1
|
Domínguez A, Gargallo R, Cuestas-Ayllón C, Grazu V, Fàbrega C, Valiuska S, Noé V, Ciudad CJ, Calderon EJ, de la Fuente JM, Eritja R, Aviñó A. Biophysical evaluation of antiparallel triplexes for biosensing and biomedical applications. Int J Biol Macromol 2024; 264:130540. [PMID: 38430998 DOI: 10.1016/j.ijbiomac.2024.130540] [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: 12/19/2023] [Revised: 02/07/2024] [Accepted: 02/27/2024] [Indexed: 03/05/2024]
Abstract
Polypyrimidine sequences can be targeted by antiparallel clamps forming triplex structures either for biosensing or therapeutic purposes. Despite its successful implementation, their biophysical properties remain to be elusive. In this work, PAGE, circular dichroism and multivariate analysis were used to evaluate the properties of PPRHs directed to SARS-CoV-2 genome. Several PPRHs designed to target various polypyrimidine sites within the viral genome were synthesized. These PPRHs displayed varying binding affinities, influenced by factors such as the length of the PPRH and its GC content. The number and position of pyrimidine interruptions relative to the 4 T loop of the PPRH was found a critical factor, affecting the binding affinity with the corresponding target. Moreover, these factors also showed to affect in the intramolecular and intermolecular equilibria of PPRHs alone and when hybridized to their corresponding targets, highlighting the polymorphic nature of these systems. Finally, the functionality of the PPRHs was evaluated in a thermal lateral flow sensing device showing a good correspondence between their biophysical properties and detection limits. These comprehensive studies contribute to the understanding of the critical factors involved in the design of PPRHs for effective targeting of biologically relevant genomes through the formation of triplex structures under neutral conditions.
Collapse
Affiliation(s)
- Arnau Domínguez
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain; Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain
| | - Raimundo Gargallo
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona (UB), 08028 Barcelona, Spain
| | - Carlos Cuestas-Ayllón
- Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain; Instituto de Nanociencia y Materiales de Aragón (INMA), Consejo Superior de Investigaciones Científicas (CSIC), 50018 Zaragoza, Spain
| | - Valeria Grazu
- Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain; Instituto de Nanociencia y Materiales de Aragón (INMA), Consejo Superior de Investigaciones Científicas (CSIC), 50018 Zaragoza, Spain
| | - Carme Fàbrega
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain; Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain
| | - Simonas Valiuska
- Department of Biochemistry and Physiology, School of Pharmacy and Food Sciences and Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona (UB), 08028 Barcelona, Spain
| | - Véronique Noé
- Department of Biochemistry and Physiology, School of Pharmacy and Food Sciences and Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona (UB), 08028 Barcelona, Spain
| | - Carlos J Ciudad
- Department of Biochemistry and Physiology, School of Pharmacy and Food Sciences and Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona (UB), 08028 Barcelona, Spain
| | - Enrique J Calderon
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas/Universidad de Sevilla, Sevilla, Spain; Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), 28029 Madrid, Spain
| | - Jesús Martínez de la Fuente
- Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain; Instituto de Nanociencia y Materiales de Aragón (INMA), Consejo Superior de Investigaciones Científicas (CSIC), 50018 Zaragoza, Spain
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain; Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain.
| | - Anna Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain; Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain.
| |
Collapse
|
2
|
Garavís M, Edwards PJB, Serrano-Chacón I, Doluca O, Filichev V, González C. Understanding intercalative modulation of G-rich sequence folding: solution structure of a TINA-conjugated antiparallel DNA triplex. Nucleic Acids Res 2024; 52:2686-2697. [PMID: 38281138 PMCID: PMC10954471 DOI: 10.1093/nar/gkae028] [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: 06/22/2023] [Revised: 12/21/2023] [Accepted: 01/06/2024] [Indexed: 01/30/2024] Open
Abstract
We present here the high-resolution structure of an antiparallel DNA triplex in which a monomer of para-twisted intercalating nucleic acid (para-TINA: (R)-1-O-[4-(1-pyrenylethynyl)phenylmethyl]glycerol) is covalently inserted as a bulge in the third strand of the triplex. TINA is a potent modulator of the hybridization properties of DNA sequences with extremely useful properties when conjugated in G-rich oligonucleotides. The insertion of para-TINA between two guanines of the triplex imparts a high thermal stabilization (ΔTM = 9ºC) to the structure and enhances the quality of NMR spectra by increasing the chemical shift dispersion of proton signals near the TINA location. The structural determination reveals that TINA intercalates between two consecutive triads, causing only local distortions in the structure. The two aromatic moieties of TINA are nearly coplanar, with the phenyl ring intercalating between the flanking guanine bases in the sequence, and the pyrene moiety situated between the Watson-Crick base pair of the two first strands. The precise position of TINA within the triplex structure reveals key TINA-DNA interactions, which explains the high stabilization observed and will aid in the design of new and more efficient binders to DNA.
Collapse
Affiliation(s)
- Miguel Garavís
- Instituto de Química Física ‘Blas Cabrera’, (IQF-CSIC), Madrid 28006, Spain
| | - Patrick J B Edwards
- School of Natural Sciences, Massey University, Palmerston North 4412, New Zealand
| | | | - Osman Doluca
- School of Natural Sciences, Massey University, Palmerston North 4412, New Zealand
| | | | - Carlos González
- Instituto de Química Física ‘Blas Cabrera’, (IQF-CSIC), Madrid 28006, Spain
| |
Collapse
|
3
|
Hussein MK, Papež M, Dhiman H, Baumann M, Galosy S, Borth N. In silico design of CMV promoter binding oligonucleotides and their impact on inhibition of gene expression in Chinese hamster ovary cells. J Biotechnol 2022; 359:185-193. [DOI: 10.1016/j.jbiotec.2022.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 09/30/2022] [Accepted: 10/04/2022] [Indexed: 10/31/2022]
|
4
|
Yun Z, Chinnathambi A, Alharbi SA, Jin Z. Biosynthesis of gold nanoparticles using Vetex negundo and evaluation of pro-apoptotic effect on human gastric cancer cell lines. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2019; 203:111749. [PMID: 31884347 DOI: 10.1016/j.jphotobiol.2019.111749] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 12/10/2019] [Accepted: 12/16/2019] [Indexed: 12/13/2022]
Abstract
Gastric cancer (GC) is mainly widespread gastrointestinal malignancy,which reports for 8% of overallcases in carcinogenesis and 10% of yearly fatality, is 4thprimary cause of cancer associated death global. The plan of the present research was to develop ethanolic extract of Vitex negundo-loaded gold nanoparticles (VN-AuNPs) and to appraise the various characteristic methods likes UV-vis spectroscopy, SAED, FTIR, XRD and HR-TEM. Additionally, the anticancer effect of VN-AuNPs on AGS cells were analysed by cell viability, apoptotic morphological changes by TUNEL, AO/EtBr and Hoechst staining, alterations of mitochondrial membrane potential (MMP) and production reactive oxygen species (ROS). Moreover, the status of apoptosis gene such as caspase-3, Bcl-2, Bcl-XL, Bax and caspase-9 expressions was analysed by using western and RT-PCR techniques. Synthesized AuNPs established by UV absorption peak of the highest at 538 and crystal nature of AuNPs was additionallyverifiedwith SAED and XRD. TEM images were illustrates size and morphological division of NPs. FTIR examinationscompletedalkene, carbodiimide and aliphatic primary amines of biomolecules werepresent in synthesized VN-AuNPs. Additionally, AuNPs were stimulatedapoptosis throughthe cytotoxicity effect,changes of MMP, generation of ROS, nuclear and apoptotic morphological alterationsvia TUNEL, AO/EtBr and Hoechst assay. Furthermore, molecular mechanisms also provoked apoptosis through modulating pro (caspase-3, Bax, Bid, caspase-9) and anti-apoptotic (Bcl-2 and Bcl-XL) mediators by western blotting and gene expression in AGS cells. This production of AuNPs from VN was eco-friendly, large-scaled up and easy.
Collapse
Affiliation(s)
- Zhou Yun
- Department of Gastroenterology, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
| | - Arunachalam Chinnathambi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Sulaiman Ali Alharbi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Zhu Jin
- Department of Gastroenterology, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China.
| |
Collapse
|
5
|
Lu L, Wang J, Miao W, Wang X, Guo G. Electrogenerated Chemiluminescence Biosensor with a Tripod Probe for the Highly Sensitive Detection of MicroRNA. Anal Chem 2018; 91:1452-1459. [DOI: 10.1021/acs.analchem.8b04271] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Liping Lu
- College of Environmental and Energy Engineering, Beijing University of Technology, Beijing 100124, China
| | - Jiaxing Wang
- College of Environmental and Energy Engineering, Beijing University of Technology, Beijing 100124, China
| | - Wujian Miao
- Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
| | - Xiayan Wang
- College of Environmental and Energy Engineering, Beijing University of Technology, Beijing 100124, China
| | - Guangsheng Guo
- College of Environmental and Energy Engineering, Beijing University of Technology, Beijing 100124, China
| |
Collapse
|
6
|
Szabat M, Kierzek E, Kierzek R. Modified RNA triplexes: Thermodynamics, structure and biological potential. Sci Rep 2018; 8:13023. [PMID: 30158667 PMCID: PMC6115336 DOI: 10.1038/s41598-018-31387-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 08/17/2018] [Indexed: 12/23/2022] Open
Abstract
The occurrence of triplexes in vivo has been well documented and is determined by the presence of long homopurine-homopyrimidine tracts. The formation of these structures is the result of conformational changes that occur in the duplex, which allow the binding of a third strand within the major groove of the helix. Formation of these noncanonical forms by introducing synthetic triplex-forming oligonucleotides (TFOs) into the cell may have applications in molecular biology, diagnostics and therapy. This study focused on the formation of RNA triplexes as well as their thermal stability and biological potential in the HeLa cell line. Thermodynamics studies revealed that the incorporation of multiple locked nucleic acid (LNA) and 2-thiouridine (2-thioU) residues increased the stability of RNA triplexes. These data suggest that the number and position of the modified nucleotides within TFOs significantly stabilize the formed structures. Moreover, specificity of the interactions between the modified TFOs and the RNA hairpin was characterized using electrophoretic mobility-shift assay (EMSA), and triplex dissociation constants have been also determined. Finally, through quantitative analysis of GFP expression, the triplex structures were shown to regulate GFP gene silencing. Together, our data provide a first glimpse into the thermodynamic, structural and biological properties of LNA- and 2-thioU modified RNA triplexes.
Collapse
Affiliation(s)
- Marta Szabat
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Elzbieta Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.
| |
Collapse
|
7
|
Ukale DU, Lönnberg T. Triplex Formation by Oligonucleotides Containing Organomercurated Base Moieties. Chembiochem 2018; 19:1096-1101. [PMID: 29575511 DOI: 10.1002/cbic.201800112] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Indexed: 12/26/2022]
Abstract
Homothymine oligonucleotides with a single 5-mercuricytosine or 5-mercuriuracil residue at their termini have been synthesized and their capacity to form triplexes has been examined with an extensive array of double-helical targets. UV and circular dichroism (CD) melting experiments revealed the formation and thermal denaturation of pyrimidine⋅purine*pyrimidine-type triple helices with all oligonucleotide combinations studied. Nearly all triplexes were destabilized upon mercuration of the 3'-terminal residue of the triplex-forming oligonucleotide, in all likelihood due to competing intramolecular HgII -mediated base pairing. Two exceptions from this general pattern were, however, observed: 5-mercuricytosine was stabilizing when placed opposite to a T⋅A or A⋅T base pair. The stabilization was further amplified in the presence of 2-mercaptoethanol (but not hexanethiol, thiophenol or cysteine), suggesting a stabilizing interaction other than HgII -mediated base pairing.
Collapse
Affiliation(s)
| | - Tuomas Lönnberg
- University of Turku, Department of Chemistry, Vatselankatu 2, 20014, Turku, Finland
| |
Collapse
|
8
|
Politi C, Ciccacci C, Novelli G, Borgiani P. Genetics and Treatment Response in Parkinson's Disease: An Update on Pharmacogenetic Studies. Neuromolecular Med 2018; 20:1-17. [PMID: 29305687 DOI: 10.1007/s12017-017-8473-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 12/29/2017] [Indexed: 01/11/2023]
Abstract
Parkinson's disease (PD) is a complex neurodegenerative disorder characterized by a progressive loss of dopamine neurons of the central nervous system. The disease determines a significant disability due to a combination of motor symptoms such as bradykinesia, rigidity and rest tremor and non-motor symptoms such as sleep disorders, hallucinations, psychosis and compulsive behaviors. The current therapies consist in combination of drugs acting to control only the symptoms of the illness by the replacement of the dopamine lost. Although patients generally receive benefits from this symptomatic pharmacological management, they also show great variability in drug response in terms of both efficacy and adverse effects. Pharmacogenetic studies highlighted that genetic factors play a relevant influence in this drug response variability. In this review, we tried to give an overview of the recent progresses in the pharmacogenetics of PD, reporting the major genetic factors identified as involved in the response to drugs and highlighting the potential use of some of these genomic variants in the clinical practice. Many genes have been investigated and several associations have been reported especially with adverse drug reactions. However, only polymorphisms in few genes, including DRD2, COMT and SLC6A3, have been confirmed as associated in different populations and in large cohorts. The identification of genomic biomarkers involved in drug response variability represents an important step in PD treatment, opening the prospective of more personalized therapies in order to identify, for each person, the better therapy in terms of efficacy and toxicity and to improve the PD patients' quality of life.
Collapse
Affiliation(s)
- Cristina Politi
- Department of Biomedicine and Prevention, Genetics Section, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy
| | - Cinzia Ciccacci
- Department of Biomedicine and Prevention, Genetics Section, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy.
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, Genetics Section, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy
| | - Paola Borgiani
- Department of Biomedicine and Prevention, Genetics Section, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy
| |
Collapse
|
9
|
Hu Y, Cecconello A, Idili A, Ricci F, Willner I. Triplex DNA Nanostructures: From Basic Properties to Applications. Angew Chem Int Ed Engl 2017; 56:15210-15233. [PMID: 28444822 DOI: 10.1002/anie.201701868] [Citation(s) in RCA: 223] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Indexed: 12/16/2022]
Abstract
Triplex nucleic acids have recently attracted interest as part of the rich "toolbox" of structures used to develop DNA-based nanostructures and materials. This Review addresses the use of DNA triplexes to assemble sensing platforms and molecular switches. Furthermore, the pH-induced, switchable assembly and dissociation of triplex-DNA-bridged nanostructures are presented. Specifically, the aggregation/deaggregation of nanoparticles, the reversible oligomerization of origami tiles and DNA circles, and the use of triplex DNA structures as functional units for the assembly of pH-responsive systems and materials are described. Examples include semiconductor-loaded DNA-stabilized microcapsules, DNA-functionalized dye-loaded metal-organic frameworks (MOFs), and the pH-induced release of the loads. Furthermore, the design of stimuli-responsive DNA-based hydrogels undergoing reversible pH-induced hydrogel-to-solution transitions using triplex nucleic acids is introduced, and the use of triplex DNA to assemble shape-memory hydrogels is discussed. An outlook for possible future applications of triplex nucleic acids is also provided.
Collapse
Affiliation(s)
- Yuwei Hu
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Alessandro Cecconello
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Andrea Idili
- Department of Chemistry, University of Rome, Tor Vergata, via della Ricerca Scientifica, 00133, Rome, Italy
| | - Francesco Ricci
- Department of Chemistry, University of Rome, Tor Vergata, via della Ricerca Scientifica, 00133, Rome, Italy
| | - Itamar Willner
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| |
Collapse
|
10
|
Hu Y, Cecconello A, Idili A, Ricci F, Willner I. Triplex-DNA-Nanostrukturen: von grundlegenden Eigenschaften zu Anwendungen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701868] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Yuwei Hu
- Institute of Chemistry; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
| | | | - Andrea Idili
- Department of Chemistry; Universität Rom; Tor Vergata, via della Ricerca Scientifica 00133 Rom Italien
| | - Francesco Ricci
- Department of Chemistry; Universität Rom; Tor Vergata, via della Ricerca Scientifica 00133 Rom Italien
| | - Itamar Willner
- Institute of Chemistry; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
| |
Collapse
|
11
|
Khan ZUH, Khan A, Chen Y, Shah NS, Muhammad N, Khan AU, Tahir K, Khan FU, Murtaza B, Hassan SU, Qaisrani SA, Wan P. Biomedical applications of green synthesized Nobel metal nanoparticles. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2017; 173:150-164. [DOI: 10.1016/j.jphotobiol.2017.05.034] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 05/23/2017] [Accepted: 05/23/2017] [Indexed: 11/26/2022]
|
12
|
Wang S, Yue L, Shpilt Z, Cecconello A, Kahn JS, Lehn JM, Willner I. Controlling the Catalytic Functions of DNAzymes within Constitutional Dynamic Networks of DNA Nanostructures. J Am Chem Soc 2017. [DOI: 10.1021/jacs.7b04531] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Shan Wang
- Institute
of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Liang Yue
- Institute
of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Zohar Shpilt
- Institute
of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Alessandro Cecconello
- Institute
of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Jason S. Kahn
- Institute
of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Jean-Marie Lehn
- Institut
de Science et d’Ingénierie Supramoléculaires
(ISIS), University of Strasbourg, 8 Rue Gaspard Monge, Strasbourg 67000, France
| | - Itamar Willner
- Institute
of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| |
Collapse
|
13
|
Effect of the 3-halo substitution of the 2′-deoxy aminopyridinyl-pseudocytidine derivatives on the selectivity and stability of antiparallel triplex DNA with a CG inversion site. Bioorg Med Chem 2017; 25:3853-3860. [DOI: 10.1016/j.bmc.2017.05.035] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 05/12/2017] [Accepted: 05/16/2017] [Indexed: 11/23/2022]
|
14
|
Gasparyan SP, Alexanyan MV, Arutyunyan GK, Kocharov SL, Martirosyan AH, Tamazyan RA, Ayvazyan AG, Panosyan HA, Danagulyan GG. Synthesis of new derivatives of 5-(3,4-dihydro-2Н-pyrrol-5-yl)-pyrimidine. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2017. [DOI: 10.1134/s1070428016110166] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
15
|
Synthesis of tetrahydrofuran-based natural products and their carba analogs via stereoselective enzyme mediated Baeyer–Villiger oxidation. Tetrahedron 2016. [DOI: 10.1016/j.tet.2015.11.048] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
16
|
Bomb R, Heckle MR, Sun Y, Mancarella S, Guntaka RV, Gerling IC, Weber KT. Myofibroblast secretome and its auto-/paracrine signaling. Expert Rev Cardiovasc Ther 2016; 14:591-8. [PMID: 26818589 DOI: 10.1586/14779072.2016.1147348] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Myofibroblasts (myoFb) are phenotypically transformed, contractile fibroblast-like cells expressing α-smooth muscle actin microfilaments. They are integral to collagen fibrillogenesis with scar tissue formation at sites of repair irrespective of the etiologic origins of injury or tissue involved. MyoFb can persist long after healing is complete, where their ongoing turnover of collagen accounts for a progressive structural remodeling of an organ (a.k.a. fibrosis, sclerosis or cirrhosis). Such persistent metabolic activity is derived from a secretome consisting of requisite components in the de novo generation of angiotensin (Ang) II. Autocrine and paracrine signaling induced by tissue AngII is expressed via AT1 receptor ligand binding to respectively promote: i) regulation of myoFb collagen synthesis via the fibrogenic cytokine TGF-β1-Smad pathway; and ii) dedifferentiation and protein degradation of atrophic myocytes immobilized and ensnared by fibrillar collagen at sites of scarring. Several cardioprotective strategies in the prevention of fibrosis and involving myofibroblasts are considered. They include: inducing myoFb apoptosis through inactivation of antiapoptotic proteins; AT1 receptor antagonist to interfere with auto-/paracrine myoFb signaling or to induce counterregulatory expression of ACE2; and attacking the AngII-AT1R-TGF-β1-Smad pathway by antibody or the use of triplex-forming oligonucleotides.
Collapse
Affiliation(s)
- Ritin Bomb
- a Division of Cardiovascular Diseases , University of Tennessee Health Science Center , Memphis , TN , USA
| | - Mark R Heckle
- b Department of Medicine , University of Tennessee Health Science Center , Memphis , TN , USA
| | - Yao Sun
- a Division of Cardiovascular Diseases , University of Tennessee Health Science Center , Memphis , TN , USA
| | - Salvatore Mancarella
- c Department of Physiology , University of Tennessee Health Science Center , Memphis , TN , USA
| | - Ramareddy V Guntaka
- d Department of Microbiology, Immunology and Biochemistry , University of Tennessee Health Science Center , Memphis , TN , USA
| | - Ivan C Gerling
- e Division of Endocrinology , University of Tennessee Health Science Center , Memphis , TN , USA
| | - Karl T Weber
- a Division of Cardiovascular Diseases , University of Tennessee Health Science Center , Memphis , TN , USA
| |
Collapse
|
17
|
Kumar P, Sharma PK, Hansen J, Jedinak L, Reslow-Jacobsen C, Hornum M, Nielsen P. Three new double-headed nucleotides with additional nucleobases connected to C-5 of pyrimidines; synthesis, duplex and triplex studies. Bioorg Med Chem 2015; 24:742-9. [PMID: 26778611 DOI: 10.1016/j.bmc.2015.12.043] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 12/22/2015] [Accepted: 12/23/2015] [Indexed: 10/22/2022]
Abstract
In the search for double-coding DNA-systems, three new pyrimidine nucleosides, each coded with an additional nucleobase anchored to the major groove face, are synthesized. Two of these building blocks carry a thymine at the 5-position of 2'-deoxyuridine through a methylene linker and a triazolomethylene linker, respectively. The third building block carries an adenine at the 6-position of pyrrolo-2'-deoxycytidine through a methylene linker. These double-headed nucleosides are introduced into oligonucleotides and their effects on the thermal stabilities of duplexes are studied. All studied double-headed nucleotide monomers reduce the thermal stability of the modified duplexes, which is partially compensated by using consecutive incorporations of the modified monomers or by flanking the new double-headed analogs with members of our former series containing propyne linkers. Also their potential in triplex-forming oligonucleotides is studied for two of the new double-headed nucleotides as well as the series of analogs with propyne linkers. The most stable triplexes are obtained with single incorporations of additional pyrimidine nucleobases connected via the propyne linker.
Collapse
Affiliation(s)
- Pawan Kumar
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark
| | - Pawan K Sharma
- Department of Chemistry, Kurukshetra University, Kurukshetra 136 119, India
| | - Jonas Hansen
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark
| | - Lukas Jedinak
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark
| | - Charlotte Reslow-Jacobsen
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark
| | - Mick Hornum
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark
| | - Poul Nielsen
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark.
| |
Collapse
|
18
|
Rieck M, Schumacher-Schuh AF, Callegari-Jacques SM, Altmann V, Schneider Medeiros M, Rieder CR, Hutz MH. Is there a role for ADORA2A polymorphisms in levodopa-induced dyskinesia in Parkinson's disease patients? Pharmacogenomics 2015; 16:573-82. [PMID: 25872644 DOI: 10.2217/pgs.15.23] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
AIM Levodopa is first line treatment of Parkinson's disease (PD). However, its use is associated with the presence of motor fluctuations and dyskinesias. In recent years, adenosine A2A receptor (A2AR) is rising as a therapeutic target for PD. The aim of the present study was to investigate whether ADORA2A is associated with levodopa adverse effects. PATIENTS & METHODS Two hundred and eight PD patients on levodopa therapy were investigated. rs2298383 and rs3761422 at the ADORA2A gene were genotyped by allelic discrimination assays. RESULTS A trend for association was observed for both polymorphism and diplotypes with dyskinesia. CONCLUSION The present results should be considered as positive preliminary evidence. Further studies are needed to determine the association between ADORA2A and dyskinesia. Original submitted 3 December 2014; Revision submitted 13 February 2015.
Collapse
Affiliation(s)
- Mariana Rieck
- Departmento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Caixa postal 15053, Porto Alegre, RS, 91501-970, Brazil
| | | | | | | | | | | | | |
Collapse
|
19
|
Unlocked nucleic acids: implications of increased conformational flexibility for RNA/DNA triplex formation. Biochem J 2015; 464:203-11. [PMID: 25226286 DOI: 10.1042/bj20141023] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Unlocked nucleic acids (UNAs) have been introduced at specific positions in short model DNA hairpins and RNA/DNA triplexes for the first time. UNA residues destabilize the hairpins and decrease triplex thermodynamic stability or suppress triplex formation for most of the evaluated structures. Nevertheless, the incorporation of UNA residues at certain positions of dsDNA was found to be energetically favourable or at least did not affect triplex stability. Notably, the most thermodynamically stable UNA-modified triplexes exhibited improved stability at both acidic and physiological pH. The specificity of the interactions between the triplex-forming oligonucleotide and dsDNA was characterized using EMSA for the most thermodynamically stable structures, and triplex dissociation constants were determined. One of the modified triplexes exhibited an improved Kd in comparison with the unmodified triplex. CD and thermal difference spectra indicated that UNA residues do not alter the overall structure of the most thermodynamically stable triplexes. In addition, incubation of the modified oligonucleotides with human serum indicated that the UNAs demonstrate the potential to improve the biological stability of nucleic acids.
Collapse
|
20
|
Liang W, Zhang W, Zhao S, Li Q, Yang Y, Liang H, Ceng R. A study of the ultrasound-targeted microbubble destruction based triplex-forming oligodexinucleotide delivery system to inhibit tissue factor expression. Mol Med Rep 2014; 11:903-9. [PMID: 25355395 PMCID: PMC4262506 DOI: 10.3892/mmr.2014.2822] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 07/21/2014] [Indexed: 12/20/2022] Open
Abstract
The efficiency of cellular uptake of triplex‑forming oligodexinucleotides (TFO), and the inhibition of tissue factor (TF) is low. The aim of the present study was to improve the absorption of TFO, and increase the inhibition of TF induced by shear stress both in vitro and in vivo, by using an ultrasound‑targeted microbubble destruction (UTMD)‑based delivery system. TFO‑conjugated lipid ultrasonic microbubbles (TFO‑M) were first constructed and characterised. The absorption of TFO was observed by a fluorescence‑based method, and the inhibition of TF by immunofluorescence and quantitative polymerase chain reaction. ECV304 human umbilical vein endothelial cells were subjected to fluid shear stress for 6 h after treatment with TFO conjugated lipid ultrasonic microbubbles without sonication (TFO‑M group); TFO alone; TFO conjugated lipid ultrasonic microbubbles, plus immediate sonication (TFO+U group and TFO‑M+U group); or mock treated with 0.9% NaCl only (SSRE group). The in vivo experiments were established in a similar manner to the in vitro experiments, except that TFO or TFO‑M was injected into rats through the tail vein. Six hours after the preparation of a carotid stenosis model, the rats were humanely sacrificed. The transfection efficiency of TFO in the TFO‑M+U group was higher as compared with the TFO‑M and TFO+U group (P<0.01). The protein and mRNA expression of TF in the TFO‑M+U group was significantly decreased both in vitro and in vivo (P<0.01), as compared with the TFO‑M, TFO+U and SSRE groups. The UTMD‑based TFO delivery system promoted the -absorption of TFO and the inhibition of TF, and was therefore considered to be favorable for preventing thrombosis induced by shear stress.
Collapse
Affiliation(s)
- Weihua Liang
- Department of Neurology, Xinqiao Hospital, The Third Military Medical University, Chongqing 400038, P.R. China
| | - Weiwei Zhang
- Deparment of Neurology, General Hospital of Beijing PLA Military Region, Beijing 100700, P.R. China
| | - Shifu Zhao
- Department of Neurology, Xinqiao Hospital, The Third Military Medical University, Chongqing 400038, P.R. China
| | - Qianning Li
- Department of Neurology, Xinqiao Hospital, The Third Military Medical University, Chongqing 400038, P.R. China
| | - Yiming Yang
- Department of Internal Medicine, The Sixteenth Hospital of PLA, Altay, Xinjiang 836500, P.R. China
| | - Hua Liang
- Department of Internal Medicine, 66083 Clinic of Beijing Military Region, Beijing 102488, P.R. China
| | - Rongchuan Ceng
- Department of Neurology, Xinqiao Hospital, The Third Military Medical University, Chongqing 400038, P.R. China
| |
Collapse
|
21
|
Huo S, Jin S, Ma X, Xue X, Yang K, Kumar A, Wang PC, Zhang J, Hu Z, Liang XJ. Ultrasmall gold nanoparticles as carriers for nucleus-based gene therapy due to size-dependent nuclear entry. ACS NANO 2014; 8:5852-62. [PMID: 24824865 PMCID: PMC4076024 DOI: 10.1021/nn5008572] [Citation(s) in RCA: 255] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 05/13/2014] [Indexed: 05/19/2023]
Abstract
The aim of this study was to determine the size-dependent penetration ability of gold nanoparticles and the potential application of ultrasmall gold nanoparticles for intranucleus delivery and therapy. We synthesized gold nanoparticles with diameters of 2, 6, 10, and 16 nm and compared their intracellular distribution in MCF-7 breast cancer cells. Nanoparticles smaller than 10 nm (2 and 6 nm) could enter the nucleus, whereas larger ones (10 and 16 nm) were found only in the cytoplasm. We then investigated the possibility of using ultrasmall 2 nm nanoparticles as carriers for nuclear delivery of a triplex-forming oligonucleotide (TFO) that binds to the c-myc promoter. Compared to free TFO, the nanoparticle-conjugated TFO was more effective at reducing c-myc RNA and c-myc protein, which resulted in reduced cell viability. Our result demonstrated that the entry of gold nanoparticles into the cell nucleus is critically dependent on the size of the nanoparticles. We developed a strategy for regulating gene expression, by directly delivering TFOs into the nucleus using ultrasmall gold nanoparticles. More importantly, guidelines were provided to choose appropriate nanocarriers for different biomedical purposes.
Collapse
Affiliation(s)
- Shuaidong Huo
- Chinese Academy of Sciences (CAS) Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, No.11, First North Road, Zhongguancun, Beijing, China 100190
- University of Chinese Academy of Sciences, Beijing, China 100049
| | - Shubin Jin
- Chinese Academy of Sciences (CAS) Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, No.11, First North Road, Zhongguancun, Beijing, China 100190
- University of Chinese Academy of Sciences, Beijing, China 100049
| | - Xiaowei Ma
- Chinese Academy of Sciences (CAS) Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, No.11, First North Road, Zhongguancun, Beijing, China 100190
- University of Chinese Academy of Sciences, Beijing, China 100049
| | - Xiangdong Xue
- Chinese Academy of Sciences (CAS) Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, No.11, First North Road, Zhongguancun, Beijing, China 100190
- University of Chinese Academy of Sciences, Beijing, China 100049
| | - Keni Yang
- Chinese Academy of Sciences (CAS) Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, No.11, First North Road, Zhongguancun, Beijing, China 100190
| | - Anil Kumar
- Chinese Academy of Sciences (CAS) Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, No.11, First North Road, Zhongguancun, Beijing, China 100190
| | - Paul C. Wang
- Molecular Imaging Laboratory, Department of Radiology, Howard University, Washington D.C. 20060, United States
| | - Jinchao Zhang
- College of Chemistry & Environmental Science, Chemical Biology Key Laboratory of Hebei Province, Hebei University, Baoding, China
| | - Zhongbo Hu
- University of Chinese Academy of Sciences, Beijing, China 100049
- Address correspondence to ,
| | - Xing-Jie Liang
- Chinese Academy of Sciences (CAS) Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, No.11, First North Road, Zhongguancun, Beijing, China 100190
- Address correspondence to ,
| |
Collapse
|
22
|
Abstract
The syncytium of cardiomyocytes in the heart is tethered within a matrix composed principally of type I fibrillar collagen. The matrix has diverse mechanical functions that ensure the optimal contractile efficiency of this muscular pump. In the diseased heart, cardiomyocytes are lost to necrotic cell death, and phenotypically transformed fibroblast-like cells-termed 'myofibroblasts'-are activated to initiate a 'reparative' fibrosis. The structural integrity of the myocardium is preserved by this scar tissue, although at the expense of its remodelled architecture, which has increased tissue stiffness and propensity to arrhythmias. A persisting population of activated myofibroblasts turns this fibrous tissue into a living 'secretome' that generates angiotensin II and its type 1 receptor, and fibrogenic growth factors (such as transforming growth factor-β), all of which collectively act as a signal-transducer-effector signalling pathway to type I collagen synthesis and, therefore, fibrosis. Persistent myofibroblasts, and the resultant fibrous tissue they produce, cause progressive adverse myocardial remodelling, a pathological hallmark of the failing heart irrespective of its etiologic origin. Herein, we review relevant cellular, subcellular, and molecular mechanisms integral to cardiac fibrosis and consequent remodelling of atria and ventricles with a heterogeneity in cardiomyocyte size. Signalling pathways that antagonize collagen fibrillogenesis provide novel strategies for cardioprotection.
Collapse
|
23
|
Marcélis L, Ghesquière J, Garnir K, Kirsch-De Mesmaeker A, Moucheron C. Photo-oxidizing RuII complexes and light: Targeting biomolecules via photoadditions. Coord Chem Rev 2012. [DOI: 10.1016/j.ccr.2012.02.012] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
24
|
Govan JM, Uprety R, Hemphill J, Lively MO, Deiters A. Regulation of transcription through light-activation and light-deactivation of triplex-forming oligonucleotides in mammalian cells. ACS Chem Biol 2012; 7:1247-56. [PMID: 22540192 DOI: 10.1021/cb300161r] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Triplex-forming oligonucleotides (TFOs) are efficient tools to regulate gene expression through the inhibition of transcription. Here, nucleobase-caging technology was applied to the temporal regulation of transcription through light-activated TFOs. Through site-specific incorporation of caged thymidine nucleotides, the TFO:DNA triplex formation is blocked, rendering the TFO inactive. However, after a brief UV irradiation, the caging groups are removed, activating the TFO and leading to the inhibition of transcription. Furthermore, the synthesis and site-specific incorporation of caged deoxycytidine nucleotides within TFO inhibitor sequences was developed, allowing for the light-deactivation of TFO function and thus photochemical activation of gene expression. After UV-induced removal of the caging groups, the TFO forms a DNA dumbbell structure, rendering it inactive, releasing it from the DNA, and activating transcription. These are the first examples of light-regulated TFOs and their application in the photochemical activation and deactivation of gene expression. In addition, hairpin loop structures were found to significantly increase the efficacy of phosphodiester DNA-based TFOs in tissue culture.
Collapse
Affiliation(s)
- Jeane M. Govan
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina
27695, United States
| | - Rajendra Uprety
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina
27695, United States
| | - James Hemphill
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina
27695, United States
| | - Mark O. Lively
- Center
for Structural Biology, Wake Forest University School of Medicine, Winston-Salem,
North Carolina 27157, United States
| | - Alexander Deiters
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina
27695, United States
| |
Collapse
|
25
|
Selim ME, Hendi AA. Gold Nanoparticles Induce Apoptosis in MCF-7 Human Breast Cancer Cells. Asian Pac J Cancer Prev 2012; 13:1617-20. [DOI: 10.7314/apjcp.2012.13.4.1617] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
26
|
Kanamori T, Masaki Y, Mizuta M, Tsunoda H, Ohkubo A, Sekine M, Seio K. DNA duplexes and triplex-forming oligodeoxynucleotides incorporating modified nucleosides forming stable and selective triplexes. Org Biomol Chem 2011; 10:1007-13. [PMID: 22146807 DOI: 10.1039/c1ob06411h] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have previously reported DNA triplexes containing the unnatural base triad G-PPI·C3, in which PPI is an indole-fused cytosine derivative incorporated into DNA duplexes and C3 is an abasic site in triplex-forming oligonucleotides (TFOs) introduced by a propylene linker. In this study, we developed a new unnatural base triad A-ψ·C(R1) where ψ and C(R1) are base moieties 2'-deoxypseudouridine and 5-substituted deoxycytidine, respectively. We examined several electron-withdrawing substituents for R1 and found that 5-bromocytosine (C(Br)) could selectively recognize ψ. In addition, we developed a new PPI derivative, PPI(Me), having a methyl group on the indole ring in order to achieve selective triplex formation between DNA duplexes incorporating various Watson-Crick base pairs, such as T-A, C-G, A-ψ, and G-PPI(Me), and TFOs containing T, C, C(Br), and C3. We studied the selective triplex formation between these duplexes and TFOs using UV-melting and gel mobility shift assays.
Collapse
|
27
|
Nyakas A, Stucki SR, Schürch S. Tandem mass spectrometry of modified and platinated oligoribonucleotides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:875-887. [PMID: 21472522 DOI: 10.1007/s13361-011-0106-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Revised: 02/04/2011] [Accepted: 02/09/2011] [Indexed: 05/30/2023]
Abstract
Therapeutic approaches for treatment of various diseases aim at the interruption of transcription or translation. Modified oligonucleotides, such as 2'-O-methyl- and methylphosphonate-derivatives, exhibit high resistance against cellular nucleases, thus rendering application for, e.g., antigene or antisense purposes possible. Other approaches are based on administration of cross-linking agents, such as cis-diamminedichloroplatinum(II) (cisplatin, DDP), which is still the most widely used anticancer drug worldwide. Due to the formation of 1,2-intrastrand cross links at adjacent guanines, replication of the double-strand is disturbed, thus resulting in significant cytotoxicity. Evidence for the gas-phase dissociation mechanism of platinated RNA is given, based on nano-electrospray ionization high-resolution multistage tandem mass spectrometry (MS(n)). Confirmation was found by investigating the fragmentation pattern of platinated and unplatinated 2'-methoxy oligoribonucleotide hexamers and their corresponding methylphosphonate derivatives. Platinated 2'-methoxy oligoribonucleotides exhibit a similar gas-phase dissociation behavior as the corresponding DNA and RNA sequences, with the 3'-C-O bond adjacent to the vicinal guanines being cleaved preferentially, leading to w(x)-ion formation. By examination of the corresponding platinated methylphosphonate derivatives of the 2'-methoxy oligoribonucleotides, the key role of the negatively charged phosphate oxygen atoms in direct proximity to the guanines was proven. The significant alteration of fragmentation due to platination is demonstrated by comparison of the fragment ion patterns of unplatinated and platinated 2'-O-methyl- and 2'-O-methyl methylphosphonate oligoribonucleotides, and the results obtained by H/D exchange experiments.
Collapse
Affiliation(s)
- Adrien Nyakas
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | | | | |
Collapse
|
28
|
Capek I. Dispersions based on noble metal nanoparticles-DNA conjugates. Adv Colloid Interface Sci 2011; 163:123-43. [PMID: 21382609 DOI: 10.1016/j.cis.2011.02.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Revised: 02/15/2011] [Accepted: 02/15/2011] [Indexed: 10/18/2022]
Abstract
Many biomolecules have specific binding properties in the nanostructure formation; they are attractive materials for nanotechnology. One such promising construction material for growing a well-defined nanostructure is deoxyribonucleic acid, due to its π-electron hydrophobic core and predictable recognition attributed to the specificity of Watson-Crick base-pairing. Hydrogen bonding provides the specificity behind the matching of complementary pairs of single-stranded (ss) DNA to hybridize into a double strand (ds) of helical DNA. The double-helical structure of DNA is determined by a subtle balance of noncovalent interactions among the DNA building blocks. The most prominent role is played by the interactions between the DNA bases, where two binding motifs can be recognized: planar hydrogen bonding and vertical stacking. DNA-based nanotechnology has generated interest in a number of applications due to the specificity, programmability, and reproducibility of DNA interaction with noble metal nanoparticles. 5' and 3' thiol moieties are used to prepare composite DNAs, DNA-gold nanoparticle conjugates and nanostructures with a variety of nanoparticle-based DNA assays. Particularly, color changes induced by the association of nanometer-sized gold particles provide a basis of a simple yet highly selective method for detecting specific biological reactions between anchored ligand molecules and receptor molecules in the milieu. Colloidal noble metal nanoparticles, in particular, have found application in a variety of assay formats in which analyte binding is coupled to particle adsorption. The extreme sensitivity of the bandwidth, the peak height, and the position of the absorption (or scattering) maximum of surface plasmon resonance spectra to environmental changes have prompted the development of approaches directly monitor the DNA hybridization. The same features that make DNA an effective molecule for the storage of genetic information also render it useful as an engineering material for the construction of smart objects at the nanometer scale because of its ability to self organize into desired structures via the specific hybridization of complementary sequences. Biocompatibility between gold nanomaterials and biological scaffolding is crucial to the development of smart biomaterials. These DNA/metal colloids are interesting for their fundamental properties as well as for applications in nanomaterials science and nanobiotechnology.
Collapse
|
29
|
Cao SQ, Okamoto I, Tsunoda H, Ohkubo A, Seio K, Sekine M. Synthesis and triplex-forming properties of oligonucleotides containing thio-substituted C-nucleoside 4-thiopseudoisocytidine. Tetrahedron Lett 2011. [DOI: 10.1016/j.tetlet.2010.11.065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
30
|
Koilan S, Hamilton D, Baburyan N, Padala MK, Weber KT, Guntaka RV. Prevention of liver fibrosis by triple helix-forming oligodeoxyribonucleotides targeted to the promoter region of type I collagen gene. Oligonucleotides 2010; 20:231-7. [PMID: 20818932 PMCID: PMC2957239 DOI: 10.1089/oli.2010.0244] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2010] [Accepted: 07/21/2010] [Indexed: 12/25/2022]
Abstract
Hepatic fibrosis leading to cirrhosis remains a global health problem. The most common etiologies are alcoholism and viral infections. Liver fibrosis is associated with major changes in both quantity and composition of extracellular matix and leads to disorganization of the liver architecture and irreversible damage to the liver function. As of now there is no effective therapy to control fibrosis. The end product of fibrosis is abnormal synthesis and accumulation of type I collagen in the extracellular matrix, which is produced by activated stellate or Ito cells in the damaged liver. Therefore, inhibition of transcription of type I collagen should in principle inhibit its production and accumulation in liver. Normally, DNA exists in a duplex form. However, under some circumstances, DNA can assume triple helical (triplex) structures. Intermolecular triplexes, formed by the addition of a sequence-specific third strand to the major groove of the duplex DNA, have the potential to serve as selective gene regulators. Earlier, we demonstrated efficient triplex formation between the exogenously added triplex-forming oligodeoxyribonucleotides (TFOs) and a specific sequence in the promoter region of the COL1A1 gene. In this study we used a rat model of liver fibrosis, induced by dimethylnitrosamine, to test whether these TFOs prevent liver fibrosis. Our results indicate that both the 25-mer and 18-mer TFOs, specific for the upstream nucleotide sequence from -141 to -165 (relative to the transcription start site) in the 5' end of collagen gene promoter, effectively prevented accumulation of liver collagen and fibrosis. We also observed improvement in liver function tests. However, mutations in the TFO that eliminated formation of triplexes are ineffective in preventing fibrosis. We believe that these TFOs can be used as potential antifibrotic therapeutic molecules.
Collapse
Affiliation(s)
- Subramaniyan Koilan
- Department of Molecular Sciences, The University of Tennessee Health Science Center, Memphis, Tennessee
| | - David Hamilton
- Department of Comparative Medicine, The University of Tennessee Health Science Center, Memphis, Tennessee
| | - Narina Baburyan
- Department of Molecular Sciences, The University of Tennessee Health Science Center, Memphis, Tennessee
| | - Mythili K. Padala
- Department of Molecular Sciences, The University of Tennessee Health Science Center, Memphis, Tennessee
| | - Karl T. Weber
- Department of Medicine, The University of Tennessee Health Science Center, Memphis, Tennessee
| | - Ramareddy V. Guntaka
- Department of Molecular Sciences, The University of Tennessee Health Science Center, Memphis, Tennessee
| |
Collapse
|
31
|
Hohoff C, Mullings EL, Heatherley SV, Freitag CM, Neumann LC, Domschke K, Krakowitzky P, Rothermundt M, Keck ME, Erhardt A, Unschuld PG, Jacob C, Fritze J, Bandelow B, Maier W, Holsboer F, Rogers PJ, Deckert J. Adenosine A(2A) receptor gene: evidence for association of risk variants with panic disorder and anxious personality. J Psychiatr Res 2010; 44:930-7. [PMID: 20334879 DOI: 10.1016/j.jpsychires.2010.02.006] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Revised: 02/02/2010] [Accepted: 02/03/2010] [Indexed: 11/19/2022]
Abstract
Adenosine A(2A) receptors are suggested to play an important role in different brain circuits and pathways involved in anxiety reactions. A variant within the corresponding ADORA2A gene (rs5751876) increased the risk for panic disorder (PD), for elevated anxiety during challenge tests in healthy probands and for anxiety-related arousal in blood-injury phobia. These multiple effects may mirror a more general effect of the SNP on basic personality traits. In the present study we therefore aimed to replicate the original finding in a large PD sample and extend it by investigating an additional proband sample characterized for different anxiety-related personality scores. In addition, as rs5751876 is assumed not to be the disease variant itself but to be in linkage disequilibrium (LD) with the true functional polymorphism other SNPs of potentially functional relevance were identified by re-sequencing the whole gene including several newly identified regions of putative regulatory potential and analysed for their impact on PD and anxious personality. We were indeed able to replicate rs5751876 as risk factor for PD, particularly PD with agoraphobia. Rs5751876 and several other variants in high LD (rs5751862, rs2298383 and rs3761422) as well as the corresponding haplotypes were also associated with different anxiety-related personality scores (Bonferroni corrected P(all) < 0.05). Of these variants, rs2298383 shows functional potential based on in silico analyses and might therefore represent the true underlying causal variant. Our data provide further support for an important role of ADORA2A variants in the pathogenesis of anxiety disorders and anxious personality reflecting their potential as basic susceptibility factors.
Collapse
Affiliation(s)
- Christa Hohoff
- Department of Psychiatry, University of Muenster, Albert-Schweitzer-Strasse 11, 48149 Muenster, Germany.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Ye S, Li H, Cao W. Electrogenerated chemiluminescence detection of adenosine based on triplex DNA biosensor. Biosens Bioelectron 2010; 26:2215-20. [PMID: 20947334 DOI: 10.1016/j.bios.2010.09.037] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Revised: 09/19/2010] [Accepted: 09/21/2010] [Indexed: 10/19/2022]
Abstract
A novel electrogenerated chemiluminescence (ECL) biosensor based on the construction of triplex DNA for the detection of adenosine was designed. The ECL biosensor employs an aptamer as a molecular recognition element, and quenches ECL of tris(2,2'-bipyridine) ruthenium (Ru(bpy)(3)(2+)) by ferrocenemonocarboxylic acid (FcA). Through self-assembly technology, the ECL probe of thiolated hairpin adenosine aptamer tagged was self-assembled onto the surface of a gold electrode with an ECL signal producer Ru(bpy)(3)(2+) derivative (Ru-DNA-1). The adenosine aptamer, including a section of triplex characteristic chain, formatted triplex DNA with two other DNAs (DNA-2, Fc-DNA-3) in the presence of triplex DNA binder coralyne chloride (CORA). Fc-DNA-3 was tagged with an ECL quencher ferrocenemonocarboxylic acid (FcA), a quenching probe. In the presence of adenosine, the aptamer sequence (Ru-DNA-1) prefers to form the aptamer-adenosine complex with hairpin configuration and the switch of the DNA-1 occurs in conjunction with the generation of a strong ECL signal owing to the dissociation of a quenching probe. Meanwhile, a control experiment was performed; the ECL-duplex biosensor was designed to detect adenosine. The detection limits were 2.7×10(-10) mol L(-1) and 2.3×10(-9) mol L(-1) for the ECL-triplex DNA biosensor and ECL-duplex DNA biosensor, respectively, which demonstrated that the ECL-triplex DNA biosensor improved the sensitivity and specificity greatly.
Collapse
Affiliation(s)
- Sujuan Ye
- State Key Laboratory Base of Eco-chemical Engineering, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | | | | |
Collapse
|
33
|
Tsai TL, Shieh DB, Yeh CS, Tzeng Y, Htet K, Chuang KS, Hwu JR, Su WC. The down regulation of target genes by photo activated DNA nanoscissors. Biomaterials 2010; 31:6545-54. [DOI: 10.1016/j.biomaterials.2010.04.058] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2010] [Accepted: 04/29/2010] [Indexed: 01/24/2023]
|
34
|
Srisawat C, Engelke DR. Selection of RNA aptamers that bind HIV-1 LTR DNA duplexes: strand invaders. Nucleic Acids Res 2010; 38:8306-15. [PMID: 20693539 PMCID: PMC3001068 DOI: 10.1093/nar/gkq696] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
RNA that can specifically bind to double-stranded DNA is of interest because it might be used as a means to regulate transcription of the target genes. To explore possible interactions between RNA and duplex DNA, we selected for RNA aptamers that can bind to the long terminal repeats (LTRs) of human immunodeficiency virus type 1 DNA. The selected aptamers were classified into four major groups based on the consensus sequences, which were found to locate in the non-stem regions of the predicted RNA secondary structures, consistent with roles in target binding. Analysis of the aptamer consensus sequences suggested that the conserved segments could form duplexes via Watson–Crick base-pairing with preferred sequences in one strand of the DNA, assuming the aptamer invaded the duplex. The aptamer binding sites on the LTR were experimentally determined to be located preferentially at these sites near the termini of double-stranded target DNA, despite selection schemes that were designed to minimize preferences for termini. The results presented here show that aptamer RNAs can be selected in vitro that strand-invade at preferred DNA duplex sequences to form stable complexes.
Collapse
Affiliation(s)
- Chatchawan Srisawat
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkoknoi, Bangkok 10700, Thailand
| | | |
Collapse
|
35
|
Martirosyan A, Tamazyan R, Gasparyan S, Alexanyan M, Panosyan H, Martirosyan V, Schinazi R. Synthesis of 6-imino-5-tetrahydro-1H-2-pyrrolylidenhexahydro-2,4-pyrimidinediones as intermediates for the synthesis of C-azanucleosides. Tetrahedron Lett 2010. [DOI: 10.1016/j.tetlet.2009.11.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
36
|
Bonnac L, Lee SE, Giuffredi GT, Elphick LM, Anderson AA, Child ES, Mann DJ, Gouverneur V. Synthesis and O-phosphorylation of 3,3,4,4-tetrafluoroaryl-C-nucleoside analogues. Org Biomol Chem 2010; 8:1445-54. [DOI: 10.1039/b922442d] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
37
|
Lu J, Li NS, Koo SC, Piccirilli JA. Synthesis of Pyridine, Pyrimidine and Pyridinone C-Nucleoside Phosphoramidites for Probing Cytosine Function in RNA. J Org Chem 2009; 74:8021-30. [DOI: 10.1021/jo9016919] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jun Lu
- Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biology and Department of Chemistry, University of Chicago, 929 East 57th Street, Chicago, Illinois 60637
| | - Nan-Sheng Li
- Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biology and Department of Chemistry, University of Chicago, 929 East 57th Street, Chicago, Illinois 60637
| | - Selene C. Koo
- Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biology and Department of Chemistry, University of Chicago, 929 East 57th Street, Chicago, Illinois 60637
| | - Joseph A. Piccirilli
- Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biology and Department of Chemistry, University of Chicago, 929 East 57th Street, Chicago, Illinois 60637
| |
Collapse
|
38
|
Nano and microtechnologies for the delivery of oligonucleotides with gene silencing properties. Molecules 2009; 14:2801-23. [PMID: 19701125 PMCID: PMC6255434 DOI: 10.3390/molecules14082801] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Revised: 07/22/2009] [Accepted: 07/27/2009] [Indexed: 01/13/2023] Open
Abstract
Oligonucleotides (ONs) are synthetic fragments of nucleic acid designed to modulate the expression of target proteins. DNA-based ONs (antisense, antigene, aptamer or decoy) and more recently a new class of RNA-based ONs, the small interfering RNAs (siRNAs), have gained great attention for the treatment of different disease states, such as viral infections, inflammation, diabetes, and cancer. However, the development of therapeutic strategies based on ONs is hampered by their low bioavailability, poor intracellular uptake and rapid degradation in biological fluids. The use of a non-viral carrier can be a powerful tool to overcome these drawbacks. Lipid or polymer-based nanotechnologies can improve biological stability and cellular uptake of ONs, with possibility of tissue and/or cellular targeting. The use of polymeric devices can also produce a prolonged release of the ON, thus reducing the need of frequent administrations. This review summarizes advantages and issues related to the main non-viral vectors used for ON delivery.
Collapse
|
39
|
Rakotondradany F, Sleiman H, Whitehead MA. Hydrogen-bond self-assembly of DNA-base analogues — Experimental results. CAN J CHEM 2009. [DOI: 10.1139/v09-028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A novel biomimetic DNA analogue with fluorescence has been synthesized to generate functional supramolecular architectures. Experimental studies show that triaminopyrimidine nucleoside (2) undergoes a sterically controlled self-assembly into hydrogen-bonded linear tapes and hexameric rosettes. Self-association of the hydrogen-bonded triaminopyrimidine–cyanuric acid complex into elongated, rodlike nanostructures was shown by dynamic light scattering and transmission electron microscopy, suggesting hierarchical formation of higher-order, π-stacked assemblies. The hydrogen-bond self-assembly of the DNA analogue decreased the fluorescence of the nucleosides. This guest-induced fluorescence quenching can be used to develop DNA-hybridization probes. MM+ molecular modelling and semi-empirical molecular orbital PM3 calculations (1) predicted the incorporation of triaminopyrimidine nucleoside into new types of artificial DNA strands and triplex formation with natural, complementary DNA strands containing thymine (1).
Collapse
Affiliation(s)
- Felaniaina Rakotondradany
- Department of Chemistry, McGill University, Otto Maass Chemistry Building, 801 Sherbrooke St. West, Montreal, QC H3A 2K6, Canada
- Imperial Oil Resources, Oil Sands Development and Research, 3535 Research Road NW, Calgary, AB T2L 2K8, Canada
| | - Hanadi Sleiman
- Department of Chemistry, McGill University, Otto Maass Chemistry Building, 801 Sherbrooke St. West, Montreal, QC H3A 2K6, Canada
- Imperial Oil Resources, Oil Sands Development and Research, 3535 Research Road NW, Calgary, AB T2L 2K8, Canada
| | - M. A. Whitehead
- Department of Chemistry, McGill University, Otto Maass Chemistry Building, 801 Sherbrooke St. West, Montreal, QC H3A 2K6, Canada
- Imperial Oil Resources, Oil Sands Development and Research, 3535 Research Road NW, Calgary, AB T2L 2K8, Canada
| |
Collapse
|
40
|
The First Postsynthetic 5′-5′ Intercalators in Triplex DNA - Solid-Phase PostsyntheticSonogashiraReaction and Homocouplings on Arylacetylenes. Helv Chim Acta 2009. [DOI: 10.1002/hlca.200800397] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
41
|
Okamoto I, Cao S, Tanaka H, Seio K, Sekine M. Synthesis of 4-Thiopseudoisocytidine and 4-Thiopseudouridine as Components of Triplex-forming Oligonucleotides. CHEM LETT 2009. [DOI: 10.1246/cl.2009.174] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
42
|
Using an aryl phenanthroimidazole moiety as a conjugated flexible intercalator to improve the hybridization efficiency of a triplex-forming oligonucleotide. Bioorg Med Chem 2008; 16:9937-47. [PMID: 18977149 DOI: 10.1016/j.bmc.2008.10.037] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2008] [Revised: 10/03/2008] [Accepted: 10/12/2008] [Indexed: 11/23/2022]
Abstract
When inserting 2-phenyl or 2-naphth-1-yl-phenanthroimidazole intercalators (X and Y, respectively) as bulges into triplex-forming oligonucleotides, both intercalators show extraordinary high thermal stability of the corresponding Hoogsteen-type triplexes and Hoogsteen-type parallel duplexes with high discrimination to Hoogsteen mismatches. Molecular modeling shows that the phenyl or the naphthyl ring stacks with the nucleobases in the TFO, while the phenanthroimidazol moiety stacks with the base pairs of the dsDNA. DNA-strands containing the intercalator X show higher thermal triplex stability than DNA-strands containing the intercalator Y. The difference can be explained by a lower degree of planarity of the intercalator in the case of naphthyl. It was also observed that triplex stability was considerably reduced when the intercalators X or Y was replaced by 2-(naphthlen-1-yl)imidazole. This confirms intercalation as the important factor for triplex stabilization and it rules out an alternative complexation of protonated imidazole with two phosphate groups. The intercalating nucleic acid monomers X and Y were obtained via a condensation reaction of 9,10-phenanthrenequinone (4) with (S)-4-(2-(2,2-dimethyl-1,3-dioxolan-4-yl)ethoxy)benzaldehyde (3a) or (S)-4-(2-(2,2-dimethyl-1,3-dioxolan-4-yl)ethoxy)-1-naphthaldehyde (3b), respectively, in the presence of acetic acid and ammonium acetate. The required monomers for DNA synthesis using amidite chemistry were obtained by standard deprotection of the hydroxy groups followed by 4,4'-dimethoxytritylation and phosphitylation.
Collapse
|
43
|
Ye Z, Houssein HSH, Mahato RI. Bioconjugation of oligonucleotides for treating liver fibrosis. Oligonucleotides 2008; 17:349-404. [PMID: 18154454 DOI: 10.1089/oli.2007.0097] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Liver fibrosis results from chronic liver injury due to hepatitis B and C, excessive alcohol ingestion, and metal ion overload. Fibrosis culminates in cirrhosis and results in liver failure. Therefore, a potent antifibrotic therapy is urgently needed to reverse scarring and eliminate progression to cirrhosis. Although activated hepatic stellate cells (HSCs) remain the principle cell type responsible for liver fibrosis, perivascular fibroblasts of portal and central veins as well as periductular fibroblasts are other sources of fibrogenic cells. This review will critically discuss various treatment strategies for liver fibrosis, including prevention of liver injury, reduction of inflammation, inhibition of HSC activation, degradation of scar matrix, and inhibition of aberrant collagen synthesis. Oligonucleotides (ODNs) are short, single-stranded nucleic acids, which disrupt expression of target protein by binding to complementary mRNA or forming triplex with genomic DNA. Triplex forming oligonucleotides (TFOs) provide an attractive strategy for treating liver fibrosis. A series of TFOs have been developed for inhibiting the transcription of alpha1(I) collagen gene, which opens a new area for antifibrotic drugs. There will be in-depth discussion on the use of TFOs and how different bioconjugation strategies can be utilized for their site-specific delivery to HSCs or hepatocytes for enhanced antifibrotic activities. Various insights developed in individual strategy and the need for multipronged approaches will also be discussed.
Collapse
Affiliation(s)
- Zhaoyang Ye
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | | | | |
Collapse
|
44
|
Abstract
We have previously demonstrated site-specific delivery of antiparallel phosphorothioate triplex forming oligonucleotide (TFO) specific to -165 to -141 promoter region of alpha1(I) collagen (abbreviated as APS165) to hepatic stellate cells (HSCs) of fibrotic rats after conjugation with mannose 6-phosphate-bovine serum albumin. However, we still need to determine whether there is correlation between transcription inhibition and triplex formation with genomic DNA. In this study, APS165 was modified with psoralen and the extent of triplex formation with alpha1(I) collagen DNA was determined in naked genomic DNA, isolated nuclei of HSC-T6 cells and whole cells by using a simple real-time PCR based method. In this method, a purification step was added to remove unbound APS165, which eliminated the possible artifacts during real-time PCR. Psoralen photoadduct formation was shown to be essential to retain triplex structure under denaturing conditions. On naked genomic DNA, 82.2% of DNA formed triplex and 36.7% of genomic DNA in isolated nuclei at 90 min contained triplex structure. As quantified by real-time PCR, 50% of genomic DNA in living cells at 12 h postincubation contained triplex structures. Furthermore, the triplex formation was dose-dependent with 26.5% and 50% of DNA having triplex structure at concentrations of 1 microM and 5 microM, respectively. Moreover, on a plasmid pCol-CAT220 containing rat alpha1(I) gene promoter (-225 to +113), 75.3% of triplex formation was observed, which was correlated with a 73.6% of transcription inhibition. These findings will further strengthen the therapeutic applications of APS165.
Collapse
Affiliation(s)
- Zhaoyang Ye
- Department of Pharmaceutical, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Ramareddy V. Guntaka
- Department of Molecular Sciences, University of Tennessee Health Science Center, Memphis, TN 38163, USA
- * Corresponding authors Ram I. Mahato, Ph.D., 26 S Dunlap Street, Feurt 413, Memphis, TN 38163, USA, Tel: (901) 448-6929, Fax: (901) 448-6092, E-mail: , Http://cop.utmem.edu/rmahato. Ramareddy V. Guntaka, Ph. D., 101 Molecular Science Bldg., Memphis, TN 38163, USA, Tel: (901) 448-8230, Fax: (901) 448-8462, E-mail:
| | - Ram I. Mahato
- Department of Pharmaceutical, University of Tennessee Health Science Center, Memphis, TN 38163, USA
- * Corresponding authors Ram I. Mahato, Ph.D., 26 S Dunlap Street, Feurt 413, Memphis, TN 38163, USA, Tel: (901) 448-6929, Fax: (901) 448-6092, E-mail: , Http://cop.utmem.edu/rmahato. Ramareddy V. Guntaka, Ph. D., 101 Molecular Science Bldg., Memphis, TN 38163, USA, Tel: (901) 448-8230, Fax: (901) 448-8462, E-mail:
| |
Collapse
|
45
|
Abstract
The synthesis of modified nucleic acids has been the subject of much study ever since the structure of DNA was elucidated by Watson and Crick at Cambridge and Wilkins and Franklin at King's College over half a century ago. This review describes recent developments in the synthesis and application of these artificial nucleic acids, predominantly the phosphoramidites which allow for easy inclusion into oligonucleotides, and is divided into three separate sections. Firstly, modifications to the base portion will be discussed followed secondly by modifications to the sugar portion. Finally, changes in the type of nucleic acid linker will be discussed in the third section. Peptide Nucleic Acids (PNAs) are not discussed in this review as they represent a separate and large area of nucleic acid mimics.
Collapse
Affiliation(s)
- Alexander J A Cobb
- School of Pharmacy, University of Reading, Whiteknights, Reading, Berks RG6 6AD, UK.
| |
Collapse
|
46
|
Boutorine AS, Escudé C. Biophysical Analysis of Triple‐Helix Formation. ACTA ACUST UNITED AC 2007; Chapter 7:Unit 7.12. [DOI: 10.1002/0471142700.nc0712s29] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
47
|
Wellington KW, Benner SA. A review: synthesis of aryl C-glycosides via the heck coupling reaction. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2007; 25:1309-33. [PMID: 17067955 DOI: 10.1080/15257770600917013] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
In this article, we focus on the synthesis of aryl C-glycosides via Heck coupling. It is organized based on the type of structures used in the assembly of the C-glycosides (also called C-nucleosides) with the following subsections: pyrimidine C-nucleosides, purine C-nucleosides, and monocyclic, bicyclic, and tetracyclic C-nucleosides. The reagents and conditions used for conducting the Heck coupling reactions are discussed. The subsequent conversion of the Heck products to the corresponding target molecules and the application of the target molecules are also described.
Collapse
Affiliation(s)
- Kevin W Wellington
- Foundation for Applied Molecular Evolution, Gainesville, Florida 32604, USA
| | | |
Collapse
|
48
|
Corral E, Kooijman H, Spek AL, Reedijk J. Nucleic acids in two dimensions: layers of base pairs linked by carboxylate. NEW J CHEM 2007. [DOI: 10.1039/b613845d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
49
|
Mahato RI, Cheng K, Guntaka RV. Modulation of gene expression by antisense and antigene oligodeoxynucleotides and small interfering RNA. Expert Opin Drug Deliv 2006; 2:3-28. [PMID: 16296732 DOI: 10.1517/17425247.2.1.3] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Antisense oligodeoxynucleotides, triplex-forming oligodeoxynucleotides and double-stranded small interfering RNAs have great potential for the treatment of many severe and debilitating diseases. Concerted efforts from both industry and academia have made significant progress in turning these nucleic acid drugs into therapeutics, and there is already one FDA-approved antisense drug in the clinic. Despite the success of one product and several other ongoing clinical trials, challenges still exist in their stability, cellular uptake, disposition, site-specific delivery and therapeutic efficacy. The principles, strategies and delivery consideration of these nucleic acids are reviewed. Furthermore, the ways to overcome the biological barriers are also discussed so that therapeutic concentrations at their target sites can be maintained for a desired period.
Collapse
MESH Headings
- Animals
- DNA/chemistry
- DNA/genetics
- DNA/metabolism
- Drug Carriers
- Gene Expression Regulation
- Gene Silencing
- Gene Targeting/methods
- Genetic Therapy/methods
- Humans
- Nucleic Acid Conformation/drug effects
- Oligonucleotides, Antisense/chemistry
- Oligonucleotides, Antisense/genetics
- Oligonucleotides, Antisense/metabolism
- Oligonucleotides, Antisense/pharmacology
- Protein Biosynthesis/drug effects
- RNA Interference
- RNA Splicing/drug effects
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Small Interfering/chemistry
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- Transcription, Genetic/drug effects
Collapse
Affiliation(s)
- Ram I Mahato
- University of Tennessee Health Science Center, Department of Pharmaceutical Sciences, 26 South Dunlap Street, Feurt Bldg RM 406, Memphis, TN 38163, USA.
| | | | | |
Collapse
|
50
|
Jain ML, Bruice TC. Solid-phase synthesis of positively charged deoxynucleic guanidine (DNG) oligonucleotide incorporating 7-deazaguanine bases. Bioorg Med Chem 2006; 14:7333-46. [PMID: 16945544 DOI: 10.1016/j.bmc.2006.05.074] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2006] [Revised: 05/31/2006] [Accepted: 05/31/2006] [Indexed: 10/24/2022]
Abstract
DNG nucleotides represent a positively charged DNA analog in which the negatively charged phosphodiester linkages of DNA are replaced by positively charged guanidinium linkages. We report herein the synthesis of 3'-end, middle, and 5'-end monomers required for the synthesis of a DNG sequence in which the natural guanine base is replaced by 7-deazaguanine (c(7)G). 7-Deazaguanine nucleobase was chosen because of their unique glycoside bond stability and their ability to prevent G-quartet formation. A facile and high yield two-step synthesis of xylo-7-deazaguanine 7, a key intermediate for introducing 3'-amino functionality, is carried out under Mitsunobu conditions. Subsequently, the 3'-Fmoc-protected thiourea monomers 13 and 19 were prepared from 7 via their corresponding 3'-amino-7-deazaguanines 11 and 18, respectively. The smooth coupling of these thiourea monomers with monomethoxytrityl (MMTr)-protected 3'-end monomer 25, prepared from 5, occurred on solid phase in 3'-->5' direction. The resultant trimeric HO-c(7)Ggc(7)Ggc(7)G-OH (1) has been designed to be included into DNA using standard DNA synthesis technology. The combination of C-c(7)G base pairing and electrostatic association of phosphodiester and guanidinium backbone allows the small synthesized DNG trimer 1 to form 1:1 complex with DNA-C pentamer.
Collapse
Affiliation(s)
- Moti L Jain
- Department of Chemistry and Biochemistry, University Of California, Santa Barbara, 93106, USA
| | | |
Collapse
|