1
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Fallah A, Havaei SA, Sedighian H, Kachuei R, Fooladi AAI. Prediction of aptamer affinity using an artificial intelligence approach. J Mater Chem B 2024; 12:8825-8842. [PMID: 39158322 DOI: 10.1039/d4tb00909f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2024]
Abstract
Aptamers are oligonucleotide sequences that can connect to particular target molecules, similar to monoclonal antibodies. They can be chosen by systematic evolution of ligands by exponential enrichment (SELEX), and are modifiable and can be synthesized. Even if the SELEX approach has been improved a lot, it is frequently challenging and time-consuming to identify aptamers experimentally. In particular, structure-based methods are the most used in computer-aided design and development of aptamers. For this purpose, numerous web-based platforms have been suggested for the purpose of forecasting the secondary structure and 3D configurations of RNAs and DNAs. Also, molecular docking and molecular dynamics (MD), which are commonly utilized in protein compound selection by structural information, are suitable for aptamer selection. On the other hand, from a large number of sequences, artificial intelligence (AI) may be able to quickly discover the possible aptamer candidates. Conversely, sophisticated machine and deep-learning (DL) models have demonstrated efficacy in forecasting the binding properties between ligands and targets during drug discovery; as such, they may provide a reliable and precise method for forecasting the binding of aptamers to targets. This research looks at advancements in AI pipelines and strategies for aptamer binding ability prediction, such as machine and deep learning, as well as structure-based approaches, molecular dynamics and molecular docking simulation methods.
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Affiliation(s)
- Arezoo Fallah
- Department of Bacteriology and Virology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Seyed Asghar Havaei
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Hamid Sedighian
- Applied Microbiology Research Center, Biomedicine Technologies Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.
| | - Reza Kachuei
- Molecular Biology Research Center, Biomedicine Technologies Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Abbas Ali Imani Fooladi
- Applied Microbiology Research Center, Biomedicine Technologies Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.
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2
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Kirsch ZJ, Ashby J, Vachet RW. Investigating Protein-Nucleic Acid Binding Interactions with Diethylpyrocarbonate Covalent Labeling-Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024. [PMID: 39208253 DOI: 10.1021/jasms.4c00285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Nucleic acids are important biomolecules that facilitate numerous cellular functions and have in recent years become promising candidates for treating disease. Consequently, there is a need for methods to characterize protein interactions with these molecules. Here, we demonstrate that diethylpyrocarbonate (DEPC) covalent labeling-mass spectrometry (CL-MS) can provide structural information for protein-nucleic acid binding by characterizing the binding sites of two DNA aptamers specific to thrombin. Reductions in thrombin labeling are observed at the pair's binding interfaces. Furthermore, we find that binding of the aptamers causes changes in labeling at residues in the thrombin active site and known exosites for each aptamer, showcasing the sensitivity of DEPC CL-MS to significant allosteric changes.
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Affiliation(s)
- Zachary J Kirsch
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Jonathan Ashby
- Department of Chemistry, Trinity College, Hartford, Connecticut 06106, United States
| | - Richard W Vachet
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
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3
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Sun H, Zhao D, He Y, Meng H, Li Z. Aptamer-Based DNA Allosteric Switch for Regulation of Protein Activity. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2402531. [PMID: 38864341 PMCID: PMC11321679 DOI: 10.1002/advs.202402531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/13/2024] [Indexed: 06/13/2024]
Abstract
Allostery is a fundamental way to regulate the function of biomolecules playing crucial roles in cell metabolism and proliferation and is deemed the second secret of life. Given the limited understanding of the structure of natural allosteric molecules, the development of artificial allosteric molecules brings a huge opportunity to transform the allosteric mechanism into practical applications. In this study, the concept of bionics is introduced into the design of artificial allosteric molecules and an allosteric DNA switch with an activity site and an allosteric site based on two aptamers for selective inhibition of thrombin activity. Compared with the single aptamer, the allosteric switch possesses a significantly enhanced inhibition ability, which can be precisely regulated by converting the switch states. Moreover, the dynamic allosteric switch is further subjected to the control of the DNA threshold circuit for realizing automatic concentration determination and activity inhibition of thrombin. These compelling results confirm that this allosteric switch equipped with self-sensing and information-processing modules puts a new slant on the research of allosteric mechanisms and further application of allosteric tactics in chemical and biomedical fields.
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Affiliation(s)
- Hongzhi Sun
- College of ChemistryInstitute of Analytical Chemistry for Life ScienceZhengzhou UniversityZhengzhou450001China
| | - Di Zhao
- College of ChemistryInstitute of Analytical Chemistry for Life ScienceZhengzhou UniversityZhengzhou450001China
| | - Yating He
- College of ChemistryInstitute of Analytical Chemistry for Life ScienceZhengzhou UniversityZhengzhou450001China
| | - Hong‐Min Meng
- College of ChemistryInstitute of Analytical Chemistry for Life ScienceZhengzhou UniversityZhengzhou450001China
| | - Zhaohui Li
- College of ChemistryInstitute of Analytical Chemistry for Life ScienceZhengzhou UniversityZhengzhou450001China
- The First Affiliated Hospital of Zhengzhou UniversityZhengzhou450052China
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4
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Troisi R, Sica F. Structural overview of DNA and RNA G-quadruplexes in their interaction with proteins. Curr Opin Struct Biol 2024; 87:102846. [PMID: 38848656 DOI: 10.1016/j.sbi.2024.102846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/03/2024] [Accepted: 05/07/2024] [Indexed: 06/09/2024]
Abstract
Since the discovery of G-quadruplex (G4) participation in vital cellular processes, the regulation of the interaction of naturally occurring G4s with the relative target proteins has emerged as a promising approach for therapeutic development. Additionally, a synthetic strategy has produced several oligonucleotide aptamers, embodying a G4 module, which exhibit relevant biological activity by binding selectively to a target protein. In this context, the G4-protein structures available in the Protein Data Bank represent a valuable molecular view of the different G4 topologies involved in protein interaction. Interestingly, recent results have shown the co-existence of G4s with other structural domains such as duplexes. Overall, these findings allow a better understanding of the mechanisms that regulate intricate biological functions and suggest new design for innovative medical treatments.
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Affiliation(s)
- Romualdo Troisi
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, via Cintia, 80126 Naples, Italy; Institute of Biostructures and Bioimaging, CNR, via Pietro Castellino 111, 80131 Naples, Italy. https://twitter.com/TroRom
| | - Filomena Sica
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, via Cintia, 80126 Naples, Italy.
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5
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Yu H, Kumar S, Frederiksen JW, Kolyadko VN, Pitoc G, Layzer J, Yan A, Rempel R, Francis S, Krishnaswamy S, Sullenger BA. Aptameric hirudins as selective and reversible EXosite-ACTive site (EXACT) inhibitors. Nat Commun 2024; 15:3977. [PMID: 38730234 PMCID: PMC11087511 DOI: 10.1038/s41467-024-48211-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 04/22/2024] [Indexed: 05/12/2024] Open
Abstract
Potent and selective inhibition of the structurally homologous proteases of coagulation poses challenges for drug development. Hematophagous organisms frequently accomplish this by fashioning peptide inhibitors combining exosite and active site binding motifs. Inspired by this biological strategy, we create several EXACT inhibitors targeting thrombin and factor Xa de novo by linking EXosite-binding aptamers with small molecule ACTive site inhibitors. The aptamer component within the EXACT inhibitor (1) synergizes with and enhances the potency of small-molecule active site inhibitors by many hundred-fold (2) can redirect an active site inhibitor's selectivity towards a different protease, and (3) enable efficient reversal of inhibition by an antidote that disrupts bivalent binding. One EXACT inhibitor, HD22-7A-DAB, demonstrates extraordinary anticoagulation activity, exhibiting great potential as a potent, rapid onset anticoagulant to support cardiovascular surgeries. Using this generalizable molecular engineering strategy, selective, potent, and rapidly reversible EXACT inhibitors can be created against many enzymes through simple oligonucleotide conjugation for numerous research and therapeutic applications.
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Affiliation(s)
- Haixiang Yu
- Department of Surgery, Duke University, Durham, NC, USA
| | - Shekhar Kumar
- Research Institute, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Vladimir N Kolyadko
- Research Institute, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - George Pitoc
- Department of Surgery, Duke University, Durham, NC, USA
| | | | - Amy Yan
- Department of Surgery, Duke University, Durham, NC, USA
| | - Rachel Rempel
- Department of Surgery, Duke University, Durham, NC, USA
| | - Samuel Francis
- Department of Emergency Medicine, Duke University Hospital, Durham, NC, USA
| | - Sriram Krishnaswamy
- Research Institute, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Bruce A Sullenger
- Department of Surgery, Duke University, Durham, NC, USA.
- Departments of Pharmacology & Cancer Biology and Biomedical Engineering, Duke University, Durham, NC, USA.
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6
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Farag M, Mouawad L. Comprehensive analysis of intramolecular G-quadruplex structures: furthering the understanding of their formalism. Nucleic Acids Res 2024; 52:3522-3546. [PMID: 38512075 DOI: 10.1093/nar/gkae182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 02/16/2024] [Accepted: 03/01/2024] [Indexed: 03/22/2024] Open
Abstract
G-quadruplexes (G4) are helical structures found in guanine-rich DNA or RNA sequences. Generally, their formalism is based on a few dozen structures, which can produce some inconsistencies or incompleteness. Using the website ASC-G4, we analyzed the structures of 333 intramolecular G4s, of all types, which allowed us to clarify some key concepts and present new information. To each of the eight distinguishable topologies corresponds a groove-width signature and a predominant glycosidic configuration (gc) pattern governed by the directions of the strands. The relative orientations of the stacking guanines within the strands, which we quantified and related to their vertical gc successions, determine the twist and tilt of the helices. The latter impact the minimum groove widths, which represent the space available for lateral ligand binding. The G4 four helices have similar twists, even when these twists are irregular, meaning that they have various angles along the strands. Despite its importance, the vertical gc succession has no strict one-to-one relationship with the topology, which explains the discrepancy between some topologies and their corresponding circular dichroism spectra. This study allowed us to introduce the new concept of platypus G4s, which are structures with properties corresponding to several topologies.
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Affiliation(s)
- Marc Farag
- Chemistry and Modeling for the Biology of Cancer, CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, Université Paris-Saclay, CS 90030, 91401 ORSAYCedex, France
| | - Liliane Mouawad
- Chemistry and Modeling for the Biology of Cancer, CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, Université Paris-Saclay, CS 90030, 91401 ORSAYCedex, France
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7
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Khoshouei A, Kempf G, Mykhailiuk V, Griessing JM, Honemann MN, Kater L, Cavadini S, Dietz H. Designing Rigid DNA Origami Templates for Molecular Visualization Using Cryo-EM. NANO LETTERS 2024; 24. [PMID: 38602296 PMCID: PMC11057029 DOI: 10.1021/acs.nanolett.4c00915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/07/2024] [Accepted: 04/09/2024] [Indexed: 04/12/2024]
Abstract
DNA origami, a method for constructing nanostructures from DNA, offers potential for diverse scientific and technological applications due to its ability to integrate various molecular functionalities in a programmable manner. In this study, we examined the impact of internal crossover distribution and the compositional uniformity of staple strands on the structure of multilayer DNA origami using cryogenic electron microscopy (cryo-EM) single-particle analysis. A refined DNA object was utilized as an alignment framework in a host-guest model, where we successfully resolved an 8 kDa thrombin binding aptamer (TBA) linked to the host object. Our results broaden the spectrum of DNA in structural applications.
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Affiliation(s)
- Ali Khoshouei
- Laboratory
for Biomolecular Nanotechnology, Department of Biosciences, School
of Natural Sciences, Technical University
of Munich, Am Coulombwall 4a, 85748 Garching, Germany
- Munich
Institute of Biomedical Engineering, Technical
University of Munich, Boltzmannstraße 11, 85748 Garching, Germany
| | - Georg Kempf
- Friedrich
Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Volodymyr Mykhailiuk
- Laboratory
for Biomolecular Nanotechnology, Department of Biosciences, School
of Natural Sciences, Technical University
of Munich, Am Coulombwall 4a, 85748 Garching, Germany
- Munich
Institute of Biomedical Engineering, Technical
University of Munich, Boltzmannstraße 11, 85748 Garching, Germany
| | - Johanna Mariko Griessing
- Laboratory
for Biomolecular Nanotechnology, Department of Biosciences, School
of Natural Sciences, Technical University
of Munich, Am Coulombwall 4a, 85748 Garching, Germany
- Munich
Institute of Biomedical Engineering, Technical
University of Munich, Boltzmannstraße 11, 85748 Garching, Germany
| | - Maximilian Nicolas Honemann
- Laboratory
for Biomolecular Nanotechnology, Department of Biosciences, School
of Natural Sciences, Technical University
of Munich, Am Coulombwall 4a, 85748 Garching, Germany
- Munich
Institute of Biomedical Engineering, Technical
University of Munich, Boltzmannstraße 11, 85748 Garching, Germany
| | - Lukas Kater
- Friedrich
Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Simone Cavadini
- Friedrich
Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Hendrik Dietz
- Laboratory
for Biomolecular Nanotechnology, Department of Biosciences, School
of Natural Sciences, Technical University
of Munich, Am Coulombwall 4a, 85748 Garching, Germany
- Munich
Institute of Biomedical Engineering, Technical
University of Munich, Boltzmannstraße 11, 85748 Garching, Germany
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8
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Johnson RE, Murray MT, Bycraft LJ, Myler P, Wetmore SD, Manderville RA. Harnessing a 4-Formyl-Aniline Handle to Tune the Stability of a DNA Aptamer-Protein Complex via Fluorescent Surrogates. Bioconjug Chem 2023; 34:2066-2076. [PMID: 37857354 DOI: 10.1021/acs.bioconjchem.3c00373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Interactions between DNA aptamers and protein targets hold promise for the development of pharmaceuticals and diagnostics. As such, the utilization of fluorescent nucleobase surrogates in studying aptamer-protein interactions is a powerful tool due to their ability to provide site-specific information through turn-on fluorescence. Unfortunately, previously described turn-on probes serving as nucleobase replacements have only been strongly disruptive to the affinity of aptamer-protein interactions. Herein, we present a modified TBA15 aptamer for thrombin containing a fluorescent surrogate that provides site-specific turn-on emission with low nanomolar affinity. The modification, referred to as AnBtz, was substituted at position T3 and provided strong turn-on emission (Irel ≈ 4) and brightness (ε·Φ > 20 000 cm-1 M-1) with an apparent dissociation constant (Kd) of 15 nM to afford a limit of detection (LOD) of 10 nM for thrombin in 20% human serum. The probe was selected through a modular "on-strand" synthesis process that utilized a 4-formyl-aniline (4FA) handle. Using this platform, we were able to enhance the affinity of the final aptamer conjugate by ∼30-fold in comparison with the initial conjugate design. Molecular dynamics simulations provide insight into the structural basis for this phenomenon and highlight the importance of targeting hydrophobic protein binding sites with fluorescent nucleobase surrogates to create new contacts with protein targets.
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Affiliation(s)
- Ryan E Johnson
- Departments of Chemistry & Toxicology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Makay T Murray
- Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
| | - Lucas J Bycraft
- Departments of Chemistry & Toxicology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Peter Myler
- Departments of Chemistry & Toxicology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Stacey D Wetmore
- Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
| | - Richard A Manderville
- Departments of Chemistry & Toxicology, University of Guelph, Guelph, ON N1G 2W1, Canada
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9
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Troisi R, Balasco N, Autiero I, Vitagliano L, Sica F. Structural Insights into Protein-Aptamer Recognitions Emerged from Experimental and Computational Studies. Int J Mol Sci 2023; 24:16318. [PMID: 38003510 PMCID: PMC10671752 DOI: 10.3390/ijms242216318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/10/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023] Open
Abstract
Aptamers are synthetic nucleic acids that are developed to target with high affinity and specificity chemical entities ranging from single ions to macromolecules and present a wide range of chemical and physical properties. Their ability to selectively bind proteins has made these compounds very attractive and versatile tools, in both basic and applied sciences, to such an extent that they are considered an appealing alternative to antibodies. Here, by exhaustively surveying the content of the Protein Data Bank (PDB), we review the structural aspects of the protein-aptamer recognition process. As a result of three decades of structural studies, we identified 144 PDB entries containing atomic-level information on protein-aptamer complexes. Interestingly, we found a remarkable increase in the number of determined structures in the last two years as a consequence of the effective application of the cryo-electron microscopy technique to these systems. In the present paper, particular attention is devoted to the articulated architectures that protein-aptamer complexes may exhibit. Moreover, the molecular mechanism of the binding process was analyzed by collecting all available information on the structural transitions that aptamers undergo, from their protein-unbound to the protein-bound state. The contribution of computational approaches in this area is also highlighted.
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Affiliation(s)
- Romualdo Troisi
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy;
- Institute of Biostructures and Bioimaging, CNR, 80131 Naples, Italy;
| | - Nicole Balasco
- Institute of Molecular Biology and Pathology, CNR c/o Department of Chemistry, University of Rome Sapienza, 00185 Rome, Italy;
| | - Ida Autiero
- Institute of Biostructures and Bioimaging, CNR, 80131 Naples, Italy;
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, CNR, 80131 Naples, Italy;
| | - Filomena Sica
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy;
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10
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Kohn EM, Konovalov K, Gomez CA, Hoover GN, Yik AKH, Huang X, Martell JD. Terminal Alkyne-Modified DNA Aptamers with Enhanced Protein Binding Affinities. ACS Chem Biol 2023; 18:1976-1984. [PMID: 37531184 DOI: 10.1021/acschembio.3c00183] [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] [Indexed: 08/03/2023]
Abstract
Nucleic acid-based receptors, known as aptamers, are relatively fast to discover and manufacture but lack the diverse functional groups of protein receptors (e.g., antibodies). The binding properties of DNA aptamers can be enhanced by attaching abiotic functional groups; for example, aromatic groups such as naphthalene slow dissociation from proteins. Although the terminal alkyne is a π-electron-rich functional group that has been used in small molecule drugs to enhance binding to proteins through noncovalent interactions, it remains unexplored for enhancing DNA aptamer binding affinity. Here, we demonstrate the utility of the terminal alkyne for improving the binding of DNA to proteins. We prepared a library of 256 terminal-alkyne-bearing variants of HD22, a DNA aptamer that binds the protein thrombin with nanomolar affinity. After a one-step thrombin-binding selection, a high-affinity aptamer containing two alkynes was discovered, exhibiting 3.2-fold tighter thrombin binding than the corresponding unmodified sequence. The tighter binding was attributable to a slower rate of dissociation from thrombin (5.2-fold slower than HD22). Molecular dynamics simulations with enhanced sampling by Replica Exchange with Solute Tempering (REST2) suggest that the π-electron-rich alkyne interacts with an asparagine side chain N-H group on thrombin, forming a noncovalent interaction that stabilizes the aptamer-protein interface. Overall, this work represents the first case of terminal alkynes enhancing the binding properties of an aptamer and underscores the utility of the terminal alkyne as an atom economical π-electron-rich functional group to enhance binding affinity with minimal steric perturbation.
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Affiliation(s)
- Eric M Kohn
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kirill Konovalov
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Theoretical Chemistry Institute, Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Christian A Gomez
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Gillian N Hoover
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Andrew Kai-Hei Yik
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Theoretical Chemistry Institute, Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Xuhui Huang
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Theoretical Chemistry Institute, Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Jeffrey D Martell
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53705, United States
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11
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Troisi R, Napolitano V, Rossitto E, Osman W, Nagano M, Wakui K, Popowicz G, Yoshimoto K, Sica F. Steric hindrance and structural flexibility shape the functional properties of a guanine-rich oligonucleotide. Nucleic Acids Res 2023; 51:8880-8890. [PMID: 37503836 PMCID: PMC10484730 DOI: 10.1093/nar/gkad634] [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: 12/15/2022] [Revised: 06/27/2023] [Accepted: 07/18/2023] [Indexed: 07/29/2023] Open
Abstract
Ligand/protein molecular recognition involves a dynamic process, whereby both partners require a degree of structural plasticity to regulate the binding/unbinding event. Here, we present the characterization of the interaction between a highly dynamic G-rich oligonucleotide, M08s-1, and its target protein, human α-thrombin. M08s-1 is the most active anticoagulant aptamer selected thus far. Circular dichroism and gel electrophoresis analyses indicate that both intramolecular and intermolecular G-quadruplex structures are populated in solution. The presence of thrombin stabilises the antiparallel intramolecular chair-like G-quadruplex conformation, that provides by far the main contribution to the biological activity of the aptamer. The crystal structure of the thrombin-oligonucleotide complex reveals that M08s-1 adopts a kinked structural organization formed by a G-quadruplex domain and a long duplex module, linked by a stretch of five purine bases. The quadruplex motif hooks the exosite I region of thrombin and the duplex region is folded towards the surface of the protein. This structural feature, which has never been observed in other anti-exosite I aptamers with a shorter duplex motif, hinders the approach of a protein substrate to the active site region and may well explain the significant increase in the anticoagulant activity of M08s-1 compared to the other anti-exosite I aptamers.
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Affiliation(s)
- Romualdo Troisi
- Department of Chemical Sciences, University of Naples Federico II, Naples 80126, Italy
| | - Valeria Napolitano
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Lichtenbergstraße 4, 85747, Garching, Germany
| | - Emanuele Rossitto
- Department of Chemical Sciences, University of Naples Federico II, Naples 80126, Italy
| | - Waleed Osman
- Research and Development Division, LinkBIO Co., Ltd., The ICI Center, 5270 Terada, Toride-shi, Ibaraki 302-0021, Japan
| | - Masanobu Nagano
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | - Koji Wakui
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | - Grzegorz M Popowicz
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Lichtenbergstraße 4, 85747, Garching, Germany
| | - Keitaro Yoshimoto
- Research and Development Division, LinkBIO Co., Ltd., The ICI Center, 5270 Terada, Toride-shi, Ibaraki 302-0021, Japan
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | - Filomena Sica
- Department of Chemical Sciences, University of Naples Federico II, Naples 80126, Italy
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12
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Santostasi G, Denas G, Pengo V. New pharmacotherapeutic options for oral anticoagulant treatment in atrial fibrillation patients aged 65 and older: factor XIa inhibitors and beyond. Expert Opin Pharmacother 2023; 24:1335-1347. [PMID: 37243619 DOI: 10.1080/14656566.2023.2219391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/22/2023] [Accepted: 05/25/2023] [Indexed: 05/29/2023]
Abstract
INTRODUCTION Although much progress has been made using anticoagulation for stroke prevention in patients with non-valvular atrial fibrillation, bleeding is still a major concern. AREAS COVERED This article reviews current pharmacotherapeutic options in this setting. Particular emphasis is placed on the ability of the new molecules to minimize the bleeding risk in elderly patients. A systematic search of PubMed, Web of Science, and the Cochrane Library up to March 2023 was carried out. EXPERT OPINION Contact phase of coagulation is a possible new target for anticoagulant therapy. Indeed, congenital or acquired deficiency of contact phase factors is associated with reduced thrombotic burden and limited risk of spontaneous bleeding. These new drugs seem particularly suitable for stroke prevention in elderly patients with non-valvular atrial fibrillation in whom the hemorrhagic risk is high. Most of anti Factor XI (FXI) drugs are for parenteral use only. A group of small molecules are for oral use and therefore are candidates to substitute direct oral anticoagulants (DOACs) for stroke prevention in elderly patients with atrial fibrillation. Doubts remain on the possibility of impaired hemostasis. Indeed, a fine calibration of inhibition of contact phase factors is crucial for an effective and safe treatment.
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Affiliation(s)
| | - Gentian Denas
- Cardiology Clinic, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, Padua University Hospital, Padua, Italy
| | - Vittorio Pengo
- Cardiology Clinic, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, Padua University Hospital, Padua, Italy
- Arianna Foundation on Anticoagulation, Bologna, Italy
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13
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Yu H, Frederiksen J, Sullenger BA. Applications and future of aptamers that achieve rapid-onset anticoagulation. RNA (NEW YORK, N.Y.) 2023; 29:455-462. [PMID: 36697262 PMCID: PMC10019365 DOI: 10.1261/rna.079503.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
In this short Perspective, we discuss the history of, and recent progress toward, the development of aptamers that can serve as rapid onset anticoagulants during cardiopulmonary bypass (CPB), extracorporeal membrane oxygenation (ECMO), and catheter-based diagnostic and interventional procedures, several million of which are performed each year worldwide. Aptamer anticoagulants provide potent and antidote-controllable anticoagulation and have low immunogenicity. New methods of aptamer isolation and engineering have not only improved the quality of aptamers, but also accelerated their development. Unfortunately, no aptamer identified to date can produce an anticoagulant effect as potent as that produced by unfractionated heparin (UFH), the standard anticoagulant for CPB. We have suggested several possible strategies to amplify the anticoagulant potency of existing aptamer anticoagulants.
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Affiliation(s)
- Haixiang Yu
- Department of Surgery, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - James Frederiksen
- Department of Surgery, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Bruce A Sullenger
- Department of Surgery, Duke University Medical Center, Durham, North Carolina 27710, USA
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
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14
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Abstract
The concentrations of specific macromolecular species can be quantified using diagnostic tools that rely on molecular recognition by nucleic acid aptamers. One such approach involves the formation of osmium tetroxide 2,2'-bipyridine protein adducts, followed by electrochemical detection of analytes that bind specifically to electrode-tethered aptamers. In conjunction with a 27-mer DNA aptamer that binds specifically to exosite II on human alpha thrombin, this technique permits, in theory, a highly sensitive diagnostic tool for the quantification of serum thrombin levels. However, thrombin's aptamer binding site is lined by two tryptophan residues and the conjugation of bulky osmium groups to these residues weakens aptamer binding by an estimated 4 to 12 kcal/mol, undermining detection sensitivity. Therefore, we have rationally modified this DNA aptamer to strengthen its thrombin binding in the presence of conjugated osmium. Specifically, aptamers carrying long hydrophobic thymine derivatives in place of guanine 21 have binding affinities for osmium-conjugated thrombin that are enhanced by 10 to 15 kcal/mol, suggesting that these modified aptamers may be effective in a highly sensitive electrochemical sensor for the quantification of low concentrations of thrombin. Our approach of using molecular simulation to subtly re-engineer a DNA aptamer may be generally applicable for the optimization of other macromolecular binding interfaces.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Loan Huynh
- Department of Chemistry, University at Albany, State University of New York, Albany, NY, USA
| | - Alan Chen
- Department of Chemistry, University at Albany, State University of New York, Albany, NY, USA
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15
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Three-dimensional ordered macroporous MOF-based smart gating membrane with size screening effect and aptamer specificity for highly efficient thrombin isolation. J Memb Sci 2023. [DOI: 10.1016/j.memsci.2022.121132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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16
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Li Y, Zhao J, Xue Z, Tsang C, Qiao X, Dong L, Li H, Yang Y, Yu B, Gao Y. Aptamer nucleotide analog drug conjugates in the targeting therapy of cancers. Front Cell Dev Biol 2022; 10:1053984. [PMID: 36544906 PMCID: PMC9760908 DOI: 10.3389/fcell.2022.1053984] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022] Open
Abstract
Aptamers are short single-strand oligonucleotides that can form secondary and tertiary structures, fitting targets with high affinity and specificity. They are so-called "chemical antibodies" and can target specific biomarkers in both diagnostic and therapeutic applications. Systematic evolution of ligands by exponential enrichment (SELEX) is usually used for the enrichment and selection of aptamers, and the targets could be metal ions, small molecules, nucleotides, proteins, cells, or even tissues or organs. Due to the high specificity and distinctive binding affinity of aptamers, aptamer-drug conjugates (ApDCs) have demonstrated their potential role in drug delivery for cancer-targeting therapies. Compared with antibodies which are produced by a cell-based bioreactor, aptamers are chemically synthesized molecules that can be easily conjugated to drugs and modified; however, the conventional ApDCs conjugate the aptamer with an active drug using a linker which may add more concerns to the stability of the ApDC, the drug-releasing efficiency, and the drug-loading capacity. The function of aptamer in conventional ApDC is just as a targeting moiety which could not fully perform the advantages of aptamers. To address these drawbacks, scientists have started using active nucleotide analogs as the cargoes of ApDCs, such as clofarabine, ara-guanosine, gemcitabine, and floxuridine, to replace all or part of the natural nucleotides in aptamer sequences. In turn, these new types of ApDCs, aptamer nucleotide analog drug conjugates, show the strength for targeting efficacy but avoid the complex drug linker designation and improve the synthetic efficiency. More importantly, these classic nucleotide analog drugs have been used for many years, and aptamer nucleotide analog drug conjugates would not increase any unknown druggability risk but improve the target tumor accumulation. In this review, we mainly summarized aptamer-conjugated nucleotide analog drugs in cancer-targeting therapies.
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Affiliation(s)
- Yongshu Li
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, China,Shenzhen Institute for Technology Innovation, National Institute of Metrology, Shenzhen, China,Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China,*Correspondence: Yongshu Li, ; Yunhua Gao,
| | - Jing Zhao
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, China
| | - Zhichao Xue
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Chiman Tsang
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong, China
| | - Xiaoting Qiao
- Shenzhen Institute for Technology Innovation, National Institute of Metrology, Shenzhen, China
| | - Lianhua Dong
- Shenzhen Institute for Technology Innovation, National Institute of Metrology, Shenzhen, China,Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Huijie Li
- Shenzhen Institute for Technology Innovation, National Institute of Metrology, Shenzhen, China
| | - Yi Yang
- Shenzhen Institute for Technology Innovation, National Institute of Metrology, Shenzhen, China
| | - Bin Yu
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Yunhua Gao
- Shenzhen Institute for Technology Innovation, National Institute of Metrology, Shenzhen, China,Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China,*Correspondence: Yongshu Li, ; Yunhua Gao,
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17
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Spiridonova VA, Naumova YO, Nikolaeva PA, Novikova TM, Kolomijtseva GY. Thermodynamics and Kinetics of Unfolding of Antiparallel G-Quadruplexes in Anti-Thrombin Aptamers. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:1292-1300. [PMID: 36509716 DOI: 10.1134/s0006297922110086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The process of unfolding of G-quadruplex structure in the RE31 DNA-aptamer and in its complex with thrombin under the action of the fluorescently labeled complementary oligonucleotides of varying length with formation of double-helix structures has been studied. It has been suggested that G-quadruplex unfolding involves formation of an intermediate complex with an oligonucleotide. Thermodynamic parameters and kinetics of unfolding of the free aptamer and its complex with thrombin differ. Extension of the oligonucleotide sequence complementary to G-quadruplex by two nucleotides to cover the so-called "hinge region" had little impact on the conformational transition of G-quadruplex of the free aptamer. However, a pronounced effect has been observed for the aptamer-protein complex. Most likely these differences could be explained by the thrombin-induced conformational transition of the aptamer involving the hinge region.
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Affiliation(s)
- Vera A Spiridonova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Yulia O Naumova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Polina A Nikolaeva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Tatiana M Novikova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Galina Ya Kolomijtseva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
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18
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Zhu M, Xu F, Miao S, Xie C, Li H, Li S, Xia F. Incorporation of a Multi-Valent Aptamer into Electrochemical Biosensors to Achieve an Improved Performance for Thrombin Analysis in Blood Serum. Chempluschem 2022; 87:e202200325. [PMID: 36410784 DOI: 10.1002/cplu.202200325] [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: 09/19/2022] [Revised: 10/10/2022] [Indexed: 11/23/2022]
Abstract
The electrochemical aptamer-based (E-AB) biosensor usually has a long reaction time when detecting thrombin. This work reports the design of an E-AB biosensor with dual recognition sites to quickly detect thrombin. Specifically, two specific recognition sites of thrombin were used to design three aptamer sequences (TBA-15, TBA-29 and TBA-U), followed by fabrication of corresponding sensors. First, we tested these three types of biosensors in tris buffer solution, and found that the response time of the TBA-U sensor to the same concentration of thrombin was about 2 hours, which is shorter than TBA-15 and TBA-29 sensors. Then, we also did the same test in 50 % diluted serum with 500 nM thrombin. The response time of the TBA-U sensor was about 2 hours, which is still faster than the 3 hours of TBA-15 sensor and the 5.5 hours for TBA-29 sensor. In addition, in terms of dynamic range and specificity, TBA-U has good performance.
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Affiliation(s)
- Man Zhu
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
| | - Fan Xu
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
| | - Siyuan Miao
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
| | - Chongyu Xie
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
| | - Hui Li
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
| | - Shaoguang Li
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
| | - Fan Xia
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
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19
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Gómez-Arconada L, Díaz-Fernández A, Ferapontova EE. Ultrasensitive disposable apatasensor for reagentless electrocatalytic detection of thrombin: An O2-Dependent hemin-G4-aptamer assay on gold screen-printed electrodes. Talanta 2022; 245:123456. [DOI: 10.1016/j.talanta.2022.123456] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 04/01/2022] [Accepted: 04/03/2022] [Indexed: 11/25/2022]
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20
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Hu X, Tang L, Zheng M, Liu J, Zhang Z, Li Z, Yang Q, Xiang S, Fang L, Ren Q, Liu X, Huang CZ, Mao C, Zuo H. Structure-Guided Designing Pre-Organization in Bivalent Aptamers. J Am Chem Soc 2022; 144:4507-4514. [PMID: 35245025 DOI: 10.1021/jacs.1c12593] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Multivalent interaction is often used in molecular design and leads to engineered multivalent ligands with increased binding avidities toward target molecules. The resulting binding avidity relies critically on the rigid scaffold that joins multiple ligands as the scaffold controls the relative spatial positions and orientations toward target molecules. Currently, no general design rules exist to construct a simple and rigid DNA scaffold for properly joining multiple ligands. Herein, we report a crystal structure-guided strategy for the rational design of a rigid bivalent aptamer with precise control over spatial separation and orientation. Such a pre-organization allows the two aptamer moieties simultaneously to bind to the target protein at their native conformations. The bivalent aptamer binding has been extensively characterized, and an enhanced binding has been clearly observed. This strategy, we believe, could potentially be generally applicable to design multivalent aptamers.
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Affiliation(s)
- Xiaoli Hu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Linlin Tang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Mengxi Zheng
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jian Liu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Zhe Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Zhe Li
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Quan Yang
- Department of Cardiology, The Fourth People's Hospital of Sichuan Province, Chengdu 610016, China
| | - Shoubo Xiang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Liang Fang
- Department of Oncology, The Ninth People's Hospital of Chongqing, Chongqing 400700, China
| | - Qiao Ren
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Xuemei Liu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Cheng Zhi Huang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Chengde Mao
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China.,Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Hua Zuo
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
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21
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Caglayan MO, Üstündağ Z, Şahin S. Spectroscopic ellipsometry methods for brevetoxin detection. Talanta 2022; 237:122897. [PMID: 34736713 DOI: 10.1016/j.talanta.2021.122897] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 08/10/2021] [Accepted: 09/19/2021] [Indexed: 11/28/2022]
Abstract
The spectroscopic ellipsometry (SE), and attenuated internal reflection spectroscopic ellipsometry (TIRE) are promising methods in label-free biosensing applications. An ellipsometer running under surface plasmon resonance (SPR) conditions has unique advantages over other SPR-based methods in terms of sensitivity and real-time/label-free measurement capability. In this study, both SE and TIRE-based brevetoxin B (BTX) sensors were developed using two anti-BTX aptamers reported before. A new aptamer sequence was also derived from these two antiBTX aptamers using predictive modeling tools and an exclusion method. All three antiBTX aptamers' analytical performances were quite competitive in terms of both detecting range and detection limits. However, the selectivity of the previously reported aptamers against analogs of BTX was poor at low detection ranges, especially for okadaic acid. Furthermore, the selectivity of the derived aptamer was lower than its predecessors. The sensors were capable of detecting BTX in the range of 0.05 nM-1600 nM in the TIRE and 0.5 nM-2000 nM in the SE configuration. The detection limits of the sensors were 1.48 nM (1.32 ng/mL) and 0.80 nM (0.72 ng/mL) for SE and TIRE configurations, respectively. Both configurations have been used successfully to detect BTX standards spiked into real fish and shrimp samples.
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Affiliation(s)
| | - Zafer Üstündağ
- Department of Chemistry, Kütahya Dumlupınar University, 43100, Kütahya, Turkey
| | - Samet Şahin
- Department of Bioengineering, Bilecik Şeyh Edebali University, 11230, Bilecik, Turkey
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22
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A Fluorescence Kinetic-Based Aptasensor Employing Stilbene Isomerization for Detection of Thrombin. MATERIALS 2021; 14:ma14226927. [PMID: 34832326 PMCID: PMC8624160 DOI: 10.3390/ma14226927] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/04/2021] [Accepted: 11/09/2021] [Indexed: 02/06/2023]
Abstract
It is important to detect thrombin due to its physiological and pathological roles, where rapid and simple analytical approaches are needed. In this study, an aptasensor based on fluorescence attenuation kinetics for the detection of thrombin is presented, which incorporates the features of stilbene and aptamer. We designed and synthesized an aptasensor by one-step coupling of stilbene compound and aptamer, which employed the adaptive binding of the aptamer with thrombin to cause a change in stilbene fluorescence attenuation kinetics. The sensor realized detection of thrombin by monitoring the variation in apparent fluorescence attenuation rate constant (kapp), which could be further used for probing of enzyme–aptamer binding. In comprehensive studies, the developed aptasensor presented satisfactory performance on repeatability, specificity, and regeneration capacity, which realized rapid sensing (10 s) with a limit of detection (LOD) of 0.205 μM. The strategy was successful across seven variants of thrombin aptasensors, with tunable kapp depending on the SITS (4-Acetamido-4′-isothiocyanato-2,2′-stilbenedisulfonic acid disodium salt hydrate) grafting site. Analyte detection mode was demonstrated in diluted serum, requiring no separation or washing steps. The new sensing mode for thrombin detection paves a way for high-throughput kinetic-based sensors for exploiting aptamers targeted at clinically relevant proteins.
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23
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Xie J, Zheng J, Hong X, Tong X, Liu X, Song Q, Liu S, Liu S. Protein-DNA complex structure modeling based on structural template. Biochem Biophys Res Commun 2021; 577:152-157. [PMID: 34517213 DOI: 10.1016/j.bbrc.2021.09.018] [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: 07/29/2021] [Revised: 09/05/2021] [Accepted: 09/06/2021] [Indexed: 10/20/2022]
Abstract
DNA-binding is an important feature of proteins, and protein-DNA interaction involves in many life processes. Various computational methods have been developed to predict protein-DNA complex structures due to the difficulty of experimentally obtaining protein-DNA complex structures. However, prediction of protein-DNA complex is still a challenging problem compared with prediction of protein-RNA complex, this may be due to the large conformational changes between bound and unbound structure in both protein and DNA. We extend PRIME 2.0 to PRIME 2.0.1 to model protein-DNA complex structures. By comparing sequence and structure alignment methods, we found that structure-based methods can find more templates than sequence-based methods. The results of all-to-all structure alignments showed that DNA structure plays an important role in prediction of protein-DNA complex structure. By exploring the relationship of sequence and structure, we found that in protein-DNA interaction, numerous structures with dissimilar sequences have similar 3D structures and perform the similar function.
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Affiliation(s)
- Juan Xie
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Jinfang Zheng
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Xu Hong
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Xiaoxue Tong
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Xudong Liu
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Qi Song
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, China
| | - Sen Liu
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, China
| | - Shiyong Liu
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.
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24
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Exosite Binding in Thrombin: A Global Structural/Dynamic Overview of Complexes with Aptamers and Other Ligands. Int J Mol Sci 2021; 22:ijms221910803. [PMID: 34639143 PMCID: PMC8509272 DOI: 10.3390/ijms221910803] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 09/24/2021] [Accepted: 10/01/2021] [Indexed: 12/13/2022] Open
Abstract
Thrombin is the key enzyme of the entire hemostatic process since it is able to exert both procoagulant and anticoagulant functions; therefore, it represents an attractive target for the developments of biomolecules with therapeutic potential. Thrombin can perform its many functional activities because of its ability to recognize a wide variety of substrates, inhibitors, and cofactors. These molecules frequently are bound to positively charged regions on the surface of protein called exosites. In this review, we carried out extensive analyses of the structural determinants of thrombin partnerships by surveying literature data as well as the structural content of the Protein Data Bank (PDB). In particular, we used the information collected on functional, natural, and synthetic molecular ligands to define the anatomy of the exosites and to quantify the interface area between thrombin and exosite ligands. In this framework, we reviewed in detail the specificity of thrombin binding to aptamers, a class of compounds with intriguing pharmaceutical properties. Although these compounds anchor to protein using conservative patterns on its surface, the present analysis highlights some interesting peculiarities. Moreover, the impact of thrombin binding aptamers in the elucidation of the cross-talk between the two distant exosites is illustrated. Collectively, the data and the work here reviewed may provide insights into the design of novel thrombin inhibitors.
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25
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Beyond G-Quadruplexes-The Effect of Junction with Additional Structural Motifs on Aptamers Properties. Int J Mol Sci 2021; 22:ijms22189948. [PMID: 34576112 PMCID: PMC8466185 DOI: 10.3390/ijms22189948] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 12/02/2022] Open
Abstract
G-quadruplexes constitute an important type of nucleic acid structure, which can be found in living cells and applied by cell machinery as pivotal regulatory elements. Importantly, robust development of SELEX technology and modern, nucleic acid-based therapeutic strategies targeted towards various molecules have also revealed a large group of potent aptamers whose structures are grounded in G-quadruplexes. In this review, we analyze further extension of tetraplexes by additional structural elements and investigate whether G-quadruplex junctions with duplex, hairpin, triplex, or second G-quadruplex motifs are favorable for aptamers stability and biological activity. Furthermore, we indicate the specific and pivotal role of the G-quadruplex domain and the additional structural elements in interactions with target molecules. Finally, we consider the potency of G-quadruplex junctions in future applications and indicate the emerging research area that is still waiting for development to obtain highly specific and effective nucleic acid-based molecular tools.
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26
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Malecka K, Ferapontova EE. Femtomolar Detection of Thrombin in Serum and Cerebrospinal Fluid via Direct Electrocatalysis of Oxygen Reduction by the Covalent G4-Hemin-Aptamer Complex. ACS APPLIED MATERIALS & INTERFACES 2021; 13:37979-37988. [PMID: 33878266 DOI: 10.1021/acsami.1c03784] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Thrombin, a serine protease playing a central role in the coagulation cascade reactions and a potent neurotoxin produced by injured brain endothelial cells, is a recognized cardiac biomarker and a critical biomarker for Alzheimer's disease development. Both in vivo and in vitro, its low physiological concentrations and nonspecific binding of other components of physiological fluids complicate electroanalysis of thrombin. Here, femtomolar levels of thrombin in serum and an artificial cerebrospinal fluid (CSF) were detected by the indicator-free electrochemical methodology exploiting the O2 reduction reaction directly, with no electron transfer mediators, electrocatalyzed by the covalent G4-hemin DNAzyme complex naturally self-assembling upon thrombin binding to the hemin-modified 29-mer DNA aptamer sequence tethered to gold via an alkanethiol linker. Coadsorbed PEG inhibited nonspecific protein binding and allowed the sought signal resolution. The proposed assay exploiting the "oxidase" activity of G4-hemin DNAzyme does not require any coreactants necessary for the traditional peroxidase activity-based assays with this DNAzyme, such as H2O2 and redox mediators, or solution deaeration and allows fast, overall 30 min analysis of thrombin in aerated buffer, CSF, and 1% human serum solutions. This pioneer approach exploiting the oxidase activity G4-hemin DNAzyme is simple, sensitive, and selective and represents a new tool for ultrasensitive electrocatalytic assays based on simple and efficient O2-dependent DNAzyme labels.
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Affiliation(s)
- Kamila Malecka
- Interdisciplinary Nanoscience Center (iNANO), Science and Technology, Aarhus University, Gustav Wieds Vej 1590-14, Aarhus C DK-8000, Denmark
- Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, Olsztyn 10-748, Poland
| | - Elena E Ferapontova
- Interdisciplinary Nanoscience Center (iNANO), Science and Technology, Aarhus University, Gustav Wieds Vej 1590-14, Aarhus C DK-8000, Denmark
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27
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Heredia FL, Roche-Lima A, Parés-Matos EI. A novel artificial intelligence-based approach for identification of deoxynucleotide aptamers. PLoS Comput Biol 2021; 17:e1009247. [PMID: 34343165 PMCID: PMC8362955 DOI: 10.1371/journal.pcbi.1009247] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 08/13/2021] [Accepted: 07/05/2021] [Indexed: 02/07/2023] Open
Abstract
The selection of a DNA aptamer through the Systematic Evolution of Ligands by EXponential enrichment (SELEX) method involves multiple binding steps, in which a target and a library of randomized DNA sequences are mixed for selection of a single, nucleotide-specific molecule. Usually, 10 to 20 steps are required for SELEX to be completed. Throughout this process it is necessary to discriminate between true DNA aptamers and unspecified DNA-binding sequences. Thus, a novel machine learning-based approach was developed to support and simplify the early steps of the SELEX process, to help discriminate binding between DNA aptamers from those unspecified targets of DNA-binding sequences. An Artificial Intelligence (AI) approach to identify aptamers were implemented based on Natural Language Processing (NLP) and Machine Learning (ML). NLP method (CountVectorizer) was used to extract information from the nucleotide sequences. Four ML algorithms (Logistic Regression, Decision Tree, Gaussian Naïve Bayes, Support Vector Machines) were trained using data from the NLP method along with sequence information. The best performing model was Support Vector Machines because it had the best ability to discriminate between positive and negative classes. In our model, an Accuracy (A) of 0.995, the fraction of samples that the model correctly classified, and an Area Under the Receiving Operating Curve (AUROC) of 0.998, the degree by which a model is capable of distinguishing between classes, were observed. The developed AI approach is useful to identify potential DNA aptamers to reduce the amount of rounds in a SELEX selection. This new approach could be applied in the design of DNA libraries and result in a more efficient and faster process for DNA aptamers to be chosen during SELEX. In this manuscript authors explain the development and validation of a novel artificial intelligence approach to support and simplify the early steps of the process from SELEX, to help discriminate binding between deoxynucleotide aptamers from those unspecified targets of DNA-binding sequences. The approach was implemented based on Natural Language Processing and Machine Learning. CountVectorizer, a Natural Language Processing method, was used to extract information from nucleotide sequences. Four Machine Learning algorithms (Logistic Regression, Decision Tree, Gaussian Naïve Bayes, and Support Vector Machines) were trained using data from the Natural Language Processing method along with sequence information. From these four trained machine learning algorithms, the best performance and selected model was Support Vectors Machines, because it had the best discriminatory metrics (i.e., Accuracy (A) = 0.995; AUROC (AU) = 0.998). In general, all models showed good metric results for predicting DNA aptamer sequences. The Machine Learning model complexity and difficult interpretation may hinder its application into the standard practice. For this reason, the development of a web-app is already taking place to facilitate the interpretation and application of the obtained results.
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Affiliation(s)
- Frances L. Heredia
- Department of Chemistry, University of Puerto Rico-Mayagüez Campus, Mayagüez, Puerto Rico, United States of America
| | - Abiel Roche-Lima
- Center for Collaborative Research in Health Disparities, University of Puerto Rico-Medical Sciences Campus, San Juan, Puerto Rico, United States of America
| | - Elsie I. Parés-Matos
- Department of Chemistry, University of Puerto Rico-Mayagüez Campus, Mayagüez, Puerto Rico, United States of America
- * E-mail:
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28
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2D titanium carbide nanosheets based fluorescent aptasensor for sensitive detection of thrombin. Talanta 2021; 228:122219. [PMID: 33773725 DOI: 10.1016/j.talanta.2021.122219] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/02/2021] [Accepted: 02/13/2021] [Indexed: 01/06/2023]
Abstract
The emerging two-dimensional titanium carbides (MXenes) have a large potential in biomedical sensing owing to their excellent electrical and optical properties. Herein, a fluorescence resonance energy transfer (FRET) aptasensor with high sensitivity and specificity was constructed with single layer Ti3C2 MXene for quantitative detection of thrombin. The dye labelled thrombin-binding aptamer (TBA) was deposited on the surface of Ti3C2, and the fluorescence of which was efficiently quenched owing to the FRET between the dye and Ti3C2. The fact that thrombin forms quadruplex with TBA on Ti3C2 surface is due to the high electronic affinity between thrombin and Ti3C2. This process will cause the subsequent detachment of dye from the surface of Ti3C2, resulting in the recovery of fluorescence. Because of the special structure and high fluorescence quenching efficiency of Ti3C2 MXene, the aptasensor shows a high sensitivity with a low detection limit for thrombin at 5.27 pM. Three different aptamers were compared, and the aptamer HD22 is most sensitive for detection of thrombin originated from its great specificity in the human plasma. Importantly, this Ti3C2 MXene-based FRET aptasensor can detect thrombin in human serum accurately. These results suggest that the Ti3C2 MXene-based FRET aptasensor hold a great prospect in clinical diagnosis in the real-world applications.
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29
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Structural Biology for the Molecular Insight between Aptamers and Target Proteins. Int J Mol Sci 2021; 22:ijms22084093. [PMID: 33920991 PMCID: PMC8071422 DOI: 10.3390/ijms22084093] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 02/07/2023] Open
Abstract
Aptamers are promising therapeutic and diagnostic agents for various diseases due to their high affinity and specificity against target proteins. Structural determination in combination with multiple biochemical and biophysical methods could help to explore the interacting mechanism between aptamers and their targets. Regrettably, structural studies for aptamer–target interactions are still the bottleneck in this field, which are facing various difficulties. In this review, we first reviewed the methods for resolving structures of aptamer–protein complexes and for analyzing the interactions between aptamers and target proteins. We summarized the general features of the interacting nucleotides and residues involved in the interactions between aptamers and proteins. Challenges and perspectives in current methodologies were discussed. Approaches for determining the binding affinity between aptamers and target proteins as well as modification strategies for stabilizing the binding affinity of aptamers to target proteins were also reviewed. The review could help to understand how aptamers interact with their targets and how alterations such as chemical modifications in the structures affect the affinity and function of aptamers, which could facilitate the optimization and translation of aptamers-based theranostics.
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30
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Structural and functional analysis of the simultaneous binding of two duplex/quadruplex aptamers to human α-thrombin. Int J Biol Macromol 2021; 181:858-867. [PMID: 33864869 DOI: 10.1016/j.ijbiomac.2021.04.076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 11/23/2022]
Abstract
The long-range communication between the two exosites of human α-thrombin (thrombin) tightly modulates the protein-effector interactions. Duplex/quadruplex aptamers represent an emerging class of very effective binders of thrombin. Among them, NU172 and HD22 aptamers are at the forefront of exosite I and II recognition, respectively. The present study investigates the simultaneous binding of these two aptamers by combining a structural and dynamics approach. The crystal structure of the ternary complex formed by the thrombin with NU172 and HD22_27mer provides a detailed view of the simultaneous binding of these aptamers to the protein, inspiring the design of novel bivalent thrombin inhibitors. The crystal structure represents the starting model for molecular dynamics studies, which point out the cooperation between the binding at the two exosites. In particular, the binding of an aptamer to its exosite reduces the intrinsic flexibility of the other exosite, that preferentially assumes conformations similar to those observed in the bound state, suggesting a predisposition to interact with the other aptamer. This behaviour is reflected in a significant increase of the anticoagulant activity of NU172 when the inactive HD22_27mer is bound to exosite II, providing a clear evidence of the synergic action of the two aptamers.
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31
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Shang X, Guan Z, Zhang S, Shi L, You H. Predicting the aptamer SYL3C-EpCAM complex's structure with the Martini-based simulation protocol. Phys Chem Chem Phys 2021; 23:7066-7079. [PMID: 33496283 DOI: 10.1039/d0cp05003b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Aptamers (small single strand DNA/RNAs) such as SYL3C are considered as ideal alternatives to antibodies in cancer related research studies. However, 3D structure predictions for aptamers and aptamer-protein complexes are scarce due to the high cost of experimental measurements and unreliable computer-based methods. Thus aptamers' diagnostic and therapeutic applications are severely restricted. To meet the challenge, we proposed a Martini-based aptamer-protein complex prediction protocol. By combining the base-base contact map from simulation and secondary structure prediction from various tools, improved secondary structure predictions can be obtained. This method reduced the risk of providing incorrect or incomplete base pairs in secondary structure prediction. Thus 3D structure modeling based on the secondary structure can be more reliable. We introduced the soft elastic network to the hairpin folded regions of the Martini ssDNAs to preserve their canonical structure. Using our protocol, we predicted the first 3D structure of the aptamer SYL3C and the SYL3C-EpCAM complex. We believe that our work could contribute to the future aptamer-related research studies and medical implications.
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Affiliation(s)
- Xu Shang
- State Key Laboratory of Computer Architecture, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China.
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Smirnov I, Kolganova N, Troisi R, Sica F, Timofeev E. Expanding the recognition interface of the thrombin-binding aptamer HD1 through modification of residues T3 and T12. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 23:863-871. [PMID: 33614235 PMCID: PMC7868722 DOI: 10.1016/j.omtn.2021.01.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 01/08/2021] [Indexed: 01/11/2023]
Abstract
Post-SELEX modification of DNA aptamers is an established strategy to improve their affinity or inhibitory characteristics. In this study, we examined the possibility of increasing the recognition interface between the thrombin-binding aptamer HD1 (TBA) and thrombin by adding a chemically modified side chain to selected nucleotide residues. A panel of 22 TBA variants with N3-modified residues T3 and T12 was prepared by a two-step modification procedure. Aptamers were characterized by a combination of biophysical and biochemical methods. We identified mutants with enhanced affinity and improved anticoagulant activity. The crystal structures of thrombin complexes with three selected modified variants revealed that the modified pyrimidine base invariably allocates in proximity to thrombin residues Tyr76 and Ile82 due to the directing role of the unmodified TT loop. The modifications induced an increase in the contact areas between thrombin and the modified TBAs. Comparative analysis of the structural, biochemical, and biophysical data suggests that the non-equivalent binding modes of the mutants with thrombin in the T3- and T12-modified series account for the observed systematic differences in their affinity characteristics. In this study, we show that extending the recognition surface between the protein and modified aptamers is a promising approach that may improve characteristics of aptamer ligands.
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Affiliation(s)
- Igor Smirnov
- Federal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, Russia
| | - Natalia Kolganova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Romualdo Troisi
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Filomena Sica
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Edward Timofeev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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Riccardi C, Napolitano E, Platella C, Musumeci D, Montesarchio D. G-quadruplex-based aptamers targeting human thrombin: Discovery, chemical modifications and antithrombotic effects. Pharmacol Ther 2020; 217:107649. [PMID: 32777331 DOI: 10.1016/j.pharmthera.2020.107649] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 07/29/2020] [Indexed: 02/07/2023]
Abstract
First studies on thrombin-inhibiting DNA aptamers were reported in 1992, and since then a large number of anticoagulant aptamers has been discovered. TBA - also named HD1, a 15-mer G-quadruplex (G4)-forming oligonucleotide - is the best characterized thrombin binding aptamer, able to specifically recognize the protein exosite I, thus inhibiting the conversion of soluble fibrinogen into insoluble fibrin strands. Unmodified nucleic acid-based aptamers, in general, and TBA in particular, exhibit limited pharmacokinetic properties and are rapidly degraded in vivo by nucleases. In order to improve the biological performance of aptamers, a widely investigated strategy is the introduction of chemical modifications in their backbone at the level of the nucleobases, sugar moieties or phosphodiester linkages. Besides TBA, also other thrombin binding aptamers, able to adopt a well-defined G4 structure, e.g. mixed duplex/quadruplex sequences, as well as homo- and hetero-bivalent constructs, have been identified and optimized. Considering the growing need of new efficient anticoagulant agents associated with the strong therapeutic potential of these thrombin inhibitors, the research on thrombin binding aptamers is still a very hot and intriguing field. Herein, we comprehensively described the state-of-the-art knowledge on the DNA-based aptamers targeting thrombin, especially focusing on the optimized analogues obtained by chemically modifying the oligonucleotide backbone, and their biological performances in therapeutic applications.
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Affiliation(s)
- Claudia Riccardi
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; Department of Advanced Medical and Surgical Sciences, 2(nd) Division of Neurology, Center for Rare Diseases and InterUniversity Center for Research in Neurosciences, University of Campania Luigi Vanvitelli, via Sergio Pansini, 5, I-80131 Naples, Italy.
| | - Ettore Napolitano
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy.
| | - Chiara Platella
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy.
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; Institute of Biostructures and Bioimages, CNR, via Mezzocannone 16, I-80134 Naples, Italy.
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy.
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34
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Lu XJ. DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL. Nucleic Acids Res 2020; 48:e74. [PMID: 32442277 PMCID: PMC7367123 DOI: 10.1093/nar/gkaa426] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 04/26/2020] [Accepted: 05/07/2020] [Indexed: 12/11/2022] Open
Abstract
Sophisticated analysis and simplified visualization are crucial for understanding complicated structures of biomacromolecules. DSSR (Dissecting the Spatial Structure of RNA) is an integrated computational tool that has streamlined the analysis and annotation of 3D nucleic acid structures. The program creates schematic block representations in diverse styles that can be seamlessly integrated into PyMOL and complement its other popular visualization options. In addition to portraying individual base blocks, DSSR can draw Watson-Crick pairs as long blocks and highlight the minor-groove edges. Notably, DSSR can dramatically simplify the depiction of G-quadruplexes by automatically detecting G-tetrads and treating them as large square blocks. The DSSR-enabled innovative schematics with PyMOL are aesthetically pleasing and highly informative: the base identity, pairing geometry, stacking interactions, double-helical stems, and G-quadruplexes are immediately obvious. These features can be accessed via four interfaces: the command-line interface, the DSSR plugin for PyMOL, the web application, and the web application programming interface. The supplemental PDF serves as a practical guide, with complete and reproducible examples. Thus, even beginners or occasional users can get started quickly, especially via the web application at http://skmatic.x3dna.org.
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Affiliation(s)
- Xiang-Jun Lu
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
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35
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Qu H, Ma Q, Wang L, Mao Y, Eisenstein M, Soh HT, Zheng L. Measuring Aptamer Folding Energy Using a Molecular Clamp. J Am Chem Soc 2020; 142:11743-11749. [PMID: 32491843 DOI: 10.1021/jacs.0c01570] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Folding energy (ΔGfold) offers a useful metric for characterizing the stability and function of aptamers. However, experimentally measuring the folding energy is challenging, and there is currently no general technique to measure this parameter directly. In this work, we present a simple approach for measuring aptamer folding energy. First, the aptamer is stretched under equilibrium conditions with a double-stranded DNA "molecular clamp" that is coupled to the aptamer ends. We then measure the total internal energy of stressed DNA molecules using time-lapse gel electrophoresis and compare the folding and unfolding behavior of molecular clamp-stressed molecules that incorporate either the aptamer or unstructured random single-stranded DNA in order to derive the aptamer folding energy. Using this approach, we measured a folding energy of 10.40 kJ/mol for the HD22 thrombin aptamer, which is consistent with other predictions and estimates. We also analyzed a simple hairpin structure, generating a folding energy result of 9.05 kJ/mol, consistent with the value predicted by computational models (9.24 kJ/mol). We believe our strategy offers an accessible and generalizable approach for obtaining such measurements with virtually any aptamer.
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Affiliation(s)
- Hao Qu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Qihui Ma
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Lu Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Yu Mao
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Michael Eisenstein
- Department of Electrical Engineering, Stanford University, Stanford, California 94305, United States.,Department of Radiology, Stanford University, Stanford, California 94305, United States
| | - Hyongsok Tom Soh
- Department of Electrical Engineering, Stanford University, Stanford, California 94305, United States.,Department of Radiology, Stanford University, Stanford, California 94305, United States
| | - Lei Zheng
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
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36
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Debiais M, Lelievre A, Smietana M, Müller S. Splitting aptamers and nucleic acid enzymes for the development of advanced biosensors. Nucleic Acids Res 2020; 48:3400-3422. [PMID: 32112111 PMCID: PMC7144939 DOI: 10.1093/nar/gkaa132] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/12/2020] [Accepted: 02/18/2020] [Indexed: 12/16/2022] Open
Abstract
In analogy to split-protein systems, which rely on the appropriate fragmentation of protein domains, split aptamers made of two or more short nucleic acid strands have emerged as novel tools in biosensor set-ups. The concept relies on dissecting an aptamer into a series of two or more independent fragments, able to assemble in the presence of a specific target. The stability of the assembled structure can further be enhanced by functionalities that upon folding would lead to covalent end-joining of the fragments. To date, only a few aptamers have been split successfully, and application of split aptamers in biosensing approaches remains as promising as it is challenging. Further improving the stability of split aptamer target complexes and with that the sensitivity as well as efficient working modes are important tasks. Here we review functional nucleic acid assemblies that are derived from aptamers and ribozymes/DNAzymes. We focus on the thrombin, the adenosine/ATP and the cocaine split aptamers as the three most studied DNA split systems and on split DNAzyme assemblies. Furthermore, we extend the subject into split light up RNA aptamers used as mimics of the green fluorescent protein (GFP), and split ribozymes.
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Affiliation(s)
- Mégane Debiais
- Institut des Biomolécules Max Mousseron, University of Montpellier, CNRS, ENCSM, Montpellier, France
| | - Amandine Lelievre
- University Greifswald, Institute for Biochemistry, Greifswald, Germany
| | - Michael Smietana
- Institut des Biomolécules Max Mousseron, University of Montpellier, CNRS, ENCSM, Montpellier, France
| | - Sabine Müller
- University Greifswald, Institute for Biochemistry, Greifswald, Germany
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37
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Troisi R, Balasco N, Vitagliano L, Sica F. Molecular dynamics simulations of human α-thrombin in different structural contexts: evidence for an aptamer-guided cooperation between the two exosites. J Biomol Struct Dyn 2020; 39:2199-2209. [PMID: 32202471 DOI: 10.1080/07391102.2020.1746693] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Human α-thrombin (thrombin) is a multifunctional enzyme that plays a pivotal role in the coagulation pathway. Thrombin activity can be effectively modulated by G-quadruplex-based oligonucleotide aptamers that specifically interact with the two positively charged regions (exosites I and II) on the protein surface. Although insightful atomic-level snapshots of the recognition between thrombin and aptamers have been recently achieved through crystallographic analyses, some dynamic aspects of this interaction have not been fully characterized. We here report molecular dynamics simulations of thrombin in different association states: ligand-free and binary/ternary complexes with the aptamers TBA (at exosite I) and HD22_27mer (at exosite II). The simulations carried out on the binary and ternary complexes formed by thrombin with these aptamers provide a dynamic view of the interactions that stabilize them in a crystal-free environment. Interestingly, the analysis of the dynamics of the exosites in different thrombin binding states clearly indicates that the HD22_27mer binding at the exosite II favours conformations of exosite I that are prone to the TBA binding. Similar effects are observed upon the binding of TBA to the exosite I. These observations provide an atomic-level picture of the exosite inter-communication in thrombin and explain the experimentally detected cooperativity of the TBA/HD22_27mer binding.
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Affiliation(s)
- Romualdo Troisi
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
| | - Nicole Balasco
- Institute of Biostructures and Bioimaging, CNR, Naples, Italy
| | | | - Filomena Sica
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
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38
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Kong D, Movahedi M, Mahdavi-Amiri Y, Yeung W, Tiburcio T, Chen D, Hili R. Evolutionary Outcomes of Diversely Functionalized Aptamers Isolated from in Vitro Evolution. ACS Synth Biol 2020; 9:43-52. [PMID: 31774997 DOI: 10.1021/acssynbio.9b00222] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Expanding the chemical diversity of aptamers remains an important thrust in the field in order to increase their functional potential. Previously, our group developed LOOPER, which enables the incorporation of up to 16 unique modifications throughout a ssDNA sequence, and applied it to the in vitro evolution of thrombin binders. As LOOPER-derived highly modified nucleic acids polymers are governed by two interrelated evolutionary variables, namely, functional modifications and sequence, the evolution of this polymer contrasts with that of canonical DNA. Herein we provide in-depth analysis of the evolution, including structure-activity relationships, mapping of evolutionary pressures on the library, and analysis of plausible evolutionary pathways that resulted in the first LOOPER-derived aptamer, TBL1. A detailed picture of how TBL1 interacts with thrombin and how it may mimic known peptide binders of thrombin is also proposed. Structural modeling and folding studies afford insights into how the aptamer displays critical modifications and also how modifications enhance the structural stability of the aptamer. A discussion of benefits and potential limitations of LOOPER during in vitro evolution is provided, which will serve to guide future evolutions of this highly modified class of aptamers.
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Affiliation(s)
- Dehui Kong
- Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia 30602, United States
| | - Matina Movahedi
- Department of Chemistry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - Yasaman Mahdavi-Amiri
- Department of Chemistry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - Wayland Yeung
- Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia 30602, United States
| | - Tristan Tiburcio
- Department of Chemistry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - Dickson Chen
- Department of Chemistry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - Ryan Hili
- Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia 30602, United States
- Department of Chemistry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
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39
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Afanasyeva A, Nagao C, Mizuguchi K. Prediction of the secondary structure of short DNA aptamers. Biophys Physicobiol 2019; 16:287-294. [PMID: 31984183 PMCID: PMC6975895 DOI: 10.2142/biophysico.16.0_287] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 07/29/2019] [Indexed: 12/20/2022] Open
Abstract
Aptamers have a spectrum of applications in biotechnology and drug design, because of the relative simplicity of experimental protocols and advantages of stability and specificity associated with their structural properties. However, to understand the structure-function relationships of aptamers, robust structure modeling tools are necessary. Several such tools have been developed and extensively tested, although most of them target various forms of biological RNA. In this study, we tested the performance of three tools in application to DNA aptamers, since DNA aptamers are the focus of many studies, particularly in drug discovery. We demonstrated that in most cases, the secondary structure of DNA can be reconstructed with acceptable accuracy by at least one of the three tools tested (Mfold, RNAfold, and CentroidFold), although the G-quadruplex motif found in many of the DNA aptamer structures complicates the prediction, as well as the pseudoknot interaction. This problem should be addressed more carefully to improve prediction accuracy.
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Affiliation(s)
- Arina Afanasyeva
- Artificial Intelligence Center for Health and Biomedical Research (ArCHER), National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
| | - Chioko Nagao
- Laboratory of In-silico Drug Design, Center for Drug Design Research (CDDR), National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
| | - Kenji Mizuguchi
- Artificial Intelligence Center for Health and Biomedical Research (ArCHER), National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan.,Laboratory of In-silico Drug Design, Center for Drug Design Research (CDDR), National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
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40
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Manochehry S, McConnell EM, Li Y. Unraveling Determinants of Affinity Enhancement in Dimeric Aptamers for a Dimeric Protein. Sci Rep 2019; 9:17824. [PMID: 31780794 PMCID: PMC6883073 DOI: 10.1038/s41598-019-54005-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 09/20/2019] [Indexed: 11/09/2022] Open
Abstract
High-affinity aptamers can be derived de novo by using stringent conditions in SELEX (Systematic Evolution of Ligands by EXponential enrichment) experiments or can be engineered post SELEX via dimerization of selected aptamers. Using electrophoretic mobility shift assays, we studied a series of heterodimeric and homodimeric aptamers, constructed from two DNA aptamers with distinct primary sequences and secondary structures, previously isolated for VEGF-165, a homodimeric protein. We investigated four factors envisaged to impact the affinity of a dimeric aptamer to a dimeric protein: (1) length of the linker between two aptamer domains, (2) linking orientation, (3) binding-site compatibility of two component aptamers in a heterodimeric aptamer, and (4) steric acceptability of the two identical aptamers in a homodimeric aptamer. All heterodimeric aptamers for VEGF-165 were found to exhibit monomeric aptamer-like affinity and the lack of affinity enhancement was attributed to binding-site overlap by the constituent aptamers. The best homodimeric aptamer showed 2.8-fold better affinity than its monomeric unit (Kd = 13.6 ± 2.7 nM compared to 37.9 ± 14 nM), however the barrier to further affinity enhancement was ascribed to steric interference of the constituent aptamers. Our findings point to the need to consider the issues of binding-site compatibility and spatial requirement of aptamers for the development of dimeric aptamers capable of bivalent recognition. Thus, determinants highlighted herein should be assessed in future multimerization efforts.
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Affiliation(s)
- Sepehr Manochehry
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St. W., Hamilton, ON, L8S 4K1, Canada
| | - Erin M McConnell
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St. W., Hamilton, ON, L8S 4K1, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St. W., Hamilton, ON, L8S 4K1, Canada. .,Department of Chemistry and Chemical Biology, McMaster University, 1280 Main St. W., Hamilton, ON, L8S 4K1, Canada.
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41
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Basavalingappa V, Bera S, Xue B, Azuri I, Tang Y, Tao K, Shimon LJW, Sawaya MR, Kolusheva S, Eisenberg DS, Kronik L, Cao Y, Wei G, Gazit E. Mechanically rigid supramolecular assemblies formed from an Fmoc-guanine conjugated peptide nucleic acid. Nat Commun 2019; 10:5256. [PMID: 31748568 PMCID: PMC6868146 DOI: 10.1038/s41467-019-13250-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 10/23/2019] [Indexed: 01/25/2023] Open
Abstract
The variety and complexity of DNA-based structures make them attractive candidates for nanotechnology, yet insufficient stability and mechanical rigidity, compared to polyamide-based molecules, limit their application. Here, we combine the advantages of polyamide materials and the structural patterns inspired by nucleic-acids to generate a mechanically rigid fluorenylmethyloxycarbonyl (Fmoc)-guanine peptide nucleic acid (PNA) conjugate with diverse morphology and photoluminescent properties. The assembly possesses a unique atomic structure, with each guanine head of one molecule hydrogen bonded to the Fmoc carbonyl tail of another molecule, generating a non-planar cyclic quartet arrangement. This structure exhibits an average stiffness of 69.6 ± 6.8 N m-1 and Young's modulus of 17.8 ± 2.5 GPa, higher than any previously reported nucleic acid derived structure. This data suggests that the unique cation-free "basket" formed by the Fmoc-G-PNA conjugate can serve as an attractive component for the design of new materials based on PNA self-assembly for nanotechnology applications.
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Affiliation(s)
- Vasantha Basavalingappa
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Santu Bera
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Bin Xue
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Key Laboratory of Intelligent Optical Sensing and Manipulation, Ministry of Education, Department of Physics, Nanjing University, 210093, Nanjing, People's Republic of China
| | - Ido Azuri
- Department of Materials and Interfaces, Weizmann Institute of Science, 76100, Rehovoth, Israel
| | - Yiming Tang
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), Fudan University, 200433, Shanghai, People's Republic of China
| | - Kai Tao
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Linda J W Shimon
- Department of Chemical Research Support, Weizmann Institute of Science, 76100, Rehovoth, Israel
| | - Michael R Sawaya
- Howard Hughes Medical Institute, UCLA-DOE Institute, Departments of Biological Chemistry and Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Sofiya Kolusheva
- Ilse Katz Institute for Nanotechnology, Ben Gurion University of the Negev, 84105, Beer Sheva, Israel
| | - David S Eisenberg
- Howard Hughes Medical Institute, UCLA-DOE Institute, Departments of Biological Chemistry and Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Leeor Kronik
- Department of Materials and Interfaces, Weizmann Institute of Science, 76100, Rehovoth, Israel
| | - Yi Cao
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Key Laboratory of Intelligent Optical Sensing and Manipulation, Ministry of Education, Department of Physics, Nanjing University, 210093, Nanjing, People's Republic of China
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), Fudan University, 200433, Shanghai, People's Republic of China
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978, Tel Aviv, Israel.
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42
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Gao H, Zhao J, Huang Y, Cheng X, Wang S, Han Y, Xiao Y, Lou X. Universal Design of Structure-Switching Aptamers with Signal Reporting Functionality. Anal Chem 2019; 91:14514-14521. [PMID: 31614078 DOI: 10.1021/acs.analchem.9b03368] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Structure-switching aptamers (SSAs) offer a promising recognition element for sensor development. However, the generation of SSAs via in vitro aptamer selection technologies or postselection engineering is challenging. Inspired by the two-domain structure of antibodies, we have devised a simple, universal strategy for engineering aptamers into SSAs with signal reporting functionality. These constructs consist of a "constant" domain, comprising a split DNAzyme G-quadruplex (G4) region for signal transduction, and a "variable" domain, comprising an aptamer sequence capable of specific target binding. In the absence of target, the G4-SSA construct folds into a parallel G4 structure with high peroxidase catalytic activity. Target binding disrupts the G4 structure, resulting in low enzymatic activity. We demonstrate that this change in DNAzyme activity enables sensitive and specific colorimetric detection of diverse targets including Hg2+, thrombin, sulfadimethoxine, cocaine, and 17β-estradiol. G4-SSAs can also achieve label-free fluorescence detection of various targets using a specific G4-binding dye. We demonstrate that diverse aptamers can be readily engineered into G4-SSA constructs independent of target class, binding affinity, aptamer length, or structure. This design strategy could broadly extend the power, accessibility, and utility of numerous SSA-based biosensors.
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Affiliation(s)
- Hualong Gao
- Department of Chemistry , Capital Normal University , Xisanhuan North Road, 105 , Beijing 100048 , China
| | - Jiaoxing Zhao
- Department of Chemistry , Capital Normal University , Xisanhuan North Road, 105 , Beijing 100048 , China
| | - Yang Huang
- Department of Chemistry , Capital Normal University , Xisanhuan North Road, 105 , Beijing 100048 , China
| | - Xiao Cheng
- Department of Chemistry , Capital Normal University , Xisanhuan North Road, 105 , Beijing 100048 , China
| | - Shuo Wang
- Department of Chemistry , Capital Normal University , Xisanhuan North Road, 105 , Beijing 100048 , China
| | - Yu Han
- Department of Chemistry , Capital Normal University , Xisanhuan North Road, 105 , Beijing 100048 , China
| | - Yi Xiao
- Department of Chemistry and Biochemistry , Florida International University , Miami , Florida 33199 , United States
| | - Xinhui Lou
- Department of Chemistry , Capital Normal University , Xisanhuan North Road, 105 , Beijing 100048 , China.,Department of Chemistry and Biochemistry , Florida International University , Miami , Florida 33199 , United States
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43
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Troisi R, Napolitano V, Spiridonova V, Russo Krauss I, Sica F. Several structural motifs cooperate in determining the highly effective anti-thrombin activity of NU172 aptamer. Nucleic Acids Res 2019; 46:12177-12185. [PMID: 30357392 PMCID: PMC6294562 DOI: 10.1093/nar/gky990] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 10/09/2018] [Indexed: 12/22/2022] Open
Abstract
Despite aptamers are very promising alternative to antibodies, very few of them are under clinical trials or are used as drugs. Among them, NU172 is currently in Phase II as anticoagulant in heart disease treatments. It inhibits thrombin activity much more effectively than TBA, the best-known thrombin binding aptamer. The crystal structure of thrombin-NU172 complex reveals a bimodular duplex/quadruplex architecture for the aptamer, which binds thrombin exosite I through a highly complementary surface involving all three loops of the G-quadruplex module. Although the duplex domain does not interact directly with thrombin, the features of the duplex/quadruplex junction and the solution data on two newly designed NU172 mutants indicate that the duplex moiety is important for the optimization of the protein-ligand interaction and for the inhibition of the enzyme activity. Our work discloses the structural features determining the inhibition of thrombin by NU172 and put the basis for the design of mutants with improved properties.
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Affiliation(s)
- Romualdo Troisi
- Department of Chemical Sciences, University of Naples 'Federico II', Naples 80126, Italy
| | - Valeria Napolitano
- Department of Chemical Sciences, University of Naples 'Federico II', Naples 80126, Italy
| | - Vera Spiridonova
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow 119992, Russia
| | - Irene Russo Krauss
- Department of Chemical Sciences, University of Naples 'Federico II', Naples 80126, Italy.,CSGI - Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, Sesto Fiorentino, FI 50019, Italy
| | - Filomena Sica
- Department of Chemical Sciences, University of Naples 'Federico II', Naples 80126, Italy
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44
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Algar WR, Jeen T, Massey M, Peveler WJ, Asselin J. Small Surface, Big Effects, and Big Challenges: Toward Understanding Enzymatic Activity at the Inorganic Nanoparticle-Substrate Interface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:7067-7091. [PMID: 30415548 DOI: 10.1021/acs.langmuir.8b02733] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Enzymes are important biomarkers for molecular diagnostics and targets for the action of drugs. In turn, inorganic nanoparticles (NPs) are of interest as materials for biological assays, biosensors, cellular and in vivo imaging probes, and vectors for drug delivery and theranostics. So how does an enzyme interact with a NP, and what are the outcomes of multivalent conjugation of its substrate to a NP? This invited feature article addresses the current state of the art in answering this question. Using gold nanoparticles (Au NPs) and semiconductor quantum dots (QDs) as illustrative materials, we discuss aspects of enzyme structure-function and the properties of NP interfaces and surface chemistry that determine enzyme-NP interactions. These aspects render the substrate-on-NP configurations far more complex and heterogeneous than the conventional turnover of discrete substrate molecules in bulk solution. Special attention is also given to the limitations of a standard kinetic analysis of the enzymatic turnover of these configurations, the need for a well-defined model of turnover, and whether a "hopping" model can account for behaviors such as the apparent acceleration of enzyme activity. A detailed and predictive understanding of how enzymes turn over multivalent NP-substrate conjugates will require a convergence of many concepts and tools from biochemistry, materials, and interface science. In turn, this understanding will help to enable rational, optimized, and value-added designs of NP bioconjugates for biomedical and clinical applications.
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Affiliation(s)
- W Russ Algar
- Department of Chemistry , University of British Columbia , 2036 Main Mall , Vancouver , British Columbia V6T 1Z1 , Canada
| | - Tiffany Jeen
- Department of Chemistry , University of British Columbia , 2036 Main Mall , Vancouver , British Columbia V6T 1Z1 , Canada
| | - Melissa Massey
- Department of Chemistry , University of British Columbia , 2036 Main Mall , Vancouver , British Columbia V6T 1Z1 , Canada
| | - William J Peveler
- Department of Chemistry , University of British Columbia , 2036 Main Mall , Vancouver , British Columbia V6T 1Z1 , Canada
- Division of Biomedical Engineering, School of Engineering , University of Glasgow , Glasgow G12 8LT , United Kingdom
| | - Jérémie Asselin
- Department of Chemistry , University of British Columbia , 2036 Main Mall , Vancouver , British Columbia V6T 1Z1 , Canada
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45
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Deore PS, Manderville RA. Aptamer-induced thermofluorimetric protein stabilization and G-quadruplex nucleic acid staining by SYPRO orange dye. NEW J CHEM 2019. [DOI: 10.1039/c9nj00188c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Serendipitously discovered nucleic acid staining by SYPRO Orange dye utilized to demonstrate proteins thermal stabilization (increase in melting temperature,Tm) as a function of increased DNA aptamer binding affinity (decrease in dissociation constant,Kd).
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Affiliation(s)
- Prashant S. Deore
- Departments of Chemistry & Toxicology
- University of Guelph
- Guelph
- Canada
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46
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Kumar N, Seminario JM. Molecular dynamics study of thrombin capture by aptamers TBA26 and TBA29 coupled to a DNA origami. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1448977] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Narendra Kumar
- Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Jorge M. Seminario
- Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA
- Department of Materials Science and Engineering, Texas A&M University, College Station, TX, USA
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47
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Matysiak S, Hellmuth K, El-Sagheer AH, Shivalingam A, Ariyurek Y, de Jong M, Hollestelle MJ, Out R, Brown T. Searching for avidity by chemical ligation of combinatorially self-assembled DNA-encoded ligand libraries. Org Biomol Chem 2018; 16:48-52. [DOI: 10.1039/c7ob02119d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA encoded ligands are self-assembled into bivalent complexes and chemically ligated to link their identities.
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Affiliation(s)
| | | | - Afaf H. El-Sagheer
- Department of Chemistry
- University of Oxford
- Chemistry Research Laboratory
- Oxford
- UK
| | - Arun Shivalingam
- Department of Chemistry
- University of Oxford
- Chemistry Research Laboratory
- Oxford
- UK
| | - Yavuz Ariyurek
- Leiden Genome Technology Center
- Leiden University Medical Center
- Leiden
- The Netherlands
| | | | - Martine J. Hollestelle
- Dep. Immunophathology and Blood Coagulation
- Sanquin Diagnostic Services
- Amsterdam
- The Netherlands
| | - Ruud Out
- Piculet-Biosciences BV
- 2333BD Leiden
- The Netherlands
| | - Tom Brown
- Department of Chemistry
- University of Oxford
- Chemistry Research Laboratory
- Oxford
- UK
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48
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McRae EKS, Booy EP, Padilla-Meier GP, McKenna SA. On Characterizing the Interactions between Proteins and Guanine Quadruplex Structures of Nucleic Acids. J Nucleic Acids 2017; 2017:9675348. [PMID: 29250441 PMCID: PMC5700478 DOI: 10.1155/2017/9675348] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 10/08/2017] [Indexed: 01/07/2023] Open
Abstract
Guanine quadruplexes (G4s) are four-stranded secondary structures of nucleic acids which are stabilized by noncanonical hydrogen bonding systems between the nitrogenous bases as well as extensive base stacking, or pi-pi, interactions. Formation of these structures in either genomic DNA or cellular RNA has the potential to affect cell biology in many facets including telomere maintenance, transcription, alternate splicing, and translation. Consequently, G4s have become therapeutic targets and several small molecule compounds have been developed which can bind such structures, yet little is known about how G4s interact with their native protein binding partners. This review focuses on the recognition of G4s by proteins and small peptides, comparing the modes of recognition that have thus far been observed. Emphasis will be placed on the information that has been gained through high-resolution crystallographic and NMR structures of G4/peptide complexes as well as biochemical investigations of binding specificity. By understanding the molecular features that lead to specificity of G4 binding by native proteins, we will be better equipped to target protein/G4 interactions for therapeutic purposes.
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Affiliation(s)
- Ewan K. S. McRae
- Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada
| | - Evan P. Booy
- Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada
| | | | - Sean A. McKenna
- Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB, Canada
- Manitoba Institute for Materials, University of Manitoba, Winnipeg, MB, Canada
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49
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Russo Krauss I, Napolitano V, Petraccone L, Troisi R, Spiridonova V, Mattia CA, Sica F. Duplex/quadruplex oligonucleotides: Role of the duplex domain in the stabilization of a new generation of highly effective anti-thrombin aptamers. Int J Biol Macromol 2017; 107:1697-1705. [PMID: 29024684 DOI: 10.1016/j.ijbiomac.2017.10.033] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 10/05/2017] [Accepted: 10/06/2017] [Indexed: 12/19/2022]
Abstract
Recently, mixed duplex/quadruplex oligonucleotides have attracted great interest for use as biomedical aptamers. In the case of anti-thrombin aptamers, the addition of duplex-forming sequences to a G-quadruplex module identical or very similar to the best-known G-quadruplex of the Thrombin Binding Aptamer (HD1) results in new or improved biological properties, such as higher activity or different recognition properties with respect to HD1. Remarkably, this bimodular fold was hypothesized, based on its sequence, for the only anti-thrombin aptamer in advanced clinical trial, NU172. Whereas cation modulation of G-quadruplex conformation and stability is well characterized, only few data from similar analysis on duplex/quadruplex oligonucleotides exist. Here we have performed a characterization of structure and stability of four different duplex/quadruplex anti-thrombin aptamers, including NU172, in the presence of different cations and in physiological-mimicking conditions in comparison to HD1, by means of spectroscopic techniques (UV and circular dichroism) and differential scanning calorimetry. Our data show a strong reciprocal influence of each domain on the stability of the other and in particular suggest a stabilizing effect of the duplex region in the presence of solutions mimicking the physiological conditions, strengthening the idea that bimodular aptamers present better therapeutic potentialities than those containing a single G-quadruplex domain.
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Affiliation(s)
- Irene Russo Krauss
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, I-80126, Naples, Italy; CSGI - Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, Via della Lastruccia 3, I-50019, Sesto Fiorentino, FI, Italy
| | - Valeria Napolitano
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, I-80126, Naples, Italy
| | - Luigi Petraccone
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, I-80126, Naples, Italy
| | - Romualdo Troisi
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, I-80126, Naples, Italy
| | - Vera Spiridonova
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Carlo Andrea Mattia
- Department of Pharmacy, University of Salerno, Via Ponte Don Melillo, I-84084, Fisciano, SA, Italy
| | - Filomena Sica
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, I-80126, Naples, Italy.
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50
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Lietard J, Abou Assi H, Gómez-Pinto I, González C, Somoza MM, Damha MJ. Mapping the affinity landscape of Thrombin-binding aptamers on 2΄F-ANA/DNA chimeric G-Quadruplex microarrays. Nucleic Acids Res 2017; 45:1619-1632. [PMID: 28100695 PMCID: PMC5389548 DOI: 10.1093/nar/gkw1357] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 12/28/2016] [Indexed: 01/13/2023] Open
Abstract
In situ fabricated nucleic acids microarrays are versatile and very high-throughput platforms for aptamer optimization and discovery, but the chemical space that can be probed against a given target has largely been confined to DNA, while RNA and non-natural nucleic acid microarrays are still an essentially uncharted territory. 2΄-Fluoroarabinonucleic acid (2΄F-ANA) is a prime candidate for such use in microarrays. Indeed, 2΄F-ANA chemistry is readily amenable to photolithographic microarray synthesis and its potential in high affinity aptamers has been recently discovered. We thus synthesized the first microarrays containing 2΄F-ANA and 2΄F-ANA/DNA chimeric sequences to fully map the binding affinity landscape of the TBA1 thrombin-binding G-quadruplex aptamer containing all 32 768 possible DNA-to-2΄F-ANA mutations. The resulting microarray was screened against thrombin to identify a series of promising 2΄F-ANA-modified aptamer candidates with Kds significantly lower than that of the unmodified control and which were found to adopt highly stable, antiparallel-folded G-quadruplex structures. The solution structure of the TBA1 aptamer modified with 2΄F-ANA at position T3 shows that fluorine substitution preorganizes the dinucleotide loop into the proper conformation for interaction with thrombin. Overall, our work strengthens the potential of 2΄F-ANA in aptamer research and further expands non-genomic applications of nucleic acids microarrays.
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Affiliation(s)
- Jory Lietard
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Althanstraße 14 (UZA II), 1090 Vienna, Austria.,Department of Chemistry, McGill University, 801 Rue Sherbrooke O, Montréal, QC H3A 0B8, Canada
| | - Hala Abou Assi
- Department of Chemistry, McGill University, 801 Rue Sherbrooke O, Montréal, QC H3A 0B8, Canada
| | | | - Carlos González
- Instituto de Química Física 'Rocasolano', CSIC, 28006 Madrid, Spain
| | - Mark M Somoza
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Althanstraße 14 (UZA II), 1090 Vienna, Austria
| | - Masad J Damha
- Department of Chemistry, McGill University, 801 Rue Sherbrooke O, Montréal, QC H3A 0B8, Canada
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