‐6615
| | - Shigeki Sasaki
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3‐1‐1 Maidashi, Higashi‐ku, Fukuoka, 812‐8582 (Japan), Fax: (+81) 92‐642‐6615
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14
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Colotti G, Ilari A. Polyamine metabolism in Leishmania: from arginine to trypanothione. Amino Acids 2010; 40:269-85. [PMID: 20512387 DOI: 10.1007/s00726-010-0630-3] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2010] [Accepted: 05/13/2010] [Indexed: 12/20/2022]
Abstract
Polyamines (PAs) are essential metabolites in eukaryotes, participating in a variety of proliferative processes, and in trypanosomatid protozoa play an additional role in the synthesis of the critical thiol trypanothione. The PAs are synthesized by a metabolic process which involves arginase (ARG), which catalyzes the enzymatic hydrolysis of L-arginine (L-Arg) to L-ornithine and urea, and ornithine decarboxylase (ODC), which catalyzes the enzymatic decarboxylation of L-ornithine in putrescine. The S-adenosylmethionine decarboxylase (AdoMetDC) catalyzes the irreversible decarboxylation of S-adenosylmethionine (AdoMet), generating the decarboxylated S-adenosylmethionine (dAdoMet), which is a substrate, together with putrescine, for spermidine synthase (SpdS). Leishmania parasites and all the other members of the trypanosomatid family depend on spermidine for growth and survival. They can synthesize PAs and polyamine precursors, and also scavenge them from the microenvironment, using specific transporters. In addition, Trypanosomatids have a unique thiol-based metabolism, in which trypanothione (N1-N8-bis(glutathionyl)spermidine, T(SH)(2)) and trypanothione reductase (TR) replace many of the antioxidant and metabolic functions of the glutathione/glutathione reductase (GR) and thioredoxin/thioredoxin reductase (TrxR) systems present in the host. Trypanothione synthetase (TryS) and TR are necessary for the protozoa survival. Consequently, enzymes involved in spermidine synthesis and its utilization, i.e. ARG, ODC, AdoMetDC, SpdS and, in particular, TryS and TR, are promising targets for drug development.
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Affiliation(s)
- Gianni Colotti
- Institute of Biology and Molecular Pathology, CNR, c/o Department of Biochemical Sciences, University Sapienza, P.le A. Moro 5, 00185, Rome, Italy.
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15
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Polyamines: fundamental characters in chemistry and biology. Amino Acids 2009; 38:393-403. [DOI: 10.1007/s00726-009-0396-7] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2009] [Accepted: 10/08/2009] [Indexed: 10/20/2022]
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16
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Harve KS, Lareu R, Rajagopalan R, Raghunath M. Understanding how the crowded interior of cells stabilizes DNA/DNA and DNA/RNA hybrids-in silico predictions and in vitro evidence. Nucleic Acids Res 2009; 38:172-81. [PMID: 19854935 PMCID: PMC2800234 DOI: 10.1093/nar/gkp884] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Amplification of DNA in vivo occurs in intracellular environments characterized by macromolecular crowding (MMC). In vitro Polymerase-chain-reaction (PCR), however, is non-crowded, requires thermal cycling for melting of DNA strands, primer-template hybridization and enzymatic primer-extension. The temperature-optima for primer-annealing and extension are strikingly disparate which predicts primers to dissociate from template during extension thereby compromising PCR efficiency. We hypothesized that MMC is not only important for the extension phase in vivo but also during PCR by stabilizing nucleotide hybrids. Novel atomistic Molecular Dynamics simulations elucidated that MMC stabilizes hydrogen-bonding between complementary nucleotides. Real-time PCR under MMC confirmed that melting-temperatures of complementary DNA-DNA and DNA-RNA hybrids increased by up to 8 degrees C with high specificity and high duplex-preservation after extension (71% versus 37% non-crowded). MMC enhanced DNA hybrid-helicity, and drove specificity of duplex formation preferring matching versus mismatched sequences, including hair-pin-forming DNA- single-strands.
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Affiliation(s)
- Karthik S Harve
- Division of Bioengineering, Faculty of Engineering, National University of Singapore, Singapore
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Pavan GM, Danani A, Pricl S, Smith DK. Modeling the Multivalent Recognition between Dendritic Molecules and DNA: Understanding How Ligand “Sacrifice” and Screening Can Enhance Binding. J Am Chem Soc 2009; 131:9686-94. [DOI: 10.1021/ja901174k] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Giovanni M. Pavan
- Molecular Simulations Engineering (MOSE) Laboratory, Department of Chemical Engineering (DICAMP), University of Trieste, Piazzale Europa 1, 34127 Trieste, Italy, Institute of Computer Integrated Manufacturing for Sustainable Innovation (ICIMSI), University for Applied Sciences of Southern Switzerland (SUPSI), Centro Galleria 2, Manno, CH-6928, Switzerland, and Department of Chemistry, University of York, Heslington, York, YO10 5DD, U.K
| | - Andrea Danani
- Molecular Simulations Engineering (MOSE) Laboratory, Department of Chemical Engineering (DICAMP), University of Trieste, Piazzale Europa 1, 34127 Trieste, Italy, Institute of Computer Integrated Manufacturing for Sustainable Innovation (ICIMSI), University for Applied Sciences of Southern Switzerland (SUPSI), Centro Galleria 2, Manno, CH-6928, Switzerland, and Department of Chemistry, University of York, Heslington, York, YO10 5DD, U.K
| | - Sabrina Pricl
- Molecular Simulations Engineering (MOSE) Laboratory, Department of Chemical Engineering (DICAMP), University of Trieste, Piazzale Europa 1, 34127 Trieste, Italy, Institute of Computer Integrated Manufacturing for Sustainable Innovation (ICIMSI), University for Applied Sciences of Southern Switzerland (SUPSI), Centro Galleria 2, Manno, CH-6928, Switzerland, and Department of Chemistry, University of York, Heslington, York, YO10 5DD, U.K
| | - David K. Smith
- Molecular Simulations Engineering (MOSE) Laboratory, Department of Chemical Engineering (DICAMP), University of Trieste, Piazzale Europa 1, 34127 Trieste, Italy, Institute of Computer Integrated Manufacturing for Sustainable Innovation (ICIMSI), University for Applied Sciences of Southern Switzerland (SUPSI), Centro Galleria 2, Manno, CH-6928, Switzerland, and Department of Chemistry, University of York, Heslington, York, YO10 5DD, U.K
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Min D, Li H, Li G, Berg BA, Fenley MO, Yang W. Efficient sampling of ion motions in molecular dynamics simulations on DNA: Variant Hamiltonian replica exchange method. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2008.02.055] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Okhrimenko O, Jelesarov I. A survey of the year 2006 literature on applications of isothermal titration calorimetry. J Mol Recognit 2008; 21:1-19. [DOI: 10.1002/jmr.859] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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McMasters S, Kelly LA. Sequence-dependent interactions of cationic naphthalimides and polynucleotides. Photochem Photobiol 2007; 83:889-96. [PMID: 17645660 DOI: 10.1111/j.1751-1097.2007.00155.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The binding interactions of three naphthalimide derivatives with heteropoly nucleic acids have been evaluated using fluorescence, absorption and circular dichroism spectroscopies. Mono- and bifunctionalized naphthalimides exhibit sequence-dependent variations in their affinity toward DNA. The heteropoly nucleic acids, [Poly(dA-dT)]2 and [Poly(dG-dC)]2, as well as calf thymus (CT) DNA, were used to understand the factors that govern binding strength and selectivity. Sequence selectivity was addressed by determining the binding constants as a function of polynucleotide composition according to the noncooperative McGhee-von Hippel binding model. Binding affinities toward [poly(dA-dT)](2) were the largest for spermine-substituted naphthalimides (Kb = 2-6 x 10(6) M(-1)). The association constants for complex formation between the cationic naphthalimides and [poly(dG-dC)]2 or CT DNA (58% A-T content) were 2-500 times smaller, depending on the naphthalimide-polynucleotide pair. The binding modes were also assessed using a combination of induced circular dichroism and salt effects to determine whether the naphthalimides associate with DNA through intercalative, electrostatic or groove-binding. The results show that the monofunctionalized spermine and pyridinium-substituted naphthalimides associate with DNA through electrostatic interactions. In contrast, intercalative interactions are predominant in the complex formed between the bifunctionalized spermine compound and all of the polynucleotides.
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Affiliation(s)
- Sun McMasters
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore, MD, USA
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