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Fàbrega C, Aviñó A, Eritja R. Chemical Modifications in Nucleic Acids for Therapeutic and Diagnostic Applications. CHEM REC 2021; 22:e202100270. [DOI: 10.1002/tcr.202100270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/26/2021] [Accepted: 11/26/2021] [Indexed: 11/08/2022]
Affiliation(s)
- Carme Fàbrega
- Department of Surfactants and Nanobiotechnology Institute for Advanced Chemistry of Catalonia (IQAC) Spanish National Research Council (CSIC) Jordi Girona 18–26 E-08034 Barcelona Spain
- Networking Center on Bioengineering Biomaterials and Nanomedicine (CIBER-BBN) E-08034 Barcelona Spain
| | - Anna Aviñó
- Department of Surfactants and Nanobiotechnology Institute for Advanced Chemistry of Catalonia (IQAC) Spanish National Research Council (CSIC) Jordi Girona 18–26 E-08034 Barcelona Spain
- Networking Center on Bioengineering Biomaterials and Nanomedicine (CIBER-BBN) E-08034 Barcelona Spain
| | - Ramon Eritja
- Department of Surfactants and Nanobiotechnology Institute for Advanced Chemistry of Catalonia (IQAC) Spanish National Research Council (CSIC) Jordi Girona 18–26 E-08034 Barcelona Spain
- Networking Center on Bioengineering Biomaterials and Nanomedicine (CIBER-BBN) E-08034 Barcelona Spain
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2
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Märcher A, Nijenhuis MAD, Gothelf KV. A Wireframe DNA Cube: Antibody Conjugate for Targeted Delivery of Multiple Copies of Monomethyl Auristatin E. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202107221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Anders Märcher
- Department of Chemistry and Interdisciplinary Nanoscience Centre (iNANO) Aarhus University Gustav Wieds Vej 14 8000 Aarhus Denmark
| | - Minke A. D. Nijenhuis
- Department of Chemistry and Interdisciplinary Nanoscience Centre (iNANO) Aarhus University Gustav Wieds Vej 14 8000 Aarhus Denmark
| | - Kurt V. Gothelf
- Department of Chemistry and Interdisciplinary Nanoscience Centre (iNANO) Aarhus University Gustav Wieds Vej 14 8000 Aarhus Denmark
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Märcher A, Nijenhuis MAD, Gothelf KV. A Wireframe DNA Cube: Antibody Conjugate for Targeted Delivery of Multiple Copies of Monomethyl Auristatin E. Angew Chem Int Ed Engl 2021; 60:21691-21696. [PMID: 34309988 DOI: 10.1002/anie.202107221] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 07/18/2021] [Indexed: 11/08/2022]
Abstract
In recent years, several antibody drug conjugates (ADC) have been accepted by the FDA as therapeutics against cancer. It is well-known that control of drug-to-antibody ratio (DAR) is vital for the success of an ADC, which inspires the advancement of better and simpler methods for tight control of DAR. We present the development of an antibody DNA wireframe cube conjugate for precise control of DAR. The DNA wireframe cube consists of four single strands, which when folded present eight single stranded domains. One domain is bound to a monofunctionalized antibody DNA conjugate, and the seven others are attached to DNA functionalized with the potent tubulin inhibitor MMAE, thereby preparing an ADC with a DAR of precisely seven. The formation of the ADC is investigated by gel electrophoresis and atomic force microscopy. Lastly, the developed MMAE loaded ADC was used for targeted drug delivery in vitro.
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Affiliation(s)
- Anders Märcher
- Department of Chemistry and Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus, Denmark
| | - Minke A D Nijenhuis
- Department of Chemistry and Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus, Denmark
| | - Kurt V Gothelf
- Department of Chemistry and Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus, Denmark
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4
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Dellafiore M, Aviñó A, Alagia A, Montserrat JM, Iribarren AM, Eritja R. siRNA Modified with 2′-Deoxy-2′-C
-methylpyrimidine Nucleosides. Chembiochem 2018; 19:1409-1413. [DOI: 10.1002/cbic.201800077] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Indexed: 01/23/2023]
Affiliation(s)
- María Dellafiore
- INGEBI (CONICET); Vuelta de Obligado 2490 -1428 Buenos Aires Argentina
| | - Anna Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC); Spanish Council for Scientific Research (CSIC); Jordi Girona 18-26 08034 Barcelona Spain
- NetworkingCenter on Bioengineering; Biomaterials and Nanomedicine (CIBER-BBN); Av. Monforte de Lemos 3-5. Pabellón 11. Planta 0 Madrid 28029 Spain
| | - Adele Alagia
- Institute for Advanced Chemistry of Catalonia (IQAC); Spanish Council for Scientific Research (CSIC); Jordi Girona 18-26 08034 Barcelona Spain
- NetworkingCenter on Bioengineering; Biomaterials and Nanomedicine (CIBER-BBN); Av. Monforte de Lemos 3-5. Pabellón 11. Planta 0 Madrid 28029 Spain
| | - Javier M. Montserrat
- Instituto de Ciencias; Universidad Nacional de General Sarmiento; J. M. Gutiérrez 1150 Los Polvorines Prov. Buenos Aires B1613GSX Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Godoy Cruz 2290 Buenos Aires C1425FQB Argentina
| | - Adolfo M. Iribarren
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Godoy Cruz 2290 Buenos Aires C1425FQB Argentina
- Laboratorio de Biotransformaciones; Universidad Nacional de Quilmes; Roque Saenz Peña352 1876 Bernal Prov Buenos Aires Argentina
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC); Spanish Council for Scientific Research (CSIC); Jordi Girona 18-26 08034 Barcelona Spain
- NetworkingCenter on Bioengineering; Biomaterials and Nanomedicine (CIBER-BBN); Av. Monforte de Lemos 3-5. Pabellón 11. Planta 0 Madrid 28029 Spain
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Alagia A, Jorge AF, Aviñó A, Cova TFGG, Crehuet R, Grijalvo S, Pais AACC, Eritja R. Exploring PAZ/3'-overhang interaction to improve siRNA specificity. A combined experimental and modeling study. Chem Sci 2018; 9:2074-2086. [PMID: 29719684 PMCID: PMC5896489 DOI: 10.1039/c8sc00010g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 01/15/2018] [Indexed: 12/29/2022] Open
Abstract
The understanding of the dynamical and mechanistic aspects that lie behind siRNA-based gene regulation is a requisite to boost the performance of siRNA therapeutics. A systematic experimental and computational study on the 3'-overhang structural requirements for the design of more specific and potent siRNA molecules was carried out using nucleotide analogues differing in structural parameters, such as sugar constraint, lack of nucleobase, distance between the phosphodiester backbone and nucleobase, enantioselectivity, and steric hindrance. The results established a set of rules governing the siRNA-mediated silencing, indicating that the thermodynamic stability of the 5'-end is a crucial determinant for antisense-mediated silencing but is not sufficient to avoid sense-mediated silencing. Both theoretical and experimental approaches consistently evidence the existence of a direct connection between the PAZ/3'-overhang binding affinity and siRNA's potency and specificity. An overall description of the systems is thus achieved by atomistic simulations and free energy calculations that allow us to propose a robust and self-contained procedure for studying the factors implied in PAZ/3'-overhang siRNA interactions. A higher RNAi activity is associated with a moderate-to-strong PAZ/3'-overhang binding. Contrarily, lower binding energies compromise siRNA potency, increase specificity, and favor siRNA downregulation by Ago2-independent mechanisms. This work provides in-depth details for the design of powerful and safe synthetic nucleotide analogues for substitution at the 3'-overhang, enabling some of the intrinsic siRNA disadvantages to be overcome.
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Affiliation(s)
- Adele Alagia
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) , Jordi Girona 18-26 , E-08034 Barcelona , Spain . ; ; Tel: +34 934006145
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN) , Jordi Girona 18-26 , E-08034 Barcelona , Spain
| | - Andreia F Jorge
- CQC , Department of Chemistry , University of Coimbra , Rua Larga , 3004-535 Coimbra , Portugal .
| | - Anna Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) , Jordi Girona 18-26 , E-08034 Barcelona , Spain . ; ; Tel: +34 934006145
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN) , Jordi Girona 18-26 , E-08034 Barcelona , Spain
| | - Tânia F G G Cova
- CQC , Department of Chemistry , University of Coimbra , Rua Larga , 3004-535 Coimbra , Portugal .
| | - Ramon Crehuet
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) , Jordi Girona 18-26 , E-08034 Barcelona , Spain . ; ; Tel: +34 934006145
| | - Santiago Grijalvo
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) , Jordi Girona 18-26 , E-08034 Barcelona , Spain . ; ; Tel: +34 934006145
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN) , Jordi Girona 18-26 , E-08034 Barcelona , Spain
| | - Alberto A C C Pais
- CQC , Department of Chemistry , University of Coimbra , Rua Larga , 3004-535 Coimbra , Portugal .
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) , Jordi Girona 18-26 , E-08034 Barcelona , Spain . ; ; Tel: +34 934006145
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN) , Jordi Girona 18-26 , E-08034 Barcelona , Spain
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Carnero A, Pérez-Rentero S, Alagia A, Aviñó A, Sanghvi YS, Fernández S, Ferrero M, Eritja R. The impact of an extended nucleobase-2′-deoxyribose linker in the biophysical and biological properties of oligonucleotides. RSC Adv 2017. [DOI: 10.1039/c6ra26852h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The introduction of a novel thymine derivative at the 3′-end of the sense strand generates more potent and selective siRNAs.
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Affiliation(s)
- Alejandro Carnero
- Departamento de Química Orgánica e Inorgánica
- Instituto Universitario de Biotecnología de Asturias
- Universidad de Oviedo
- 33006-Oviedo
- Spain
| | - Sónia Pérez-Rentero
- Dpt. Chemical & Biomolecular Nanotechnology
- Institute for Advanced Chemistry of Catalonia (IQAC)
- CSIC
- 08034-Barcelona
- Spain
| | - Adele Alagia
- Dpt. Chemical & Biomolecular Nanotechnology
- Institute for Advanced Chemistry of Catalonia (IQAC)
- CSIC
- 08034-Barcelona
- Spain
| | - Anna Aviñó
- Dpt. Chemical & Biomolecular Nanotechnology
- Institute for Advanced Chemistry of Catalonia (IQAC)
- CSIC
- 08034-Barcelona
- Spain
| | | | - Susana Fernández
- Departamento de Química Orgánica e Inorgánica
- Instituto Universitario de Biotecnología de Asturias
- Universidad de Oviedo
- 33006-Oviedo
- Spain
| | - Miguel Ferrero
- Departamento de Química Orgánica e Inorgánica
- Instituto Universitario de Biotecnología de Asturias
- Universidad de Oviedo
- 33006-Oviedo
- Spain
| | - Ramon Eritja
- Dpt. Chemical & Biomolecular Nanotechnology
- Institute for Advanced Chemistry of Catalonia (IQAC)
- CSIC
- 08034-Barcelona
- Spain
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Kumar V, Gothelf KV. Synthesis and biophysical properties of (L)-aTNA based G-quadruplexes. Org Biomol Chem 2016; 14:1540-4. [PMID: 26731694 DOI: 10.1039/c5ob02525g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Novel G-quadruplex structures are constructed by acyclic (L)-threninol nucleic acid and their synthesis and biophysical properties are described. Pyrene excimer fluorescence and circular dichroism (CD) data revealed that four strands of aTNA are oriented in antiparallel direction.
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Affiliation(s)
- Vipin Kumar
- Danish National Research Foundation Center for DNA Nanotechnology, iNANO and Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark.
| | - Kurt V Gothelf
- Danish National Research Foundation Center for DNA Nanotechnology, iNANO and Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark.
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8
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Alagia A, Eritja R. siRNA and RNAi optimization. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:316-29. [PMID: 26840434 DOI: 10.1002/wrna.1337] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 12/17/2015] [Accepted: 12/18/2015] [Indexed: 12/12/2022]
Abstract
The discovery and examination of the posttranscriptional gene regulatory mechanism known as RNA interference (RNAi) contributed to the identification of small interfering RNA (siRNA) and the comprehension of its enormous potential for clinical purposes. Theoretically, the ability of specific target gene downregulation makes the RNAi pathway an appealing solution for several diseases. Despite numerous hurdles resulting from the inherent properties of siRNA molecule and proper delivery to the target tissue, more than 50 RNA-based drugs are currently under clinical testing. In this work, we analyze the recent literature in the optimization of siRNA molecules. In detail, we focused on describing the most recent advances of siRNA field aimed at optimize siRNA pharmacokinetic properties. Special attention has been given in describing the impact of RNA modifications in the potential off-target effects (OTEs) such as saturation of the RNAi machinery, passenger strand-mediated silencing, immunostimulation, and miRNA-like OTEs as well as to recent developments on the delivery issue. The novel delivery systems and modified siRNA provide significant steps toward the development of reliable siRNA molecules for therapeutic use. WIREs RNA 2016, 7:316-329. doi: 10.1002/wrna.1337 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Adele Alagia
- Chemical and Biomolecular Nanotechnology, CIBER-BBN, Institute for Advanced Chemistry of Catalonia, IQAC-CSIC, Barcelona, Spain
| | - Ramon Eritja
- Chemical and Biomolecular Nanotechnology, CIBER-BBN, Institute for Advanced Chemistry of Catalonia, IQAC-CSIC, Barcelona, Spain
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9
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Modulation of the RNA Interference Activity Using Central Mismatched siRNAs and Acyclic Threoninol Nucleic Acids (aTNA) Units. Molecules 2015; 20:7602-19. [PMID: 25919280 PMCID: PMC6272285 DOI: 10.3390/molecules20057602] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 04/21/2015] [Accepted: 04/22/2015] [Indexed: 02/06/2023] Open
Abstract
The understanding of the mechanisms behind nucleotide recognition by Argonaute 2, core protein of the RNA-induced silencing complex, is a key aspect in the optimization of small interfering RNAs (siRNAs) activity. To date, great efforts have been focused on the modification of certain regions of siRNA, such as the 3'/5'-termini and the seed region. Only a few reports have described the roles of central positions flanking the cleavage site during the silence process. In this study, we investigate the potential correlations between the thermodynamic and silencing properties of siRNA molecules carrying, at internal positions, an acyclic L-threoninol nucleic acid (aTNA) modification. Depending on position, the silencing is weakened or impaired. Furthermore, we evaluate the contribution of mismatches facing either a natural nucleotide or an aTNA modification to the siRNA potency. The position 11 of the antisense strand is more permissive to mismatches and aTNA modification, in respect to the position 10. Additionally, comparing the ON-/OFF-target silencing of central mismatched siRNAs with 5'-terminal modified siRNA, we concluded: (i) central perturbation of duplex pairing features weights more on potency rather than silencing asymmetry; (ii) complete bias for the ON-target silencing can be achieved with single L-threoninol modification near the 5'-end of the sense strand.
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Pérez-Rentero S, Gargallo R, González C, Eritja R. Modulation of the stability of i-motif structures using an acyclic threoninol cytidine derivative. RSC Adv 2015. [DOI: 10.1039/c5ra10096h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The effect of aTNA (acyclic threoninol nucleic acids) units on the stability of intramolecular i-motifs was investigated by spectroscopic techniques.
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Affiliation(s)
- Sonia Pérez-Rentero
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC)
- CIBER-BBN
- E-08034 Barcelona
- Spain
| | - Raimundo Gargallo
- Department of Analytical Chemistry
- University of Barcelona
- E-08028 Barcelona
- Spain
| | - Carlos González
- Institute of Physical Chemistry “Rocasolano”
- CSIC
- E-28006 Madrid
- Spain
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC)
- CIBER-BBN
- E-08034 Barcelona
- Spain
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