1
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Crespo-Hernández CE. Special issue on nucleic acid photophysics. Photochem Photobiol 2024; 100:257-261. [PMID: 38501585 DOI: 10.1111/php.13923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/02/2024] [Accepted: 02/03/2024] [Indexed: 03/20/2024]
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2
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Krul SE, Costa GJ, Hoehn SJ, Valverde D, Oliveira LMF, Borin AC, Crespo-Hernández CE. Resolving Ultrafast Photoinitiated Dynamics of the Hachimoji 5-Aza-7-Deazaguanine Nucleobase: Impact of Synthetically Expanding the Genetic Alphabet. Photochem Photobiol 2022; 99:693-705. [PMID: 35938218 DOI: 10.1111/php.13688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 08/05/2022] [Indexed: 11/29/2022]
Abstract
The guanine derivative, 5-aza-7-deazaguanine (5N7C G) has recently been proposed as one of four unnatural bases, termed Hachimoji (8-letter) to expand the genetic code. We apply steady-state and time-resolved spectroscopy to investigate its electronic relaxation mechanism and probe the effect of atom substitution on the relaxation mechanism in polar protic and polar aprotic solvents. Mapping of the excited state potential energy surfaces is performed, from which the critical points are optimized by using the state-of-art Extended Multi-State Complete Active Space Second-Order Perturbation Theory. It is demonstrated that excitation to the lowest energy 1 ππ* state of 5N7C G results in complex dynamics leading to ca. 10 to 30-fold slower relaxation (depending on solvent) compared to guanine. A significant conformational change occurs at the S1 minimum, resulting in a 10-fold greater fluorescence quantum yield compared to guanine. The fluorescence quantum yield and S1 decay lifetime increase going from water to acetonitrile to propanol. The solvent-dependent results are supported by the quantum chemical calculations showing an increase in the energy barrier between the S1 minimum and the S1 /S0 conical intersection going from water to propanol. The longer lifetimes might make 5N7C G more photochemical active to adjacent nucleobases than guanine or other nucleobases within DNA.
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Affiliation(s)
- Sarah E Krul
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Ave, Cleveland, Ohio, 44106, United States
| | - Gustavo J Costa
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000. São Paulo, SP, Brazil
| | - Sean J Hoehn
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Ave, Cleveland, Ohio, 44106, United States
| | - Danillo Valverde
- Unité de Chimie Physique Theorique et Structurale, Namur Institute of Structured Matter, Université de Namur, B-5000, Namur, Belgium
| | - Leonardo M F Oliveira
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000. São Paulo, SP, Brazil
| | - Antonio Carlos Borin
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000. São Paulo, SP, Brazil
| | - Carlos E Crespo-Hernández
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Ave, Cleveland, Ohio, 44106, United States
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3
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Homaeigohar S, Liu Q, Kordbacheh D. Biomedical Applications of Antiviral Nanohybrid Materials Relating to the COVID-19 Pandemic and Other Viral Crises. Polymers (Basel) 2021; 13:2833. [PMID: 34451371 PMCID: PMC8401873 DOI: 10.3390/polym13162833] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 08/12/2021] [Accepted: 08/20/2021] [Indexed: 01/19/2023] Open
Abstract
The COVID-19 pandemic has driven a global research to uncover novel, effective therapeutical and diagnosis approaches. In addition, control of spread of infection has been targeted through development of preventive tools and measures. In this regard, nanomaterials, particularly, those combining two or even several constituting materials possessing dissimilar physicochemical (or even biological) properties, i.e., nanohybrid materials play a significant role. Nanoparticulate nanohybrids have gained a widespread reputation for prevention of viral crises, thanks to their promising antimicrobial properties as well as their potential to act as a carrier for vaccines. On the other hand, they can perform well as a photo-driven killer for viruses when they release reactive oxygen species (ROS) or photothermally damage the virus membrane. The nanofibers can also play a crucial protective role when integrated into face masks and personal protective equipment, particularly as hybridized with antiviral nanoparticles. In this draft, we review the antiviral nanohybrids that could potentially be applied to control, diagnose, and treat the consequences of COVID-19 pandemic. Considering the short age of this health problem, trivially the relevant technologies are not that many and are handful. Therefore, still progressing, older technologies with antiviral potential are also included and discussed. To conclude, nanohybrid nanomaterials with their high engineering potential and ability to inactivate pathogens including viruses will contribute decisively to the future of nanomedicine tackling the current and future pandemics.
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Affiliation(s)
- Shahin Homaeigohar
- School of Science and Engineering, University of Dundee, Dundee DD1 4HN, UK;
| | - Qiqi Liu
- School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China;
| | - Danial Kordbacheh
- School of Science and Engineering, University of Dundee, Dundee DD1 4HN, UK;
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4
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Liczner C, Duke K, Juneau G, Egli M, Wilds CJ. Beyond ribose and phosphate: Selected nucleic acid modifications for structure-function investigations and therapeutic applications. Beilstein J Org Chem 2021; 17:908-931. [PMID: 33981365 PMCID: PMC8093555 DOI: 10.3762/bjoc.17.76] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/14/2021] [Indexed: 12/16/2022] Open
Abstract
Over the past 25 years, the acceleration of achievements in the development of oligonucleotide-based therapeutics has resulted in numerous new drugs making it to the market for the treatment of various diseases. Oligonucleotides with alterations to their scaffold, prepared with modified nucleosides and solid-phase synthesis, have yielded molecules with interesting biophysical properties that bind to their targets and are tolerated by the cellular machinery to elicit a therapeutic outcome. Structural techniques, such as crystallography, have provided insights to rationalize numerous properties including binding affinity, nuclease stability, and trends observed in the gene silencing. In this review, we discuss the chemistry, biophysical, and structural properties of a number of chemically modified oligonucleotides that have been explored for gene silencing.
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Affiliation(s)
- Christopher Liczner
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Kieran Duke
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Gabrielle Juneau
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Martin Egli
- Department of Biochemistry, Vanderbilt Institute of Chemical Biology, and Center for Structural Biology, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Christopher J Wilds
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
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5
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Levina A, Repkova M, Shikina N, Ismagilov Z, Kupryushkin M, Pavlova A, Mazurkova N, Pyshnyi D, Zarytova V. Pronounced therapeutic potential of oligonucleotides fixed on inorganic nanoparticles against highly pathogenic H5N1 influenza A virus in vivo. Eur J Pharm Biopharm 2021; 162:92-98. [PMID: 33753212 DOI: 10.1016/j.ejpb.2021.03.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 12/20/2020] [Accepted: 03/14/2021] [Indexed: 11/26/2022]
Abstract
This study describes the effective attack of oligonucleotides on the viral genome of highly pathogenic H5N1 influenza A virus (IAV) in vivo using for the first time the new delivery system consisting of biocompatible low-toxic titanium dioxide nanoparticles and immobilized polylysine-containing oligonucleotides with the native (ODN) and partially modified (ODNm) internucleotide bonds. Intraperitoneal injection of the TiO2•PL-ODN nanocomposite provided 65-70% survival of mice, while intraperitoneal or oral administration of TiO2•PL-ODNm was somewhat more efficient (~80% survival). The virus titer in the lung was reduced by two-three orders of magnitude. The nanocomposites are nontoxic to mice under the used conditions. TiO2 nanoparticles, unbound ODN, and the nanocomposite bearing the random oligonucleotide showed an insignificant protective effect, which indicates the ability of targeted oligonucleotides delivered in mice in the nanocomposites to site-specifically interact with complementary RNAs. The protection of oligonucleotides in nanocomposites by TiO2 nanoparticles and partial modification of the internucleotide bonds provides a continued presence of oligonucleotides in the body for the effective and specific action on the viral RNA. The proposed oligonucleotide delivery system can claim not only to effectively inhibit IAV genes but also to turn off other genes responsible for diseases caused by nucleic acids.
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Affiliation(s)
- Asya Levina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of RAS, pr. Lavrent'eva 8, 630090 Novosibirsk, Russia
| | - Marina Repkova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of RAS, pr. Lavrent'eva 8, 630090 Novosibirsk, Russia
| | - Nadezhda Shikina
- Boreskov Institute of Catalysis, Siberian Branch of RAS, pr. Lavrent'eva 5, 630090 Novosibirsk, Russia
| | - Zinfer Ismagilov
- Boreskov Institute of Catalysis, Siberian Branch of RAS, pr. Lavrent'eva 5, 630090 Novosibirsk, Russia
| | - Maxim Kupryushkin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of RAS, pr. Lavrent'eva 8, 630090 Novosibirsk, Russia
| | - Anna Pavlova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of RAS, pr. Lavrent'eva 8, 630090 Novosibirsk, Russia
| | - Natalia Mazurkova
- FBRI State Research Centre of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, Russia
| | - Dmitrii Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of RAS, pr. Lavrent'eva 8, 630090 Novosibirsk, Russia
| | - Valentina Zarytova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of RAS, pr. Lavrent'eva 8, 630090 Novosibirsk, Russia.
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6
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Novopashina DS, Vorobyeva MA, Venyaminova A. Recent Advances in the Synthesis of High Boron-Loaded Nucleic Acids for BNCT. Front Chem 2021; 9:619052. [PMID: 33791278 PMCID: PMC8005562 DOI: 10.3389/fchem.2021.619052] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 02/02/2021] [Indexed: 12/05/2022] Open
Abstract
Boron clusters attract considerable attention as promising therapeutic tools for boron neutron capture therapy (BNCT). They combine high boron content with high chemical and biological stability, biorthogonality, and low toxicity. The development of oligonucleotide-based constructs and nucleic acid-like molecules, such as oligomeric phosphate diesters, bearing one or multiple boron clusters permits to create potential high boron-loaded agents for BNCT with good bioavailability, specifically interacting with nucleic acids inside the cell. Here, we shortly review the strategies and solutions in the design of oligonucleotide conjugates with boron clusters in light of the requirements for effective BNCT and future prospects of their practical use.
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Affiliation(s)
- Darya Sergeevna Novopashina
- Laboratory of RNA Chemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | | | - Alya Venyaminova
- Laboratory of RNA Chemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
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7
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Victorio CBL, Novera W, Tham JY, Watanabe S, Vasudevan SG, Chacko AM. Peptide-Conjugated Phosphorodiamidate Morpholino Oligomers for In Situ Live-Cell Molecular Imaging of Dengue Virus Replication. Int J Mol Sci 2020; 21:E9260. [PMID: 33291644 PMCID: PMC7730579 DOI: 10.3390/ijms21239260] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/15/2020] [Accepted: 12/01/2020] [Indexed: 01/01/2023] Open
Abstract
Current methods to detect and monitor pathogens in biological systems are largely limited by the tradeoffs between spatial context and temporal detail. A new generation of molecular tracking that provides both information simultaneously involves in situ detection coupled with non-invasive imaging. An example is antisense imaging that uses antisense oligonucleotide probes complementary to a target nucleotide sequence. In this study, we explored the potential of repurposing antisense oligonucleotides initially developed as antiviral therapeutics as molecular probes for imaging of viral infections in vitro and in vivo. We employed nuclease-resistant phosphorodiamidate synthetic oligonucleotides conjugated with cell-penetrating peptides (i.e., PPMOs) previously established as antivirals for dengue virus serotype-2 (DENV2). As proof of concept, and before further development for preclinical testing, we evaluated its validity as in situ molecular imaging probe for tracking cellular DENV2 infection using live-cell fluorescence imaging. Although the PPMO was designed to specifically target the DENV2 genome, it was unsuitable as in situ molecular imaging probe. This study details our evaluation of the PPMOs to assess specific and sensitive molecular imaging of DENV2 infection and tells a cautionary tale for those exploring antisense oligonucleotides as probes for non-invasive imaging and monitoring of pathogen infections in experimental animal models.
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Affiliation(s)
- Carla Bianca Luena Victorio
- Laboratory for Translational and Molecular Imaging, Cancer and Stem Cell Biology Programme, Duke-NUS Medical School, Singapore 169857, Singapore; (C.B.L.V.); (W.N.); (J.Y.T.)
| | - Wisna Novera
- Laboratory for Translational and Molecular Imaging, Cancer and Stem Cell Biology Programme, Duke-NUS Medical School, Singapore 169857, Singapore; (C.B.L.V.); (W.N.); (J.Y.T.)
| | - Jing Yang Tham
- Laboratory for Translational and Molecular Imaging, Cancer and Stem Cell Biology Programme, Duke-NUS Medical School, Singapore 169857, Singapore; (C.B.L.V.); (W.N.); (J.Y.T.)
| | - Satoru Watanabe
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (S.W.); (S.G.V.)
| | - Subhash G. Vasudevan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (S.W.); (S.G.V.)
| | - Ann-Marie Chacko
- Laboratory for Translational and Molecular Imaging, Cancer and Stem Cell Biology Programme, Duke-NUS Medical School, Singapore 169857, Singapore; (C.B.L.V.); (W.N.); (J.Y.T.)
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8
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Khan M, Yan L, Lv B, Ji N, Shah S, Liu X, Song Z, Zhao Y, Wang X, Lv Z. The preparation of endotoxin-free genetically engineered murine B1 antisense RNA. Anal Biochem 2020; 599:113737. [PMID: 32305428 DOI: 10.1016/j.ab.2020.113737] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 04/08/2020] [Accepted: 04/10/2020] [Indexed: 12/09/2022]
Abstract
One of the major limitations in the production of genetically engineered RNA from Escherichia coli (E. coli) is contamination by endotoxin. Here we report the first method that is capable of removing endotoxin from genetically engineered RNA. As a proof of concept, we transformed E. coli with a plasmid containing a tandem short interspersed nuclear elements from the mouse genome (SINE B1 elements). We then evaluated several extraction methods (SDS-NaCl centrifugation, SDS-NaCl filtration, TRIzol and SDS hot-phenol) and refinements thereof, and measured the resulting RNA yield, RNA purity, RNA integrity and endotoxin content. SDS-NaCl filtration with 2 mol/L NaCl, incorporating DEPC as an RNA protective agent, effectively removed endotoxin and resulted in a good RNA yield. Triton X-114 phase separation further reduced the endotoxin content of SDS-NaCl filtration-extracted RNA. RNA extracted by SDS-NaCl filtration with Triton X-114 phase separation did not cause adverse reactions in BALB/c mice and did not induce fever in rabbits when injected into these animals. The RNA met the requirements of nucleic acid reagents for in vivo experiments on animals.
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Affiliation(s)
- Murad Khan
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, 050017, Hebei Province, China
| | - Lifang Yan
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, 050017, Hebei Province, China
| | - Baixue Lv
- Department of Ultrasound, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, Hubei Province, China; Hubei Province Key Laboratory of Molecular Imaging, Wuhan, 430022, Hubei Province, China
| | - Ning Ji
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, 050017, Hebei Province, China
| | - Suleman Shah
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, 050017, Hebei Province, China
| | - Xin Liu
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, 050017, Hebei Province, China
| | - Zhixue Song
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, 050017, Hebei Province, China
| | - Yufang Zhao
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, 050017, Hebei Province, China
| | - Xiufang Wang
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, 050017, Hebei Province, China.
| | - Zhanjun Lv
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, 050017, Hebei Province, China.
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9
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Hendrikse SIS, Gras SL, Ellis AV. Opportunities and Challenges in DNA-Hybrid Nanomaterials. ACS NANO 2019; 13:8512-8516. [PMID: 31415144 DOI: 10.1021/acsnano.9b06186] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Nature has inspired the development of many life-like materials. Although still simplistic, key biological functionalities have been incorporated, enabling a wide variety of applications. DNA-based systems, in particular, show high promise due to their ability to merge specific Watson-Crick base pairing with unique properties that are also programmable, scalable, or dynamic. By combining the fields of DNA-based covalent polymers, DNA origami, and DNA-functionalized supramolecular polymers, new frontiers in next-generation DNA-based hybrid materials that can outperform current bioartificial systems will be realized. Many challenges must still be overcome before this emerging technology can be materialized.
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10
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Juliano RL, Wang L, Tavares F, Brown EG, James L, Ariyarathna Y, Ming X, Mao C, Suto M. Structure-activity relationships and cellular mechanism of action of small molecules that enhance the delivery of oligonucleotides. Nucleic Acids Res 2019; 46:1601-1613. [PMID: 29361039 PMCID: PMC5829638 DOI: 10.1093/nar/gkx1320] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 01/15/2018] [Indexed: 02/06/2023] Open
Abstract
The pharmacological effects of antisense and siRNA oligonucleotides are hindered by the tendency of these molecules to become entrapped in endomembrane compartments thus failing to reach their targets in the cytosol or nucleus. We have previously used high throughput screening to identify small molecules that enhance the escape of oligonucleotides from intracellular membrane compartments and have termed such molecules OECs (oligonucleotide enhancing compounds). Here, we report on the structure-activity relationships of a family of OECs that are analogs of a hit that emerged from our original screen. These studies demonstrate key roles for the lipophilic aromatic groups, the tertiary nitrogen, and the carbamate moiety of the parent compound. We have also investigated the intracellular site of action of the OECs and have shown that activity is due to the release of oligonucleotides from intermediate endosomal compartments rather than from early endosomes or from highly acidic downstream compartments. At high concentrations of OECs toxicity occurs in a manner that is independent of caspases or of lysosomal cathepsins but instead involves increased plasma membrane permeability. Thus, in addition to describing specific characteristics of this family of OECs, the current study provides insights into basic mechanisms of oligonucleotide trafficking and their implications for oligonucleotide delivery.
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Affiliation(s)
- Rudolph L Juliano
- Initos Pharmaceuticals LLC, Chapel Hill, NC 27599, USA.,UNC Eshelman School of Pharmacy, Chapel Hill, NC 27599, USA
| | - Ling Wang
- Initos Pharmaceuticals LLC, Chapel Hill, NC 27599, USA
| | - Francis Tavares
- Chemogenics Biopharma, Research Triangle Park, NC 27709, USA
| | - Edward G Brown
- Chemogenics Biopharma, Research Triangle Park, NC 27709, USA
| | - Lindsey James
- UNC Eshelman School of Pharmacy, Chapel Hill, NC 27599, USA
| | | | - Xin Ming
- Department of Cancer Biology and Comprehensive Cancer Center, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Chengqiong Mao
- Department of Cancer Biology and Comprehensive Cancer Center, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Mark Suto
- Southern Research Institute, Birmingham, AL 35205, USA
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11
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Némethová V, Rázga F. Chronic myelogenous leukemia on target. Cancer Med 2018; 7:3406-3410. [PMID: 29905026 PMCID: PMC6051163 DOI: 10.1002/cam4.1604] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 05/03/2018] [Accepted: 05/15/2018] [Indexed: 12/12/2022] Open
Abstract
Chronic myelogenous leukemia (CML) is commonly treated with tyrosine kinase inhibitors (TKIs) that inhibit the pro-leukemic activity of the BCR-ABL1 oncoprotein. Despite the therapeutic progress mediated by TKI use, off-target effects, treatment-induced drug resistance, and the limited effect of these drugs on CML stem cells (SCs) are major drawbacks frequently resulting in insufficient or unsustainable treatment. Therefore, intense research efforts have focused on development of improved TKIs and alternative treatment strategies to eradicate CML SCs. Alongside efforts to design superior protein inhibitors, the need to overcome the poor therapeutic effect of TKIs on CML SCs has led to a renaissance of antisense strategies, as they are reported as effective in more primitive cell types. Despite the greater drug design flexibility offered by antisense sequence variability and remarkable chemical improvements, antisense drugs exhibit unacceptable levels of off-target effects, precluding them from large-scale clinical testing. Recent advances in antisense drug design have led to a pioneering mRNA recognition concept that may offer a helping hand in eliminating off-target effects, and has potential to bridge the gap between research and clinical practice.
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Affiliation(s)
- Veronika Némethová
- Department for Biomaterials Research, Polymer Institute of the Slovak Academy of Sciences, Bratislava, Slovakia
| | - Filip Rázga
- Department for Biomaterials Research, Polymer Institute of the Slovak Academy of Sciences, Bratislava, Slovakia
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12
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Juliano RL. Intracellular Trafficking and Endosomal Release of Oligonucleotides: What We Know and What We Don't. Nucleic Acid Ther 2018; 28:166-177. [PMID: 29708838 DOI: 10.1089/nat.2018.0727] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Understanding the cellular uptake and intracellular trafficking of oligonucleotides provides an important basic underpinning for the developing field of oligonucleotide-based therapeutics. Whether delivered as "free" oligonucleotides, as ligand-oligonucleotide conjugates, or in association with various nanocarriers, all forms of oligonucleotide enter cells by endocytosis and are initially ensconced within membrane-limited vesicles. Accordingly, the locus and extent of release to the cytosol and nucleus are key determinants of the pharmacological actions of oligonucleotides. A number of recent studies have explored the intracellular trafficking of various forms of oligonucleotides and their release from endomembrane compartments. These studies reveal a surprising convergence on an early-intermediate compartment in the trafficking pathway as the key locus of release for oligonucleotides administered in "free" form as well as those delivered with lipid complexes. Thus, oligonucleotide release from multivesicular bodies or from late endosomes seems to be the crucial endogenous process for attaining pharmacological effects. This intrinsic process of oligonucleotide release may be amplified by delivery agents such as lipid complexes or small molecule enhancers.
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Affiliation(s)
- R L Juliano
- Initos Pharmaceuticals LLC, UNC Eshelman School of Pharmacy, University of North Carolina , Chapel Hill, North Carolina
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13
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Klimov LO, Seryapina AA, Zarytova VF, Levina AS, Markel AL. Antisense oligonucleotides for the arterial hypertension mechanisms study and therapy. Vavilovskii Zhurnal Genet Selektsii 2018. [DOI: 10.18699/vj18.354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Arterial hypertension is one of the most common chronic diseases in adults all over the world. This pathology can not only reduce patients’ life quality, but can also be accompanied by a number of complications. Despite the fact that there is a large group of antihypertensive drugs on the market, mainly representing different combinations of inhibitors of the renin-angiotensin system, adrenoreceptor blockers in combination with diuretics, there is no generally accepted “gold standard” for drugs that would not have side effects. The review discusses the main aspects of antisense oligonucleotides use in the context of arterial hypertension. It is well known that the medical implementation of antisense oligonucleotides aims to block the expression of particular genes involved in the pathology development, and a key advantage of this technique is a high selectivity of the effect. However, with the undoubted advantages of the method, there are difficulties in its application, related both to the properties of the oligonucleotides themselves (insufficient stability and poor penetration into cells), and to the variety of mechanisms of the origin of a particular pathology, arterial hypertension, in our case. The review provides a brief description of the main molecular targets for antisense treatment of hypertensive disease. The newest targets for therapy with oligonucleotides – microRNAs – are discussed. The main modifications of antisense nucleotides, designed to increase the duration of their effects and simplify the delivery of this type of drugs to the targets are discussed, in particular, combining antisense oligonucleotides with adenovirus-based expression vectors. Particular attention is given to antisense oligonucleotides in the complex with nanoparticles. The review discusses the results of the use of titanium dioxide (TiO2) containing antisense nanocomposites for the angiotensin converting enzyme in rats with stress induced arterial hypertension (ISIAH). It was shown that the use of antisense oligonucleotides continues to be a promising technique for studying the mechanisms of various forms of hypertensive disease and has a high potential for therapeutic use.
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Affiliation(s)
| | - A. A. Seryapina
- Novosibirsk State University; Institute of Cytology and Genetics SB RAS
| | - V. F. Zarytova
- Novosibirsk State University; Institute of Chemical Biology and Fundamental Medicine SB RAS
| | - A. S. Levina
- Novosibirsk State University; Institute of Chemical Biology and Fundamental Medicine SB RAS
| | - A. L. Markel
- Novosibirsk State University; Institute of Cytology and Genetics SB RAS
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14
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Liu C, Zhao Y, Yin S, Liu S, Zhang H, Wang X, Lv Z. The expression and construction of engineering Escherichia coli producing humanized AluY RNAs. Microb Cell Fact 2017; 16:183. [PMID: 29084536 PMCID: PMC5663053 DOI: 10.1186/s12934-017-0800-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 10/25/2017] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Exogenous RNAs can specifically up-regulate or down-regulate gene expression after they enter into cells. Alu RNAs are the main constituent of human transcriptome and participate in gene expression regulation. AluY elements belong to a subfamily of Alus and are the youngest Alus. In this paper, we established the technology method of preparing genetically engineered humanized AluY RNAs (AluY RNAs) from Escherichia coli (E. coli) strains. This technology method also can be used to prepare other genetically engineered humanized RNAs that can be used for cytology experiments. RESULTS Different copies of human AluY elements were inserted into pET-28α plasmid (pET) to construct pET-AluY plasmids that were transformed into BMBL21-DE3 (DE3) E. coli. Isopropylthio-β-D-galactoside (IPTG) induction inhibited transformed bacterial growth after DE3 E. coli were transformed by pET-AluY × 8 plasmid (8 copies of AluYs were inserted into pET); northern blotting was used to detect the amount of AluY RNAs after 2, 4, 6, 8, 10, 12, 14 and 16 h inducing with IPTG. The results showed that the amount of AluY RNAs was the highest at 4 h; 1, 2, 4, 8 or 14 copies of AluY elements were inserted into the pET to construct pET-AluY plasmids that were transformed into DE3 bacteria, the northern blotting results showed that AluY RNAs production amount increased with the increase of AluY copy number; pET-AluY × 8 DE3 bacteria did not produce AluY RNAs without IPTG induction, AluY RNA production kept similar when inducing by 0.1-0.4 mg/ml IPTG induction, however, AluY RNA production slightly decreased if deviating from the above concentration range; pET-AluY × 8 DE3 bacteria were cultured at 34, 37 or 40 °C and the results showed that AluY RNA production was the highest under 37 °C cultivation; pET-AluY × 8 plasmid was transformed into three kinds of BL21 bacteria, including DE3, BMBL21-DE3-pLysS (pLysS) and Trans BL 21 (TransBL), the results showed that AluY RNA production was the highest when using DE3 bacteria. CONCLUSIONS The optimal conditions of producing AluY RNAs were: a kind of host bacteria of DE3, an engineering bacteria concentration of OD600 1.0, an IPTG concentration of 0.2 mg/ml, a culturing temperature of 37 °C and a culturing time of 4 h. Pure AluY RNAs occupied 15.8% of extractive total RNAs and the mean yield of pure AluY RNAs in 100 ml bacteria solution was 0.46 mg.
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Affiliation(s)
- Chao Liu
- Department of Genetics, Hebei Key Lab of Laboratory Animal, Hebei Medical University, Shijiazhuang, 050017, Hebei Province, China
| | - Yuehua Zhao
- School of Stomatology, Hebei Medical University, Shijiazhuang, 050017, Hebei Province, China
| | - Shuxian Yin
- School of Stomatology, Hebei Medical University, Shijiazhuang, 050017, Hebei Province, China
| | - Shufeng Liu
- Department of Genetics, Hebei Key Lab of Laboratory Animal, Hebei Medical University, Shijiazhuang, 050017, Hebei Province, China
| | - Huanling Zhang
- Department of Genetics, Hebei Key Lab of Laboratory Animal, Hebei Medical University, Shijiazhuang, 050017, Hebei Province, China
| | - Xiufang Wang
- Department of Genetics, Hebei Key Lab of Laboratory Animal, Hebei Medical University, Shijiazhuang, 050017, Hebei Province, China.
| | - Zhanjun Lv
- Department of Genetics, Hebei Key Lab of Laboratory Animal, Hebei Medical University, Shijiazhuang, 050017, Hebei Province, China.
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Krasheninina OA, Fishman VS, Novopashina DS, Venyaminova AG. 5′-Bispyrene molecular beacons for RNA detection. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2017. [DOI: 10.1134/s1068162017030086] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Krasheninina OA, Lomzov AA, Fishman VS, Novopashina DS, Venyaminova AG. Rational design and studies of excimer forming novel dual probes to target RNA. Bioorg Med Chem 2017; 25:2244-2250. [PMID: 28279557 DOI: 10.1016/j.bmc.2017.02.042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 01/31/2017] [Accepted: 02/22/2017] [Indexed: 11/18/2022]
Abstract
In this paper, we report structure-based rational design and physico-chemical and biological studies of novel pyrene excimer forming dual probes for visualization of intracellular RNAs. Herein, the probes based on 2'-O-methyl RNA with linkers of different structure and length between pyrene moiety and ribose are studied with respect to their hybridization and spectral properties. We found optimal linkers that provide more intense excimer emission (at ∼480nm) of RNA-bound probes; particularly, the length of the linker arm of the 3'-component of dual probes plays a key role in formation of pyrene excimer. Calculated molecular dynamics trajectories and probability distributions of pyrene-pyrene dimer formation upon hybridization of the dual probes with RNA target are in agreement with the obtained fluorescence spectroscopy data for the corresponding duplexes. Our study demonstrates the excellent binding properties of new dual probes to structured RNA and their feasibility for the visualization of intracellular RNA targets.
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Affiliation(s)
- O A Krasheninina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev Ave., Novosibirsk 630090, Russia; Novosibirsk State University, 2 Pirogov str., Novosibirsk 630090, Russia.
| | - A A Lomzov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev Ave., Novosibirsk 630090, Russia; Novosibirsk State University, 2 Pirogov str., Novosibirsk 630090, Russia
| | - V S Fishman
- Institute of Cytology and Genetics SB RAS, 10 Lavrentiev Ave., Novosibirsk 630090, Russia
| | - D S Novopashina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev Ave., Novosibirsk 630090, Russia; Novosibirsk State University, 2 Pirogov str., Novosibirsk 630090, Russia
| | - A G Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev Ave., Novosibirsk 630090, Russia
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17
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Rocha CSJ, Lundin KE, Behlke MA, Zain R, El Andaloussi S, Smith CIE. Four Novel Splice-Switch Reporter Cell Lines: Distinct Impact of Oligonucleotide Chemistry and Delivery Vector on Biological Activity. Nucleic Acid Ther 2016; 26:381-391. [PMID: 27629437 DOI: 10.1089/nat.2016.0631] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
New advances in oligonucleotide (ON) chemistry emerge continuously, and over the last few years, several aspects of ON delivery have been improved. However, clear knowledge regarding how certain chemistries behave alone, or in combination with various delivery vectors, is limited. Moreover, characterization is frequently limited to a single reporter cell line and, when different cell types are studied, experiments are commonly not carried out under similar conditions, hampering comparative analysis. To address this, we have developed a small "tissue" library of new, stable, pLuc/705 splice-switching reporter cell lines (named HuH7_705, U-2 OS_705, C2C12_705, and Neuro-2a_705). Our data show that, indeed, the cell type used in activity screenings influences the efficiency of ONs of different chemistry (phosphorothioate with locked nucleic acid or 2'-O-methyl with or without N,N-diethyl-4-(4-nitronaphthalen-1-ylazo)-phenylamine). Likewise, the delivery method, Lipofectamine® 2000, PepFect14 nanoparticles, or "naked" uptake, also demonstrates cell-type-dependent outcomes. Taken together, these cell lines can potentially become useful tools for future in vitro evaluation of new nucleic acid-based oligomers as well as delivery compounds for splice-switching approaches and cell-specific therapies.
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Affiliation(s)
- Cristina S J Rocha
- 1 Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital , Huddinge, Sweden
| | - Karin E Lundin
- 1 Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital , Huddinge, Sweden
| | - Mark A Behlke
- 2 Integrated DNA Technologies, Inc. , Coralville, Iowa
| | - Rula Zain
- 1 Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital , Huddinge, Sweden .,3 Department of Clinical Genetics, Centre for Rare Diseases, Karolinska University Hospital , Stockholm, Sweden
| | - Samir El Andaloussi
- 1 Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital , Huddinge, Sweden .,4 Department of Physiology, Anatomy and Genetics, University of Oxford , Oxford, United Kingdom
| | - C I Edvard Smith
- 1 Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital , Huddinge, Sweden
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Kuznetsov NA, Kupryushkin MS, Abramova TV, Kuznetsova AA, Miroshnikova AD, Stetsenko DA, Pyshnyi DV, Fedorova OS. New oligonucleotide derivatives as unreactive substrate analogues and potential inhibitors of human apurinic/apyrimidinic endonuclease APE1. MOLECULAR BIOSYSTEMS 2016; 12:67-75. [PMID: 26548492 DOI: 10.1039/c5mb00692a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Human apurinic/apyrimidinic endonuclease APE1 is one of the key enzymes of the base excision DNA repair system. The main biological function of APE1 is the hydrolysis of the phosphodiester bond on the 5'-side of an apurinic/apyrimidinic site (AP-site) to give the 5'-phosphate and 3'-hydroxyl group. It has long been known that AP-sites have mutagenic and cytotoxic effects and their accumulation in DNA is a potential hazard to the cell lifecycle. The structural and biochemical studies of APE1 are complicated by its high catalytic activity towards the AP-site and its cyclic or acyclic analogues. This work has focussed on the design, synthesis and analysis of oligonucleotide derivatives as potentially unreactive APE1 substrates. We have shown that the replacement of oxygen atoms in the phosphate group on the 5'-side from the AP-site analogue tetrahydrofuran (F) considerably decreases the rate of enzymatic hydrolysis of modified oligonucleotides. We have calculated that a N3'-P5' phosphoramidate linkage is hydrolysed about 30 times slower than the native phosphodiester bond while phosphorothioate or primary phosphoramidate linkages are cleaved more than three orders of magnitude slower. The value of IC50 of the oligonucleotide duplex containing a primary phosphoramidate linkage is 2.5 × 10(-7) M, which is in accordance with the APE1 association constant of DNA duplexes containing AP-sites. Thus, it is demonstrated that oligonucleotide duplexes with chemical modifications could be used as unreactive substrates and potential competitive inhibitors of APE1.
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Affiliation(s)
- Nikita A Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia. and Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Maxim S Kupryushkin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.
| | - Tatyana V Abramova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.
| | - Alexandra A Kuznetsova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.
| | - Anastasia D Miroshnikova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.
| | - Dmitry A Stetsenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia. and Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Dmitrii V Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia. and Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Olga S Fedorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia. and Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
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Preparation of a paclitaxel-loaded cationic nanoemulsome and its biodistribution via direct intratumoral injection. Colloids Surf B Biointerfaces 2016; 142:81-88. [DOI: 10.1016/j.colsurfb.2016.02.046] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Revised: 02/21/2016] [Accepted: 02/22/2016] [Indexed: 12/18/2022]
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20
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Kel'in AV, Zlatev I, Harp J, Jayaraman M, Bisbe A, O'Shea J, Taneja N, Manoharan RM, Khan S, Charisse K, Maier MA, Egli M, Rajeev KG, Manoharan M. Structural Basis of Duplex Thermodynamic Stability and Enhanced Nuclease Resistance of 5'-C-Methyl Pyrimidine-Modified Oligonucleotides. J Org Chem 2016; 81:2261-79. [PMID: 26940174 DOI: 10.1021/acs.joc.5b02375] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Although judicious use of chemical modifications has contributed to the success of nucleic acid therapeutics, poor systemic stability remains a major hurdle. The introduction of functional groups around the phosphate backbone can enhance the nuclease resistance of oligonucleotides (ONs). Here, we report the synthesis of enantiomerically pure (R)- and (S)-5'-C-methyl (C5'-Me) substituted nucleosides and their incorporation into ONs. These modifications generally resulted in a decrease in thermal stability of oligonucleotide (ON) duplexes in a manner dependent on the stereoconfiguration at C5' with greater destabilization characteristic of (R)-epimers. Enhanced stability against snake venom phosphodiesterase resulted from modification of the 3'-end of an ON with either (R)- or (S)-C5'-Me nucleotides. The (S)-isomers with different 2'-substituents provided greater resistance against 3'-exonucleases than the corresponding (R)-isomers. Crystal structure analyses of RNA octamers with (R)- or (S)-5'-C-methyl-2'-deoxy-2'-fluorouridine [(R)- or (S)-C5'-Me-2'-FU, respectively] revealed that the stereochemical orientation of the C5'-Me and the steric effects that emanate from the alkyl substitution are the dominant determinants of thermal stability and are likely molecular origins of resistance against nucleases. X-ray and NMR structural analyses showed that the (S)-C5'-Me epimers are spatially and structurally more similar to their natural 5' nonmethylated counterparts than the corresponding (R)-epimers.
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Affiliation(s)
- Alexander V Kel'in
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Ivan Zlatev
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Joel Harp
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University, School of Medicine , Nashville, Tennessee 37232, United States
| | - Muthusamy Jayaraman
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Anna Bisbe
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Jonathan O'Shea
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Nate Taneja
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Rajar M Manoharan
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Saeed Khan
- Department of Chemistry and Biochemistry, University of California , Los Angeles, California 90095, United States
| | - Klaus Charisse
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Martin A Maier
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Martin Egli
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University, School of Medicine , Nashville, Tennessee 37232, United States
| | | | - Muthiah Manoharan
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
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