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Nasiri M, Bahadorani M, Dellinger K, Aravamudhan S, Vivero-Escoto JL, Zadegan R. Improving DNA nanostructure stability: A review of the biomedical applications and approaches. Int J Biol Macromol 2024; 260:129495. [PMID: 38228209 PMCID: PMC11060068 DOI: 10.1016/j.ijbiomac.2024.129495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 01/10/2024] [Accepted: 01/12/2024] [Indexed: 01/18/2024]
Abstract
DNA's programmable, predictable, and precise self-assembly properties enable structural DNA nanotechnology. DNA nanostructures have a wide range of applications in drug delivery, bioimaging, biosensing, and theranostics. However, physiological conditions, including low cationic ions and the presence of nucleases in biological systems, can limit the efficacy of DNA nanostructures. Several strategies for stabilizing DNA nanostructures have been developed, including i) coating them with biomolecules or polymers, ii) chemical cross-linking of the DNA strands, and iii) modifications of the nucleotides and nucleic acids backbone. These methods significantly enhance the structural stability of DNA nanostructures and thus enable in vivo and in vitro applications. This study reviews the present perspective on the distinctive properties of the DNA molecule and explains various DNA nanostructures, their advantages, and their disadvantages. We provide a brief overview of the biomedical applications of DNA nanostructures and comprehensively discuss possible approaches to improve their biostability. Finally, the shortcomings and challenges of the current biostability approaches are examined.
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Affiliation(s)
- Mahboobeh Nasiri
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina Agriculture and Technical State University, USA
| | - Mehrnoosh Bahadorani
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina Agriculture and Technical State University, USA
| | - Kristen Dellinger
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina Agriculture and Technical State University, USA
| | - Shyam Aravamudhan
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina Agriculture and Technical State University, USA
| | - Juan L Vivero-Escoto
- Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Reza Zadegan
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina Agriculture and Technical State University, USA.
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2
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Thiede J, Rothenbühler S, Iacovache I, Langenegger SM, Zuber B, Häner R. Supramolecular assembly of pyrene-DNA conjugates: influence of pyrene substitution pattern and implications for artificial LHCs. Org Biomol Chem 2023; 21:7908-7912. [PMID: 37750811 PMCID: PMC10566252 DOI: 10.1039/d3ob01375h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 09/20/2023] [Indexed: 09/27/2023]
Abstract
The supramolecular self-assembly of pyrene-DNA conjugates into nanostructures is presented. DNA functionalized with different types of pyrene isomers at the 3'-end self-assemble into nano-objects. The shape of the nanostructures is influenced by the type of pyrene isomer appended to the DNA. Multilamellar vesicles are observed with the 1,6- and 1,8-isomers, whereas conjugates of the 2,7-isomer exclusively assemble into spherical nanoparticles. Self-assembled nano-spheres obtained with the 2,7-dialkynyl pyrene isomer were used for the construction of an artificial light-harvesting complex (LHC) in combination with Cy3 as the energy acceptor.
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Affiliation(s)
- Jan Thiede
- Department of Chemistry, Biochemistry, and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
| | - Simon Rothenbühler
- Department of Chemistry, Biochemistry, and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
| | - Ioan Iacovache
- Institute of Anatomy, University of Bern, Baltzerstrasse 2, CH-3012 Bern, Switzerland
| | - Simon M Langenegger
- Department of Chemistry, Biochemistry, and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
| | - Benoît Zuber
- Institute of Anatomy, University of Bern, Baltzerstrasse 2, CH-3012 Bern, Switzerland
| | - Robert Häner
- Department of Chemistry, Biochemistry, and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
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Nakamura M, Yoshioka H, Takada T. Conformational Switching of Pyrenes Associated on Hairpin Loop Region by DNA B‐Z Transition. ChemistrySelect 2022. [DOI: 10.1002/slct.202200696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Mitsunobu Nakamura
- Department of Applied Chemistry University of Hyogo 2167 Shosha Himeji Hyogo 671–2280 Japan
| | - Hibiki Yoshioka
- Department of Applied Chemistry University of Hyogo 2167 Shosha Himeji Hyogo 671–2280 Japan
| | - Tadao Takada
- Department of Applied Chemistry University of Hyogo 2167 Shosha Himeji Hyogo 671–2280 Japan
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Nakamura M, Takada T, Yamana K. Controlling Pyrene Association in DNA Duplexes by B‐ to Z‐DNA Transitions. Chembiochem 2019; 20:2949-2954. [DOI: 10.1002/cbic.201900350] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Indexed: 12/23/2022]
Affiliation(s)
- Mitsunobu Nakamura
- Department of Applied ChemistryUniversity of Hyogo 2167 Shosha Himeji Hyogo 671–2280 Japan
| | - Tadao Takada
- Department of Applied ChemistryUniversity of Hyogo 2167 Shosha Himeji Hyogo 671–2280 Japan
| | - Kazushige Yamana
- Department of Applied ChemistryUniversity of Hyogo 2167 Shosha Himeji Hyogo 671–2280 Japan
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Nejad MI, Guo X, Housh K, Nel C, Yang Z, Price NE, Wang Y, Gates KS. Preparation and Purification of Oligodeoxynucleotide Duplexes Containing a Site-Specific, Reduced, Chemically Stable Covalent Interstrand Cross-Link Between a Guanine Residue and an Abasic Site. Methods Mol Biol 2019; 1973:163-175. [PMID: 31016701 DOI: 10.1007/978-1-4939-9216-4_10] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Methods for the preparation of DNA duplexes containing interstrand covalent cross-links may facilitate research in the fields of biochemistry, molecular biology, nanotechnology, and materials science. Here we report methods for the synthesis and isolation of DNA duplexes containing a site-specific, chemically stable, reduced covalent interstrand cross-link between a guanine residue and an abasic site. The method uses experimental techniques and equipment that are common in most biochemical laboratories and inexpensive, commercially available oligonucleotides and reagents.
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Affiliation(s)
| | - Xu Guo
- Department of Chemistry, University of Missouri, Columbia, MO, USA
| | - Kurt Housh
- Department of Chemistry, University of Missouri, Columbia, MO, USA
| | - Christopher Nel
- Department of Chemistry, University of Missouri, Columbia, MO, USA
| | - Zhiyu Yang
- Department of Chemistry, University of Missouri, Columbia, MO, USA
| | - Nathan E Price
- Department of Chemistry, University of California Riverside, Riverside, CA, USA
| | - Yinsheng Wang
- Department of Chemistry, University of California Riverside, Riverside, CA, USA
| | - Kent S Gates
- Department of Chemistry, University of Missouri, Columbia, MO, USA. .,Department of Biochemistry, University of Missouri, Columbia, MO, USA.
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Synthesis, Characterization, and Application of Poly(4,4'-Cyclohexylidene Bisphenol Oxalate) for Solid-Phase Extraction of DNA. BIOMED RESEARCH INTERNATIONAL 2019; 2019:7064073. [PMID: 30868072 PMCID: PMC6379882 DOI: 10.1155/2019/7064073] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 12/23/2018] [Accepted: 01/09/2019] [Indexed: 11/17/2022]
Abstract
The present study has synthesized poly(4,4'-cyclohexylidene bisphenol oxalate) by the condensation of oxalyl chloride with 4,4'-cyclohexylidene bisphenol, where its efficacy was tested for the solid-phase extraction of DNA. The synthesized polymer in the form of a white powder was characterized by FTIR, TGA-DTG, SEM, and BET analysis. The study utilized solid-phase application of the resulting polymer to extract DNA. The analysis of results provided the information that the extraction efficiency is a strong dependent of polymer amount and binding buffer type. Among the three types of buffers tested, the GuHCl buffer produced the most satisfactory results in terms of yield and efficiency of extraction. Moreover, the absorbance ratio of A260/A280 in all of the samples varied from 1.682 to 1.491, thereby confirming the capability of poly(4,4'-cyclohexylidene bisphenol oxalate) to elute pure DNA. The results demonstrated an increased DNA binding capacity with respect to increased percentage of the polymer. The study has concluded that poly(bisphenol Z oxalate) can be applied as one of the potential candidates for the high efficiency extraction of DNA by means of a simple, cost-effective, and environmentally friendly approach compared to the other traditional solid-phase methods.
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Jaleel JA, Ashraf SM, Rathinasamy K, Pramod K. Carbon dot festooned and surface passivated graphene-reinforced chitosan construct for tumor-targeted delivery of TNF-α gene. Int J Biol Macromol 2019; 127:628-636. [PMID: 30708020 DOI: 10.1016/j.ijbiomac.2019.01.174] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 01/18/2019] [Accepted: 01/28/2019] [Indexed: 12/11/2022]
Abstract
Gene therapy is a promising alternative that ensures effective treatment and cure for cancer. Here, we report graphene-reinforced chitosan (CS) construct based non-viral vector for tumor-targeted gene therapy. The therapeutic gene, pDNA-TNF-α, was loaded on to chitosan-carboxylated graphene oxide (CS-CGO) construct via electrostatic interaction. The pDNA-TNF-α-CS-CGO thus obtained was further passivated with 4,7,10-trioxa-1,13-tridecanediamine for protecting the vector from the mononuclear phagocyte system that contributes to the prolongation of circulation half-life. The surface passivated carrier (PEG-pDNA-TNF-α-CS-CGO) then festooned with the folic acid derived carbon dots (C-dots) for targeting folate receptors that are overexpressed in most of the cancer cells. The results of TEM images and zeta potential values ensured the occurrence of desired changes in each stage of C-dot-PEG-pDNA-TNF-α-CS-CGO formulation. After 14 days of incubation, the anti-angiogenesis effect was observed for final formulation in the chorioallantoic membrane. The results of in vitro gene expression study in cancer cell line show a comparatively higher transfection efficacy of the developed system (C-dot-PEG-pDNA-TNF-α-CS-CGO) than pDNA-TNF-α. The efficiency of the developed gene delivery system was further confirmed using a developed and validated artificial tumor cell apparatus.
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Affiliation(s)
- Jumana Abdul Jaleel
- College of Pharmaceutical Sciences, Govt. Medical College, Kozhikode, Kerala, India
| | - Shabeeba M Ashraf
- School of Biotechnology, National Institute of Technology Calicut, Calicut, India
| | - Krishnan Rathinasamy
- School of Biotechnology, National Institute of Technology Calicut, Calicut, India
| | - K Pramod
- College of Pharmaceutical Sciences, Govt. Medical College, Kozhikode, Kerala, India.
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Nakamura M, Matsui Y, Takada T, Yamana K. Chromophore Arrays Constructed in the Major Groove of DNA Duplexes Using a Post-Synthetic Strategy. ChemistrySelect 2019. [DOI: 10.1002/slct.201803464] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Mitsunobu Nakamura
- Department of Applied Chemistry; University of Hyogo; 2167 Shosha, Himeji Hyogo 671-2280 Japan
| | - Yuki Matsui
- Department of Applied Chemistry; University of Hyogo; 2167 Shosha, Himeji Hyogo 671-2280 Japan
| | - Tadao Takada
- Department of Applied Chemistry; University of Hyogo; 2167 Shosha, Himeji Hyogo 671-2280 Japan
| | - Kazushige Yamana
- Department of Applied Chemistry; University of Hyogo; 2167 Shosha, Himeji Hyogo 671-2280 Japan
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Gamboa Varela J, Gates KS. Simple, High-Yield Syntheses of DNA Duplexes Containing Interstrand DNA-DNA Cross-Links Between an N(4) -Aminocytidine Residue and an Abasic Site. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2016; 65:5.16.1-5.16.15. [PMID: 27248783 PMCID: PMC5000854 DOI: 10.1002/cpnc.3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The protocol describes the preparation and purification of interstrand DNA-DNA cross-links derived from the reaction of an N(4) -aminocytidine residue with an abasic site in duplex DNA. The procedures employ inexpensive, commercially available chemicals and enzymes to carry out post-synthetic modification of commercially available oligodeoxynucleotides. The yield of cross-linked duplex is typically better than 90%. If purification is required, the cross-linked duplex can be readily separated from single-stranded DNA starting materials by denaturing gel electrophoresis. The resulting covalent hydrazone-based cross-links are stable under physiologically relevant conditions and may be useful for biophysical studies, structural analyses, DNA repair studies, and materials science applications. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
| | - Kent S Gates
- Department of Chemistry, University of Missouri, Columbia, Missouri
- Department of Biochemistry, University of Missouri, Columbia, Missouri
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Zhang X, Price NE, Fang X, Yang Z, Gu LQ, Gates KS. Characterization of Interstrand DNA-DNA Cross-Links Using the α-Hemolysin Protein Nanopore. ACS NANO 2015; 9:11812-9. [PMID: 26563913 PMCID: PMC4826734 DOI: 10.1021/acsnano.5b03923] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Nanopore-based sensors have been studied extensively as potential tools for DNA sequencing, characterization of epigenetic modifications such as 5-methylcytosine, and detection of microRNA biomarkers. In the studies described here, the α-hemolysin protein nanopore embedded in a lipid bilayer was used for the detection and characterization of interstrand cross-links in duplex DNA. Interstrand cross-links are important lesions in medicinal chemistry and toxicology because they prevent the strand separation that is required for read-out of genetic information from DNA in cells. In addition, interstrand cross-links are used for the stabilization of duplex DNA in structural biology and materials science. Cross-linked DNA fragments produced unmistakable current signatures in the nanopore experiment. Some cross-linked substrates gave irreversible current blocks of >10 min, while others produced long current blocks (10-100 s) before the double-stranded DNA cross-link translocated through the α-hemolysin channel in a voltage-driven manner. The duration of the current block for the different cross-linked substrates examined here may be dictated by the stability of the duplex region left in the vestibule of the nanopore following partial unzipping of the cross-linked DNA. Construction of calibration curves measuring the frequency of cross-link blocking events (1/τon) as a function of cross-link concentration enabled quantitative determination of the amounts of cross-linked DNA present in samples. The unique current signatures generated by cross-linked DNA in the α-HL nanopore may enable the detection and characterization of DNA cross-links that are important in toxicology, medicine, and materials science.
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Affiliation(s)
- Xinyue Zhang
- University of Missouri, Department of Bioengineering and Dalton Cardiovascular Research Center, Columbia, MO 65211
| | - Nathan E. Price
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211
| | - Xi Fang
- University of Missouri, Department of Bioengineering and Dalton Cardiovascular Research Center, Columbia, MO 65211
| | - Zhiyu Yang
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211
| | - Li-Qun Gu
- University of Missouri, Department of Bioengineering and Dalton Cardiovascular Research Center, Columbia, MO 65211
- Address correspondence to: ; phone: (573) 882-6763 and ; phone: (573) 882-2057
| | - Kent S. Gates
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211
- University of Missouri, Department of Biochemistry, Columbia, MO 65211
- Address correspondence to: ; phone: (573) 882-6763 and ; phone: (573) 882-2057
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Gamboa Varela J, Gates KS. A simple, high-yield synthesis of DNA duplexes containing a covalent, thermally cleavable interstrand cross-link at a defined location. Angew Chem Int Ed Engl 2015; 54:7666-9. [PMID: 25967397 PMCID: PMC4532324 DOI: 10.1002/anie.201502566] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Indexed: 12/31/2022]
Abstract
Interstrand DNA-DNA cross-links are highly toxic to cells because these lesions block the extraction of information from the genetic material. The pathways by which cells repair cross-links are important, but not well understood. The preparation of chemically well-defined cross-linked DNA substrates represents a significant challenge in the study of cross-link repair. Here a simple method is reported that employs "post-synthetic" modifications of commercially available 2'-deoxyoligonucleotides to install a single cross-link in high yield at a specified location within a DNA duplex. The cross-linking process exploits the formation of a hydrazone between a non-natural N(4) -amino-2'-deoxycytidine nucleobase and the aldehyde residue of an abasic site in duplex DNA. The resulting cross-link is stable under physiological conditions, but can be readily dissociated and re-formed through heating-cooling cycles.
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Affiliation(s)
| | - Kent S Gates
- Department of Chemistry, University of Missouri, Columbia, MO 65211 (USA).
- Department of Biochemistry, University of Missouri, Columbia, MO 65211 (USA).
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Gamboa Varela J, Gates KS. A Simple, High-Yield Synthesis of DNA Duplexes Containing a Covalent, Thermally Cleavable Interstrand Cross-Link at a Defined Location. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502566] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Chen W, Schuster GB. Precise Sequence Control in Linear and Cyclic Copolymers of 2,5-Bis(2-thienyl)pyrrole and Aniline by DNA-Programmed Assembly. J Am Chem Soc 2013; 135:4438-49. [DOI: 10.1021/ja312507z] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Wen Chen
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332,
United States
| | - Gary B. Schuster
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332,
United States
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