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Ivanov GS, Tribulovich VG, Pestov NB, David TI, Amoah AS, Korneenko TV, Barlev NA. Artificial genetic polymers against human pathologies. Biol Direct 2022; 17:39. [PMID: 36474260 PMCID: PMC9727881 DOI: 10.1186/s13062-022-00353-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
Originally discovered by Nielsen in 1991, peptide nucleic acids and other artificial genetic polymers have gained a lot of interest from the scientific community. Due to their unique biophysical features these artificial hybrid polymers are now being employed in various areas of theranostics (therapy and diagnostics). The current review provides an overview of their structure, principles of rational design, and biophysical features as well as highlights the areas of their successful implementation in biology and biomedicine. Finally, the review discusses the areas of improvement that would allow their use as a new class of therapeutics in the future.
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Affiliation(s)
- Gleb S Ivanov
- Institute of Cytology, Tikhoretsky Ave 4, Saint Petersburg, Russia, 194064
- St. Petersburg State Technological Institute (Technical University), Saint Petersburg, Russia, 190013
| | - Vyacheslav G Tribulovich
- St. Petersburg State Technological Institute (Technical University), Saint Petersburg, Russia, 190013
| | - Nikolay B Pestov
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products, Moscow, Russia, 108819
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia, 141701
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia, 117997
- Institute of Biomedical Chemistry, Moscow, Russia, 119121б
| | - Temitope I David
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia, 141701
| | - Abdul-Saleem Amoah
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia, 141701
| | - Tatyana V Korneenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia, 117997
| | - Nikolai A Barlev
- Institute of Cytology, Tikhoretsky Ave 4, Saint Petersburg, Russia, 194064.
- Institute of Biomedical Chemistry, Moscow, Russia, 119121б.
- School of Medicine, Nazarbayev University, 010000, Astana, Kazakhstan.
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Nuclease resistance and protein recognition properties of DNA and hybrid PNA-DNA four-way junctions. Biophys Chem 2022; 289:106863. [DOI: 10.1016/j.bpc.2022.106863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 11/18/2022]
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Troisi M, Klein M, Smith AC, Moorhead G, Kebede Y, Huang R, Parker E, Herrada H, Wade E, Smith S, Broome P, Halsell J, Estevez L, Bell AJ. Conformation and protein interactions of intramolecular DNA and phosphorothioate four-way junctions. Exp Biol Med (Maywood) 2020; 246:707-717. [PMID: 33342281 DOI: 10.1177/1535370220973970] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The objectives of this study are to evaluate the structure and protein recognition features of branched DNA four-way junctions in an effort to explore the therapeutic potential of these molecules. The classic immobile DNA 4WJ, J1, is used as a matrix to design novel intramolecular junctions including natural and phosphorothioate bonds. Here we have inserted H2-type mini-hairpins into the helical termini of the arms of J1 to generate four novel intramolecular four-way junctions. Hairpins are inserted to reduce end fraying and effectively eliminate potential nuclease binding sites. We compare the structure and protein recognition features of J1 with four intramolecular four-way junctions: i-J1, i-J1(PS1), i-J1(PS2) and i-J1(PS3). Circular dichroism studies suggest that the secondary structure of each intramolecular 4WJ is composed predominantly of B-form helices. Thermal unfolding studies indicate that intramolecular four-way junctions are significantly more stable than J1. The Tm values of the hairpin four-way junctions are 25.2° to 32.2°C higher than the control, J1. With respect to protein recognition, gel shift assays reveal that the DNA-binding proteins HMGBb1 and HMGB1 bind the hairpin four-way junctions with affinity levels similar to control, J1. To evaluate nuclease resistance, four-way junctions are incubated with DNase I, exonuclease III (Exo III) and T5 exonuclease (T5 Exo). The enzymes probe nucleic acid cleavage that occurs non-specifically (DNase I) and in a 5'→3' (T5 Exo) and 3'→5' direction (Exo III). The nuclease digestion assays clearly show that the intramolecular four-way junctions possess significantly higher nuclease resistance than the control, J1.
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Affiliation(s)
- Maria Troisi
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, CA 92110, USA
| | - Mitchell Klein
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, CA 92110, USA
| | - Andrew C Smith
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, CA 92110, USA
| | - Gaston Moorhead
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, CA 92110, USA
| | - Yonatan Kebede
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, CA 92110, USA
| | - Raymond Huang
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, CA 92110, USA
| | - Elliott Parker
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, CA 92110, USA
| | - Hector Herrada
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, CA 92110, USA
| | - Elizabeth Wade
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, CA 92110, USA
| | - Samara Smith
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, CA 92110, USA
| | - Payson Broome
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, CA 92110, USA
| | - Jonah Halsell
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, CA 92110, USA
| | - Louis Estevez
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, CA 92110, USA
| | - Anthony J Bell
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, CA 92110, USA
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Duan T, He L, Tokura Y, Liu X, Wu Y, Shi Z. Construction of tunable peptide nucleic acid junctions. Chem Commun (Camb) 2018; 54:2846-2849. [PMID: 29364308 DOI: 10.1039/c8cc00108a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We report here the construction of 3-way and 4-way peptide nucleic acid (PNA) junctions as basic structural units for PNA nanostructuring. The incorporation of amino acid residues into PNA chains makes PNA nanostructures with more structural complexity and architectural flexibility possible, as exemplified by building 3-way PNA junctions with tunable nanopores. Given that PNA nanostructures have good thermal and enzymatic stabilities, they are expected to have broad potential applications in biosensing, drug delivery and bioengineering.
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Affiliation(s)
- Tanghui Duan
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Luoyu Road 1037, 430074 Hongshan, Wuhan, P. R. China.
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Iverson D, Serrano C, Brahan AM, Shams A, Totsingan F, Bell AJ. Supporting data for the characterization of PNA-DNA four-way junctions. Data Brief 2015; 5:756-60. [PMID: 26693508 PMCID: PMC4659781 DOI: 10.1016/j.dib.2015.10.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 10/12/2015] [Accepted: 10/13/2015] [Indexed: 11/24/2022] Open
Abstract
Holliday or DNA four-way junctions (4WJs) are cruciform/bent structures composed of four DNA duplexes. 4WJs are key intermediates in homologous genetic recombination and double-strand break repair. To investigate 4WJs in vitro, junctions are assembled using four asymmetric DNA strands. The presence of four asymmetric strands about the junction branch point eliminates branch migration, and effectively immobilizes the resulting 4WJ. The purpose of these experiments is to show that immobile 4WJs composed of DNA and peptide nucleic acids (PNAs) can be distinguished from contaminating labile nucleic acid structures. These data compare the electrophoretic mobility of hybrid PNA-DNA junctions vs. i) a classic immobile DNA 4WJ, J1 and ii) contaminating nucleic acid structures.
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Affiliation(s)
- Douglas Iverson
- Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, MS, USA
| | - Crystal Serrano
- Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, MS, USA
| | - Ann Marie Brahan
- Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, MS, USA
| | - Arik Shams
- Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, MS, USA
| | | | - Anthony J Bell
- Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, MS, USA
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