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Maity B, Moorthy H, Govindaraju T. Intrinsically Disordered Ku Protein-Derived Cell-Penetrating Peptides. ACS BIO & MED CHEM AU 2023; 3:471-479. [PMID: 38144254 PMCID: PMC10739243 DOI: 10.1021/acsbiomedchemau.3c00032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 10/08/2023] [Accepted: 10/09/2023] [Indexed: 12/26/2023]
Abstract
Efficient delivery of bioactive ingredients into cells is a major challenge. Cell-penetrating peptides (CPPs) have emerged as promising vehicles for this purpose. We have developed novel CPPs derived from the flexible and disordered tail extensions of DNA-binding Ku proteins. Ku-P4, the lead CPP identified in this study, is biocompatible and displays high internalization efficacy. Biophysical studies show that the proline residue is crucial for preserving the intrinsically disordered state and biocompatibility. DNA binding studies showed effective DNA condensation to form a positively charged polyplex. The polyplex exhibited effective penetration through the cell membrane and delivered the plasmid DNA inside the cell. These novel CPPs have the potential to enhance the cellular uptake and therapeutic efficacy of peptide-drug or gene conjugates.
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Affiliation(s)
- Biswanath Maity
- Bioorganic Chemistry Laboratory, New
Chemistry Unit, and School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research
(JNCASR), Jakkur P.O., Bengaluru 560064, Karnataka India
| | - Hariharan Moorthy
- Bioorganic Chemistry Laboratory, New
Chemistry Unit, and School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research
(JNCASR), Jakkur P.O., Bengaluru 560064, Karnataka India
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory, New
Chemistry Unit, and School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research
(JNCASR), Jakkur P.O., Bengaluru 560064, Karnataka India
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Morozov VN, Klimovich MA, Shibaeva AV, Klimovich ON, Koshevaya ED, Kolyvanova MA, Kuzmin VA. Optical Polymorphism of Liquid-Crystalline Dispersions of DNA at High Concentrations of Crowding Polymer. Int J Mol Sci 2023; 24:11365. [PMID: 37511123 PMCID: PMC10379083 DOI: 10.3390/ijms241411365] [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: 06/10/2023] [Revised: 07/03/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
Optically active liquid-crystalline dispersions (LCD) of nucleic acids, obtained by polymer- and salt-induced (psi-) condensation, e.g., by mixing of aqueous saline solutions of low molecular weight DNA (≤106 Da) and polyethylene glycol (PEG), possess an outstanding circular dichroism (CD) signal (so-called psi-CD) and are of interest for sensor applications. Typically, such CD signals are observed in PEG content from ≈12.5% to ≈22%. However, in the literature, there are very conflicting data on the existence of psi-CD in DNA LCDs at a higher content of crowding polymer up to 30-40%. In the present work, we demonstrate that, in the range of PEG content in the system above ≈24%, optically polymorphic LCDs can be formed, characterized by both negative and positive psi-CD signals, as well as by ones rather slightly differing from the spectrum of isotropic DNA solution. Such a change in the CD signal is determined by the concentration of the stock solution of PEG used for the preparation of LCDs. We assume that various saturation of polymer chains with water molecules may affect the amount of active water, which in turn leads to a change in the hydration of DNA molecules and their transition from B-form to Z-form.
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Affiliation(s)
- Vladimir N Morozov
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygina, 119334 Moscow, Russia
| | - Mikhail A Klimovich
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygina, 119334 Moscow, Russia
- Burnazyan Federal Medical Biophysical Center, Federal Medical Biological Agency of the Russian Federation, 23 Marshala Novikova, 123182 Moscow, Russia
| | - Anna V Shibaeva
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygina, 119334 Moscow, Russia
| | - Olga N Klimovich
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygina, 119334 Moscow, Russia
| | - Ekaterina D Koshevaya
- Burnazyan Federal Medical Biophysical Center, Federal Medical Biological Agency of the Russian Federation, 23 Marshala Novikova, 123182 Moscow, Russia
| | - Maria A Kolyvanova
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygina, 119334 Moscow, Russia
- Burnazyan Federal Medical Biophysical Center, Federal Medical Biological Agency of the Russian Federation, 23 Marshala Novikova, 123182 Moscow, Russia
| | - Vladimir A Kuzmin
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygina, 119334 Moscow, Russia
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Pratihar S, Suseela YV, Govindaraju T. Threading Intercalator-Induced Nanocondensates and Role of Endogenous Metal Ions in Decondensation for DNA Delivery. ACS APPLIED BIO MATERIALS 2020; 3:6979-6991. [PMID: 35019357 DOI: 10.1021/acsabm.0c00870] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The interplay of condensation and decondensation of DNA plays a crucial role in chromosome maintenance and gene expression. The molecular architectonics governing the chromatin condensation-decondensation cycle are worth studying, as DNA performs unique and distinct roles in each state and switches between two states without the loss of structural and functional integrity. This phenomenon has been adapted and implemented in transfection studies. Effective gene delivery into the cells to achieve respectable transfection efficiency has remained a challenge and emphasizes the need for understanding the steps involved in DNA delivery and transfection. Especially, recognizing the factors that effectively regulate DNA decondensation can provide logical solutions to the hurdles affecting the transfection efficiency. We designed a set of small molecule-based threading intercalation ligands as model condensing agents to study various factors influencing the DNA condensation and decondensation process. This study revealed condensation of DNA into nanocondensate by the threading intercalator and endogenous stimuli induced effective decondensation. Further, DNA nanocondensates are tracked using the intrinsic fluorescence in the lower pH of endocytic pathway and were evaluated as nonviral vectors for in cellulo delivery of plasmids. The correlation of decondensation of DNA nanocondensate with endogenous metal ions at their physiological concentrations provided valuable insights and implications for intracellular DNA delivery.
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Affiliation(s)
- Sumon Pratihar
- Bioorganic Chemistry Laboratory, New Chemistry Unit and School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, P.O., Bengaluru, Karnataka 560064, India
| | - Yelisetty Venkata Suseela
- Bioorganic Chemistry Laboratory, New Chemistry Unit and School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, P.O., Bengaluru, Karnataka 560064, India
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit and School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, P.O., Bengaluru, Karnataka 560064, India
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Dinda SK, Polepalli S, Rao CP. Binding of Fe( ii)-complex of phenanthroline appended glycoconjugate with DNA, plasmid and an agglutinin protein. NEW J CHEM 2020. [DOI: 10.1039/d0nj01524e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A phenanthroline appended glycoconjugate and its Fe(ii) complex have been synthesized and characterized thoroughly. The Fe-complex interacts with DNA and WGA protein and alter their structures as studied by spectroscopy and microscopy.
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Affiliation(s)
- Subrata Kumar Dinda
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai–400 076
- India
| | - Sirilata Polepalli
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai–400 076
- India
| | - Chebrolu Pulla Rao
- Department of Chemistry
- Indian Institute of Technology Tirupati
- Settipalli post
- Tirupati–517506
- India
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Tartakoff SS, Finan JM, Curtis EJ, Anchukaitis HM, Couture DJ, Glazier S. Investigations into the DNA-binding mode of doxorubicinone. Org Biomol Chem 2019; 17:1992-1998. [PMID: 30406253 DOI: 10.1039/c8ob02344a] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cancer treatment is one of the major challenges facing the modern biomedical profession. Development of new small-molecule chemotherapeutics requires an understanding of the mechanism of action for these treatments, as well as the structure-activity relationship. Study of the well-known DNA-intercalating agent, doxorubicin, and its aglycone, doxorubicinone, was undertaken using a variety of spectroscopic and calorimetric techniques. It was found that, despite conservation of the planar, aromatic portion of doxorubicin, the agylcone does not intercalate; it instead likely binds to the DNA minor-groove.
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Erlitzki N, Huang K, Xhani S, Farahat AA, Kumar A, Boykin DW, Poon GMK. Investigation of the electrostatic and hydration properties of DNA minor groove-binding by a heterocyclic diamidine by osmotic pressure. Biophys Chem 2017; 231:95-104. [PMID: 28363467 DOI: 10.1016/j.bpc.2017.02.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Revised: 02/18/2017] [Accepted: 02/21/2017] [Indexed: 12/29/2022]
Abstract
Previous investigations of sequence-specific DNA binding by model minor groove-binding compounds showed that the ligand/DNA complex was destabilized in the presence of compatible co-solutes. Inhibition was interpreted in terms of osmotic stress theory as the uptake of significant numbers of excess water molecules from bulk solvent upon complex formation. Here, we interrogated the AT-specific DNA complex formed with the symmetric heterocyclic diamidine DB1976 as a model for minor groove DNA recognition using both ionic (NaCl) and non-ionic cosolutes (ethylene glycol, glycine betaine, maltose, nicotinamide, urea). While the non-ionic cosolutes all destabilized the ligand/DNA complex, their quantitative effects were heterogeneous in a cosolute- and salt-dependent manner. Perturbation with NaCl in the absence of non-ionic cosolute showed that preferential hydration water was released upon formation of the DB1976/DNA complex. As salt probes counter-ion release from charged groups such as the DNA backbone, we propose that the preferential hydration uptake in DB1976/DNA binding observed in the presence of osmolytes reflects the exchange of preferentially bound cosolute with hydration water in the environs of the bound DNA, rather than a net uptake of hydration waters by the complex.
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Affiliation(s)
- Noa Erlitzki
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - Kenneth Huang
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - Suela Xhani
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - Abdelbasset A Farahat
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States; Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Arvind Kumar
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - David W Boykin
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - Gregory M K Poon
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, United States.
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Kenney RM, Buxton KE, Glazier S. Investigating the impacts of DNA binding mode and sequence on thermodynamic quantities and water exchange values for two small molecule drugs. Biophys Chem 2016; 216:9-18. [PMID: 27322498 DOI: 10.1016/j.bpc.2016.05.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Revised: 05/02/2016] [Accepted: 05/09/2016] [Indexed: 10/21/2022]
Abstract
Doxorubicin and nogalamycin are antitumor antibiotics that interact with DNA via intercalation and threading mechanisms, respectively. Because the importance of water, particularly its impact on entropy changes, has been established in other biological processes, we investigated the role of water in these two drug-DNA binding events. We used the osmotic stress method to calculate the number of water molecules exchanged (Δnwater), and isothermal titration calorimetry to measure Kbinding, ΔH, and ΔS for two synthetic DNAs, poly(dA·dT) and poly(dG·dC), and calf thymus DNA (CT DNA). For nogalamycin, Δnwater<0 for CT DNA and poly(dG·dC). For doxorubicin, Δnwater>0 for CT DNA and Δnwater<0 for poly(dG·dC). For poly(dA·dT), Δnwater~0 with both drugs. Net enthalpy changes were always negative, but net entropy changes depended on the drug. The effect of water exchange on the overall sign of entropy change appears to be smaller than other contributions.
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Affiliation(s)
- Rachael M Kenney
- Department of Chemistry, St. Lawrence University, 23 Romoda Drive, Canton, NY, USA; Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Katherine E Buxton
- Department of Chemistry, St. Lawrence University, 23 Romoda Drive, Canton, NY, USA; Department of Chemistry, University of Wisconsin, Madison, WI, USA.
| | - Samantha Glazier
- Department of Chemistry, St. Lawrence University, 23 Romoda Drive, Canton, NY, USA.
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Yaku H, Murashima T, Miyoshi D, Sugimoto N. In vitro assays predictive of telomerase inhibitory effect of G-quadruplex ligands in cell nuclei. J Phys Chem B 2013; 118:2605-14. [PMID: 24328194 DOI: 10.1021/jp410669t] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
G-quadruplex-binding and telomerase-inhibiting capacities of G-quadruplex ligands were examined under a cell nuclei-mimicking condition including excess double-stranded DNA (λ DNA) and molecular crowding cosolute (PEG 200). Under the cell nuclei-mimicking condition, a cationic porphyrin (TMPyP4) did not bind to the G-quadruplex despite the high affinity (Ka = 3.6 × 10(6) M(-1)) under a diluted condition without λ DNA and PEG 200. Correspondingly, TMPyP4 inhibited telomerase activity under the diluted condition (IC50 = 1.6 μM) but not under the cell nuclei-mimicking condition. In contrast, the Ka and IC50 values of an anionic copper phthalocyanine (Cu-APC) under the diluted (2.8 × 10(4) M(-1) and 0.86 μM) and the cell nuclei-mimicking (2.8 × 10(4) M(-1) and 2.1 μM) conditions were similar. In accordance with these results, 10 μM TMPyP4 did not affect the proliferation of HeLa cells, while Cu-APC efficiently inhibited the proliferation (IC50 = 1.4 μM). These results show that the cell nuclei-mimicking condition is effective to predict capacities of G-quadruplex ligands in the cell. In addition, the antiproliferative effect of Cu-APC on normal cells was smaller than that on HeLa cells, indicating that the cell nuclei-mimicking condition is also useful to predict side effects of ligands.
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Affiliation(s)
- Hidenobu Yaku
- Advanced Technology Research Laboratories, Panasonic Corporation, 3-4 Hikaridai, Seika-cho, Soraku-gun, Kyoto 619-0237, Japan
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Yaku H, Murashima T, Tateishi-Karimata H, Nakano SI, Miyoshi D, Sugimoto N. Study on effects of molecular crowding on G-quadruplex-ligand binding and ligand-mediated telomerase inhibition. Methods 2013; 64:19-27. [PMID: 23562626 DOI: 10.1016/j.ymeth.2013.03.028] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Revised: 03/21/2013] [Accepted: 03/25/2013] [Indexed: 01/24/2023] Open
Abstract
The telomere G-quadruplex-binding and telomerase-inhibiting capacity of two cationic (TMPyP4 and PIPER) and two anionic (phthalocyanine and Hemin) G-quadruplex-ligands were examined under conditions of molecular crowding (MC). Osmotic experiments showed that binding of the anionic ligands, which bind to G-quadruplex DNA via π-π stacking interactions, caused some water molecules to be released from the G-quadruplex/ligand complex; in contrast, a substantial number of water molecules were taken up upon electrostatic binding of the cationic ligands to G-quadruplex DNA. These behaviors of water molecules maintained or reduced the binding affinity of the anionic and the cationic ligands, respectively, under MC conditions. Consequently, the anionic ligands (phthalocyanine and Hemin) robustly inhibited telomerase activity even with MC; in contrast, the inhibition of telomerase caused by cationic TMPyP4 was drastically reduced by MC. These results allow us to conclude that the binding of G-quadruplex-ligands to G-quadruplex via non-electrostatic interactions is preferable for telomerase inhibition under physiological conditions.
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Key Words
- 5,10,15,20-tetra-(N-methyl-4-pyridyl)porphyrin
- Cancer
- Cu-APC
- EG
- Fe(III)-protoporphyrin IX
- G-quadruplex-ligand
- Hemin
- MC
- Molecular crowding
- N,N′-bis[2-(1-piperidino)ethyl]-3,4,9,10-perylenetetracarboxylic diimide
- PEG
- PIPER
- TMPyP4
- Telomerase
- Water molecule
- copper(II) phthalocyanine 3,4′,4′′,4′′′-tetrasulfonic acid tetrasodium salt
- double-stranded DNA
- dsDNA
- ethylene glycol
- molecular crowding
- poly ethylene glycol
- tsTRAP assay
- two-step telomere repeat amplification protocol assay
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Affiliation(s)
- Hidenobu Yaku
- Advanced Technology Research Laboratories, Panasonic Corporation, 3-4 Hikaridai, Seika-cho, Soraku-gun, Kyoto 619-0237, Japan; Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan; Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
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