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Napolitano E, Criscuolo A, Riccardi C, Esposito CL, Catuogno S, Coppola G, Roviello GN, Montesarchio D, Musumeci D. Directing in Vitro Selection towards G-quadruplex-forming Aptamers to Inhibit HMGB1 Pathological Activity. Angew Chem Int Ed Engl 2024; 63:e202319828. [PMID: 38358301 DOI: 10.1002/anie.202319828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/09/2024] [Accepted: 02/14/2024] [Indexed: 02/16/2024]
Abstract
In the search for novel, effective inhibitors of High-Mobility Group Box1 (HMGB1)-a protein involved in various inflammatory and autoimmune diseases as well as in cancer-we herein discovered a set of anti-HMGB1 G-quadruplex(G4)-forming aptamers by using an in vitro selection procedure applied to a doped library of guanine-rich oligonucleotides. The selected DNA sequences were then studied in a pseudo-physiological buffer mimicking the extracellular medium, where HMGB1 exerts its pathological activity, using spectroscopic, electrophoretic, and chromatographic techniques. All the oligonucleotides proved to fold into monomeric G4s and in some cases also dimeric species, stable at physiological temperature. Remarkably, the protein preferentially recognized the sequences forming dimeric parallel G4 structures, as evidenced by a properly designed chemiluminescent binding assay which also highlighted a good selectivity of these aptamers for HMGB1. Moreover, all aptamers showed anti-HMGB1 activity, inhibiting protein-induced cell migration. The acquired data allowed identifying L12 as the best anti-HMGB1 aptamer, featured by high thermal and enzymatic stability, no toxicity at least up to 5 μM concentration on healthy cells, along with potent anti-HMGB1 activity (IC50 ca. 28 nM) and good binding affinity for the protein, thus indicating it as a very promising lead candidate for in vivo studies.
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Affiliation(s)
- Ettore Napolitano
- Department of Chemical Sciences, University of Napoli Federico II, via Cintia 21, 80126, Napoli, Italy
| | - Andrea Criscuolo
- Department of Chemical Sciences, University of Napoli Federico II, via Cintia 21, 80126, Napoli, Italy
| | - Claudia Riccardi
- Department of Chemical Sciences, University of Napoli Federico II, via Cintia 21, 80126, Napoli, Italy
| | - Carla L Esposito
- Institute of Experimental Endocrinology and Oncology "Gaetano Salvatore" (IEOS), National Research Council (CNR), Via Sergio Pansini 5, 80131, Napoli, Italy
| | - Silvia Catuogno
- Institute of Experimental Endocrinology and Oncology "Gaetano Salvatore" (IEOS), National Research Council (CNR), Via Sergio Pansini 5, 80131, Napoli, Italy
| | - Gabriele Coppola
- Institute of Experimental Endocrinology and Oncology "Gaetano Salvatore" (IEOS), National Research Council (CNR), Via Sergio Pansini 5, 80131, Napoli, Italy
| | - Giovanni N Roviello
- Institute of Biostructures and Bioimaging (IBB), National Research Council of Italy (CNR), 80145, Napoli, Italy
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Napoli Federico II, via Cintia 21, 80126, Napoli, Italy
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Napoli Federico II, via Cintia 21, 80126, Napoli, Italy
- Institute of Biostructures and Bioimaging (IBB), National Research Council of Italy (CNR), 80145, Napoli, Italy
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Riccardi C, Pérez de Carvasal K, Platella C, Meyer A, Smietana M, Morvan F, Montesarchio D. Probing naphthalene diimide and 3-hydroxypropylphosphate as end-conjugating moieties for improved thrombin binding aptamers: Structural and biological effects. Bioorg Chem 2023; 141:106917. [PMID: 37865055 DOI: 10.1016/j.bioorg.2023.106917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/27/2023] [Accepted: 10/09/2023] [Indexed: 10/23/2023]
Abstract
The limitations associated with the in vivo use of the thrombin binding aptamer (TBA or TBA15) have dramatically stimulated the search of suitable chemically modified analogues in order to discover effective and reversible inhibitors of thrombin activity. In this context, we previously proposed cyclic and pseudo-cyclic TBA analogues with improved stability that proved to be more active than the parent aptamer. Herein, we have investigated a novel library of TBA derivatives carrying naphthalene diimide (NDI) moieties at the 3'- or 5'-end. In a subset of the investigated oligonucleotides, additional 3-hydroxypropylphosphate (HPP) groups were introduced at one or both ends of the TBA sequence. Evaluation of the G-quadruplex thermal stability, serum nuclease resistance and in vitro anticoagulant activity of the new TBA analogues allowed rationalizing the effect of these appendages on the activity of the aptamer on the basis of their relative position. Notably, most of the different TBA analogues tested were more potent thrombin inhibitors than unmodified TBA. Particularly, the analogue carrying an NDI group at the 5'-end and an HPP group at the 3'-end, named N-TBA-p, exhibited enhanced G-quadruplex thermal stability (ΔTm + 14° C) and ca. 10-fold improved nuclease resistance in serum compared to the native aptamer. N-TBA-p also induced prolonged and dose-dependent clotting times, showing a ca. 11-fold higher anticoagulant activity compared to unmodified TBA, as determined by spectroscopic methods. Overall, N-TBA-p proved to be in vitro a more efficient thrombin inhibitor than all the best ones previously investigated in our group. Its interesting features, associated with its easy preparation, make it a very promising candidate for future in vivo studies.
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Affiliation(s)
- Claudia Riccardi
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Kévan Pérez de Carvasal
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, 34095 Montpellier, France
| | - Chiara Platella
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Albert Meyer
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, 34095 Montpellier, France
| | - Michael Smietana
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, 34095 Montpellier, France
| | - François Morvan
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, 34095 Montpellier, France.
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy.
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Pérez de Carvasal K, Nicollet L, Smietana M, Morvan F. Stabilization of DNA Duplexes and Hairpins by Charge-Transfer Interactions Using DAN:NDI Pairs. Langmuir 2023; 39:7418-7425. [PMID: 37196178 DOI: 10.1021/acs.langmuir.3c00619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Electron-rich 1,5-dialkoxynaphthalene (DAN) and electron-deficient 1,8,4,5-naphthalenetetracarboxylic diimide (NDI) are known to interact through the formation of charge-transfer complexes. The introduction of DAN and NDI into various DNA duplexes and hairpins was investigated by ultraviolet (UV) melting curve analysis. The positioning of the DAN:NDI pair was found to strongly influence the stability of DNA duplex and hairpins. In particular, while the introduction of one DAN/NDI pair in front of each other in the center of a DNA duplex led to a decrease of the thermal stability (ΔTm - 6 °C), the addition of a second pair restored or even increased the stability. In contrast, the introduction of DAN:NDI pairs at the end of a duplex always induced a strong stabilization (ΔTm up to +20 °C). Finally, a DAN:NDI pair positioned in the loop of a hairpin induced a stronger stabilization than a T4 loop (ΔTm + 10 °C). Based on charge-transfer interactions, the strong stabilizations observed allow the preparation of highly stabilized DNA nanostructures opening the way to numerous applications in nanotechnology.
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Affiliation(s)
- Kévan Pérez de Carvasal
- Université de Montpellier, CNRS, ENSCM, Institut des Biomolécules Max Mousseron, 34293 Montpellier, France
| | - Laura Nicollet
- Université de Montpellier, CNRS, ENSCM, Institut des Biomolécules Max Mousseron, 34293 Montpellier, France
| | - Michael Smietana
- Université de Montpellier, CNRS, ENSCM, Institut des Biomolécules Max Mousseron, 34293 Montpellier, France
| | - François Morvan
- Université de Montpellier, CNRS, ENSCM, Institut des Biomolécules Max Mousseron, 34293 Montpellier, France
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de Carvasal KP, Vergoten G, Vasseur JJ, Smietana M, Morvan F. Supramolecular Recognition of Phosphodiester-Based Donor and Acceptor Oligomers Forming Gels in Water. Biomacromolecules 2023; 24:756-765. [PMID: 36724436 DOI: 10.1021/acs.biomac.2c01203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Inspired by automated DNA synthesis, electron-rich dialkoxynaphthalene (DAN) donor and electron-deficient naphthalene-tetracarboxylic diimide (NDI) acceptor phosphodiester-linked homohexamers were synthesized by the phosphoramidite method. Two types of hexamers were prepared, one with only one phosphodiester between the aromatics (i.e., DAN or NDI) and a second with two phosphodiesters around a propanediol between the aromatics, leading to the latter more flexible and more hydrophilic hexamers. The folding properties of these homohexamers alone or mixed together, in water only, were studied by UV-visible absorption spectroscopy and atomic force microscopy (AFM). AFM imaging revealed that a 1:1 mixture of hexaDAN and hexaNDI formed fibers by charge transfer donor-acceptor recognition leading to a hydrogel after drying. The organization of the resulting structures is strongly dependent on the nature of the complementary partner, leading to the formation of mono- or multilayer hydrogel networks with different compactness.
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Affiliation(s)
- Kévan Pérez de Carvasal
- Université de Montpellier, CNRS, ENSCM, Institut des Biomolécules Max Mousseron, Montpellier 34293, France
| | - Gérard Vergoten
- Université de Lille, Inserm, INFINITE - U1286, Institut de Chimie Pharmaceutique Albert Lespagnol (ICPAL), Faculté de Pharmacie, 3 rue du Professeur Laguesse, Lille 59006, France
| | - Jean-Jacques Vasseur
- Université de Montpellier, CNRS, ENSCM, Institut des Biomolécules Max Mousseron, Montpellier 34293, France
| | - Michael Smietana
- Université de Montpellier, CNRS, ENSCM, Institut des Biomolécules Max Mousseron, Montpellier 34293, France
| | - François Morvan
- Université de Montpellier, CNRS, ENSCM, Institut des Biomolécules Max Mousseron, Montpellier 34293, France
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Riccardi C, D’Aria F, Fasano D, Digilio FA, Carillo MR, Amato J, De Rosa L, Paladino S, Melone MAB, Montesarchio D, Giancola C. Truncated Analogues of a G-Quadruplex-Forming Aptamer Targeting Mutant Huntingtin: Shorter Is Better! Int J Mol Sci 2022; 23:ijms232012412. [PMID: 36293267 PMCID: PMC9604342 DOI: 10.3390/ijms232012412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/13/2022] [Accepted: 10/13/2022] [Indexed: 11/16/2022] Open
Abstract
Two analogues of the MS3 aptamer, which was previously shown to have an exquisite capability to selectively bind and modulate the activity of mutant huntingtin (mHTT), have been here designed and evaluated in their physicochemical and biological properties. Featured by a distinctive propensity to form complex G-quadruplex structures, including large multimeric aggregates, the original 36-mer MS3 has been truncated to give a 33-mer (here named MS3-33) and a 17-mer (here named MS3-17). A combined use of different techniques (UV, CD, DSC, gel electrophoresis) allowed a detailed physicochemical characterization of these novel G-quadruplex-forming aptamers, tested in vitro on SH-SY5Y cells and in vivo on a Drosophila Huntington’s disease model, in which these shorter MS3-derived oligonucleotides proved to have improved bioactivity in comparison with the parent aptamer.
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Affiliation(s)
- Claudia Riccardi
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Federica D’Aria
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy
| | - Dominga Fasano
- Department of Advanced Medical and Surgical Sciences, 2nd Division of Neurology, Center for Rare Diseases and InterUniversity Center for Research in Neurosciences, University of Campania Luigi Vanvitelli, 80131 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy
| | - Filomena Anna Digilio
- Research Institute on Terrestrial Ecosystems (IRET), UOS Naples-CNR, 80131 Naples, Italy
| | - Maria Rosaria Carillo
- Department of Experimental Medicine, University of Campania Luigi Vanvitelli, 80138 Naples, Italy
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy
| | - Laura De Rosa
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy
| | - Simona Paladino
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy
| | - Mariarosa Anna Beatrice Melone
- Department of Advanced Medical and Surgical Sciences, 2nd Division of Neurology, Center for Rare Diseases and InterUniversity Center for Research in Neurosciences, University of Campania Luigi Vanvitelli, 80131 Naples, Italy
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, Temple University, Philadelphia, PA 19122-6078, USA
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
- Correspondence: (D.M.); (C.G.)
| | - Concetta Giancola
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy
- Correspondence: (D.M.); (C.G.)
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Soni S, Jain U, Burke DH, Chauhan N. Development of Nanomaterial-Modified Impedimetric Aptasensor—A Single-Step Strategy for 3,4-Methylenedioxymethylamphetamine Detection. Biosensors 2022; 12:538. [PMID: 35884341 PMCID: PMC9312850 DOI: 10.3390/bios12070538] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 07/10/2022] [Accepted: 07/13/2022] [Indexed: 12/13/2022]
Abstract
Developing rapid, sensitive detection methods for 3,4-Methylenedioxymethylamphetamine (MDMA) is crucial to reduce its current misuse in the world population. With that aim, we developed an aptamer-modified tin nanoparticle (SnNP)-based nanoarchitecture as an electrochemical sensor in this study. This platform exhibited a high electron transfer rate with enhanced conductivity arising from its large surface area in comparison to the bare electrode. This observation was explained by the 40-fold higher electroactive surface area of SnNPs@Au, which provided a large space for 1.0 μM AptMDMA (0.68 ± 0.36 × 1012 molecule/cm2) immobilization and yielded a significant electrochemical response in the presence of MDMA. Furthermore, the AptMDMA-modified SnNPs@Au sensing platform proved to be a simple yet ultrasensitive analytical device for MDMA detection in spiked biological and water samples. This novel electrochemical aptasensor showed good linearity in the range of 0.01–1.0 nM for MDMA (R2 = 0.97) with a limit of detection of 0.33 nM and a sensitivity of 0.54 ohm/nM. In addition, the device showed high accuracy and stability along with signal recoveries in the range of 92–96.7% (Relative Standard Deviation, RSD, 1.1–2.18%). In conclusion, the proposed aptasensor developed here is the first to combine SnNPs and aptamers for illicit compound detection, and it offers a reliable platform for recreational drug detection.
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Riccardi C, D’Aria F, Digilio FA, Carillo MR, Amato J, Fasano D, De Rosa L, Paladino S, Melone MAB, Montesarchio D, Giancola C. Fighting the Huntington's Disease with a G-Quadruplex-Forming Aptamer Specifically Binding to Mutant Huntingtin Protein: Biophysical Characterization, In Vitro and In Vivo Studies. Int J Mol Sci 2022; 23:4804. [PMID: 35563194 PMCID: PMC9101412 DOI: 10.3390/ijms23094804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 04/23/2022] [Accepted: 04/24/2022] [Indexed: 02/07/2023] Open
Abstract
A set of guanine-rich aptamers able to preferentially recognize full-length huntingtin with an expanded polyglutamine tract has been recently identified, showing high efficacy in modulating the functions of the mutated protein in a variety of cell experiments. We here report a detailed biophysical characterization of the best aptamer in the series, named MS3, proved to adopt a stable, parallel G-quadruplex structure and show high nuclease resistance in serum. Confocal microscopy experiments on HeLa and SH-SY5Y cells, as models of non-neuronal and neuronal cells, respectively, showed a rapid, dose-dependent uptake of fluorescein-labelled MS3, demonstrating its effective internalization, even in the absence of transfecting agents, with no general cytotoxicity. Then, using a well-established Drosophila melanogaster model for Huntington's disease, which expresses the mutated form of human huntingtin, a significant improvement in the motor neuronal function in flies fed with MS3 was observed, proving the in vivo efficacy of this aptamer.
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Affiliation(s)
- Claudia Riccardi
- Department of Chemical Sciences, University of Naples Federico II, 80126 Napoli, Italy;
| | - Federica D’Aria
- Department of Pharmacy, University of Naples Federico II, 80131 Napoli, Italy; (F.D.); (J.A.)
| | - Filomena Anna Digilio
- Research Institute on Terrestrial Ecosystems (IRET), UOS Naples-CNR, 80131 Napoli, Italy; (F.A.D.); (M.R.C.)
| | - Maria Rosaria Carillo
- Research Institute on Terrestrial Ecosystems (IRET), UOS Naples-CNR, 80131 Napoli, Italy; (F.A.D.); (M.R.C.)
- Department of Experimental Medicine, University of Campania Luigi Vanvitelli, 80138 Napoli, Italy
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, 80131 Napoli, Italy; (F.D.); (J.A.)
| | - Dominga Fasano
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Napoli, Italy; (D.F.); (L.D.R.); (S.P.)
- Center for Rare Diseases and Inter University Center for Research in Neurosciences, Department of Advanced Medical and Surgical Sciences, 2nd Division of Neurology, University of Campania Luigi Vanvitelli, 80131 Napoli, Italy;
| | - Laura De Rosa
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Napoli, Italy; (D.F.); (L.D.R.); (S.P.)
| | - Simona Paladino
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Napoli, Italy; (D.F.); (L.D.R.); (S.P.)
| | - Mariarosa Anna Beatrice Melone
- Center for Rare Diseases and Inter University Center for Research in Neurosciences, Department of Advanced Medical and Surgical Sciences, 2nd Division of Neurology, University of Campania Luigi Vanvitelli, 80131 Napoli, Italy;
- Center for Biotechnology, Sbarro Institute for Cancer Research and Molecular Medicine, Temple University, Philadelphia, PA 19122, USA
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, 80126 Napoli, Italy;
| | - Concetta Giancola
- Department of Pharmacy, University of Naples Federico II, 80131 Napoli, Italy; (F.D.); (J.A.)
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Troisi R, Sica F. Aptamers: Functional-Structural Studies and Biomedical Applications. Int J Mol Sci 2022; 23:4796. [PMID: 35563186 DOI: 10.3390/ijms23094796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 04/24/2022] [Indexed: 11/26/2022] Open
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Busschaert N, Maity D, Samanta PK, English NJ, Hamilton AD. Improving structural stability and anticoagulant activity of a thrombin binding aptamer by aromatic modifications. Chembiochem 2022; 23:e202100670. [PMID: 34985829 DOI: 10.1002/cbic.202100670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/04/2022] [Indexed: 11/07/2022]
Abstract
The thrombin binding aptamer (TBA) is a 15-mer DNA oligonucleotide (5'-GGTTGGTGTGGTTGG-3'), that can form a stable intramolecular antiparallel chair-like G-quadruplex structure. This aptamer shows anticoagulant properties by interacting with one of the two anion binding sites of thrombin, namely the fibrinogen-recognition exosite. Here, we demonstrate that terminal modification of TBA with aromatic fragments such as coumarin, pyrene and perylene diimide (PDI), improves the G-quadruplex stability. The large aromatic surface of these dyes can π-π stack to the G-quadruplex or to each other, thereby stabilizing the aptamer. With respect to the original TBA, monoPDI-functionalized TBA exhibited the most remarkable improvement in melting temperature (ΔT m ≈ +18 °C) and displayed enhanced anticoagulant activity.
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Affiliation(s)
- Nathalie Busschaert
- Tulane University, Department of Chemistry, 6400 Freret St, 70118, New Orleans, UNITED STATES
| | | | - Pralok K Samanta
- University College Dublin, School of Chemical and Bioprocess engineering, IRELAND
| | - Niall J English
- University College Dublin, School of chemical and Bioprocess engineering, IRELAND
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