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Di Mauro V, Lauta FC, Modica J, Appleton SL, De Franciscis V, Catalucci D. Diagnostic and Therapeutic Aptamers: A Promising Pathway to Improved Cardiovascular Disease Management. JACC Basic Transl Sci 2024; 9:260-277. [PMID: 38510714 PMCID: PMC10950404 DOI: 10.1016/j.jacbts.2023.06.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 06/29/2023] [Indexed: 03/22/2024]
Abstract
Despite advances in care, cardiovascular diseases remain the leading cause of death worldwide. As a result, identifying suitable biomarkers for early diagnosis and improving therapeutic and diagnostic strategies is crucial. Because of their significant advantages over other therapeutic approaches, nucleic-based therapies, particularly aptamers, are gaining increased attention. Aptamers are innovative synthetic polymers or oligomers of single-stranded DNA (ssDNA) or RNA molecules that can form 3-dimensional structures and thus interact with their targets with high specificity and affinity. Furthermore, they outperform classical protein-based antibodies in terms of in vitro selection, production, ease of modification and conjugation, high stability, low immunogenicity, and suitability for nanoparticle functionalization for targeted drug delivery. This work aims to review the advances made in the aptamers' field in biomarker detection, diagnosis, imaging, and targeted therapy, which highlight their huge potential in the management of cardiovascular diseases.
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Affiliation(s)
- Vittoria Di Mauro
- Veneto Institute of Molecular Medicine, Padua, Italy
- Institute of Genetic and Biomedical Research, Milan, Milan Italy
- Humanitas Cardio Center, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | | | - Jessica Modica
- Institute of Genetic and Biomedical Research, Milan, Milan Italy
- Humanitas Cardio Center, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Silvia Lucia Appleton
- Institute of Genetic and Biomedical Research, Milan, Milan Italy
- Humanitas Cardio Center, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | | | - Daniele Catalucci
- Institute of Genetic and Biomedical Research, Milan, Milan Italy
- Humanitas Cardio Center, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
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2
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Binet T, Padiolleau-Lefèvre S, Octave S, Avalle B, Maffucci I. Comparative Study of Single-stranded Oligonucleotides Secondary Structure Prediction Tools. BMC Bioinformatics 2023; 24:422. [PMID: 37940855 PMCID: PMC10634105 DOI: 10.1186/s12859-023-05532-5] [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: 04/20/2023] [Accepted: 10/13/2023] [Indexed: 11/10/2023] Open
Abstract
BACKGROUND Single-stranded nucleic acids (ssNAs) have important biological roles and a high biotechnological potential linked to their ability to bind to numerous molecular targets. This depends on the different spatial conformations they can assume. The first level of ssNAs spatial organisation corresponds to their base pairs pattern, i.e. their secondary structure. Many computational tools have been developed to predict the ssNAs secondary structures, making the choice of the appropriate tool difficult, and an up-to-date guide on the limits and applicability of current secondary structure prediction tools is missing. Therefore, we performed a comparative study of the performances of 9 freely available tools (mfold, RNAfold, CentroidFold, CONTRAfold, MC-Fold, LinearFold, UFold, SPOT-RNA, and MXfold2) on a dataset of 538 ssNAs with known experimental secondary structure. RESULTS The minimum free energy-based tools, namely mfold and RNAfold, and some tools based on artificial intelligence, namely CONTRAfold and MXfold2, provided the best results, with [Formula: see text] of exact predictions, whilst MC-fold seemed to be the worst performing tool, with only [Formula: see text] of exact predictions. In addition, UFold and SPOT-RNA are the only options for pseudoknots prediction. Including in the analysis of mfold and RNAfold results 5-10 suboptimal solutions further improved the performances of these tools. Nevertheless, we could observe issues in predicting particular motifs, such as multiple-ways junctions and mini-dumbbells, or the ssNAs whose structure has been determined in complex with a protein. In addition, our benchmark shows that some effort has to be paid for ssDNA secondary structure predictions. CONCLUSIONS In general, Mfold, RNAfold, and MXfold2 seem to currently be the best choice for the ssNAs secondary structure prediction, although they still show some limits linked to specific structural motifs. Nevertheless, actual trends suggest that artificial intelligence has a high potential to overcome these remaining issues, for example the recently developed UFold and SPOT-RNA have a high success rate in predicting pseudoknots.
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Affiliation(s)
- Thomas Binet
- Université de technologie de Compiègne, UPJV, CNRS, Enzyme and Cell Engineering, Centre de recherche Royallieu - CS 60 319, 60203, Compiègne Cedex, France
| | - Séverine Padiolleau-Lefèvre
- Université de technologie de Compiègne, UPJV, CNRS, Enzyme and Cell Engineering, Centre de recherche Royallieu - CS 60 319, 60203, Compiègne Cedex, France
| | - Stéphane Octave
- Université de technologie de Compiègne, UPJV, CNRS, Enzyme and Cell Engineering, Centre de recherche Royallieu - CS 60 319, 60203, Compiègne Cedex, France
| | - Bérangère Avalle
- Université de technologie de Compiègne, UPJV, CNRS, Enzyme and Cell Engineering, Centre de recherche Royallieu - CS 60 319, 60203, Compiègne Cedex, France.
| | - Irene Maffucci
- Université de technologie de Compiègne, UPJV, CNRS, Enzyme and Cell Engineering, Centre de recherche Royallieu - CS 60 319, 60203, Compiègne Cedex, France.
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3
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Krishnan H, Gopinath SCB. A potent anticoagulant hybrid of snake venom derived FIX-binding protein and anti-factor IX RNA aptamer: Assessed by in-silico and electrochemical analyses. Int J Biol Macromol 2023; 247:125740. [PMID: 37423441 DOI: 10.1016/j.ijbiomac.2023.125740] [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: 02/14/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/11/2023]
Abstract
Anticoagulant therapies are crucial in the management of surgical complications as well as the prophylaxis of thrombosis. Many studies are being conducted on the Habu snake-venom anticoagulant, FIX-binding protein (FIX-Bp), for its greater potency and strong affinity to FIX clotting factor. On the other hand, the capacity to promptly reverse such acute anticoagulation is equally important. Combining a reversible anticoagulant with FIX-Bp may be advantageous in maintaining the balance between adequate anticoagulation and repealing when necessary. In this study, authors integrated FIX-Bp and RNA aptamer-based anticoagulants into a single target, FIX clotting factor, in order to achieve a robust anticoagulant effect. An in-silico and electrochemical approach were used to investigate the combination of FIX-Bp and RNA aptamers as a bivalent anticoagulant and to verify the competing or predominant binding sites of each anticoagulant. The in-silico analysis discovered that both the venom- and aptamer-anticoagulant had a strong affinity for the FIX protein at the Gla-domain and EGF-1 domain by holding 9 conventional hydrogen bonds with the binding energy of -34.859 kcal/mol. The electrochemical technique verified that both anticoagulants had different binding sites. The impedance load upon RNA aptamer binding to FIX protein was 14 %, whereas the addition of FIX-Bp caused a significant impedance rise of 37 %. This indicates that the addition of aptamers prior to FIX-Bp is a promising strategy for the conception of a hybrid anticoagulant.
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Affiliation(s)
- Hemavathi Krishnan
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), 01000 Kangar, Perlis, Malaysia
| | - Subash C B Gopinath
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), 01000 Kangar, Perlis, Malaysia; Faculty of Chemical Engineering & Technology, Universiti Malaysia Perlis (UniMAP), 02600 Arau, Perlis, Malaysia; Micro System Technology, Centre of Excellence (CoE), Universiti Malaysia Perlis (UniMAP), Pauh Campus, 02600 Arau, Perlis, Malaysia; Department of Computer Science and Engineering, Faculty of Science and Information Technology, Daffodil International University, Daffodil Smart City, Birulia, Savar, Dhaka 1216, Bangladesh.
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4
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Kou HS, Lo ST, Wang CC. One Single Tube Reaction of Aptasensor-Based Magnetic Sensing System for Selective Fluorescent Detection of VEGF in Plasma. BIOSENSORS 2023; 13:574. [PMID: 37366939 DOI: 10.3390/bios13060574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/16/2023] [Accepted: 05/22/2023] [Indexed: 06/28/2023]
Abstract
In this study, a simple, easy and convenient fluorescent sensing system for the detection of the vascular endothelial growth factor (VEGF) based on VEGF aptamers, aptamer-complementary fluorescence-labeled probe and streptavidin magnetic beads was developed in one single tube. The VEGF is the most important biomarker in cancer, and it is investigated that the serum VEGF level varied according to the different types and courses of cancers. Hence, efficient quantification of VEGF is able to improve the accuracy of cancer diagnoses and the precision of disease surveillance. In this research, the VEGF aptamer was designed to be able to bind with the VEGF by forming G-quadruplex secondary structures; then, the magnetic beads would capture the non-binding aptamers due to non-steric interference; and finally, the fluorescence-labeled probes were hybridized with the aptamers captured by the magnetic beads. Therefore, the fluorescent intensity in the supernatant would specifically reflect the present VEGF. After an overall optimization, the optimal conditions for the detection of VEGF were as followed, KCl, 50 μM; pH 7.0; aptamer, 0.1 μM; and magnetic beads, 10 μL (4 μg/μL). The VEGF could be well quantified within a range of 0.2-2.0 ng/mL in plasma, and the calibration curve possessed a good linearity (y = 1.0391x + 0.5471, r = 0.998). The detection limit (LOD) was calculated to be 0.0445 ng/mL according to the formula (LOD = 3.3 × σ/S). The specificity of this method was also investigated under the appearance of many other serum proteins, and the data showed good specificity in this aptasensor-based magnetic sensing system. This strategy provided a simple, sensitive and selective biosensing platform for the detection of serum VEGF. Finally, it was expected that this detection technique can be used to promote more clinical applications.
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Affiliation(s)
- Hwang-Shang Kou
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Shao-Tsung Lo
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Chun-Chi Wang
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan
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5
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Yoshikawa AM, Rangel AE, Zheng L, Wan L, Hein LA, Hariri AA, Eisenstein M, Soh HT. A massively parallel screening platform for converting aptamers into molecular switches. Nat Commun 2023; 14:2336. [PMID: 37095144 PMCID: PMC10126150 DOI: 10.1038/s41467-023-38105-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 04/14/2023] [Indexed: 04/26/2023] Open
Abstract
Aptamer-based molecular switches that undergo a binding-induced conformational change have proven valuable for a wide range of applications, such as imaging metabolites in cells, targeted drug delivery, and real-time detection of biomolecules. Since conventional aptamer selection methods do not typically produce aptamers with inherent structure-switching functionality, the aptamers must be converted to molecular switches in a post-selection process. Efforts to engineer such aptamer switches often use rational design approaches based on in silico secondary structure predictions. Unfortunately, existing software cannot accurately model three-dimensional oligonucleotide structures or non-canonical base-pairing, limiting the ability to identify appropriate sequence elements for targeted modification. Here, we describe a massively parallel screening-based strategy that enables the conversion of virtually any aptamer into a molecular switch without requiring any prior knowledge of aptamer structure. Using this approach, we generate multiple switches from a previously published ATP aptamer as well as a newly-selected boronic acid base-modified aptamer for glucose, which respectively undergo signal-on and signal-off switching upon binding their molecular targets with second-scale kinetics. Notably, our glucose-responsive switch achieves ~30-fold greater sensitivity than a previously-reported natural DNA-based switch. We believe our approach could offer a generalizable strategy for producing target-specific switches from a wide range of aptamers.
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Affiliation(s)
- Alex M Yoshikawa
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
| | | | - Liwei Zheng
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA
| | - Leighton Wan
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Linus A Hein
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Amani A Hariri
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA
| | - Michael Eisenstein
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - H Tom Soh
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA.
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
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6
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Wei LN, Luo L, Wang BZ, Lei HT, Guan T, Shen YD, Wang H, Xu ZL. Biosensors for detection of paralytic shellfish toxins: Recognition elements and transduction technologies. Trends Food Sci Technol 2023. [DOI: 10.1016/j.tifs.2023.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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7
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Sun D, Sun M, Zhang J, Lin X, Zhang Y, Lin F, Zhang P, Yang C, Song J. Computational tools for aptamer identification and optimization. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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8
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Cagirici HB, Budak H, Sen TZ. G4Boost: a machine learning-based tool for quadruplex identification and stability prediction. BMC Bioinformatics 2022; 23:240. [PMID: 35717172 PMCID: PMC9206279 DOI: 10.1186/s12859-022-04782-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 06/09/2022] [Indexed: 11/10/2022] Open
Abstract
Background G-quadruplexes (G4s), formed within guanine-rich nucleic acids, are secondary structures involved in important biological processes. Although every G4 motif has the potential to form a stable G4 structure, not every G4 motif would, and accurate energy-based methods are needed to assess their structural stability. Here, we present a decision tree-based prediction tool, G4Boost, to identify G4 motifs and predict their secondary structure folding probability and thermodynamic stability based on their sequences, nucleotide compositions, and estimated structural topologies.
Results G4Boost predicted the quadruplex folding state with an accuracy greater then 93% and an F1-score of 0.96, and the folding energy with an RMSE of 4.28 and R2 of 0.95 only by the means of sequence intrinsic feature. G4Boost was successfully applied and validated to predict the stability of experimentally-determined G4 structures, including for plants and humans. Conclusion G4Boost outperformed the three machine-learning based prediction tools, DeepG4, Quadron, and G4RNA Screener, in terms of both accuracy and F1-score, and can be highly useful for G4 prediction to understand gene regulation across species including plants and humans. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04782-z.
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Affiliation(s)
- H Busra Cagirici
- US Department of Agriculture - Agricultural Research Service, Crop Improvement Genetics Research Unit, Western Regional Research Center, 800 Buchanan St, Albany, CA, 94710, USA
| | | | - Taner Z Sen
- US Department of Agriculture - Agricultural Research Service, Crop Improvement Genetics Research Unit, Western Regional Research Center, 800 Buchanan St, Albany, CA, 94710, USA.
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9
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Lin YC, Chen WY, Hwu ET, Hu WP. In-Silico Selection of Aptamer Targeting SARS-CoV-2 Spike Protein. Int J Mol Sci 2022; 23:ijms23105810. [PMID: 35628622 PMCID: PMC9143595 DOI: 10.3390/ijms23105810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 05/11/2022] [Accepted: 05/18/2022] [Indexed: 11/16/2022] Open
Abstract
Aptamers are single-stranded, short DNA or RNA oligonucleotides that can specifically bind to various target molecules. To diagnose the infected cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in time, numerous conventional methods are applied for viral detection via the amplification and quantification of DNA or antibodies specific to antigens on the virus. Herein, we generated a large number of mutated aptamer sequences, derived from a known sequence of receptor-binding domain (RBD)-1C aptamer, specific to the RBD of SARS-CoV-2 spike protein (S protein). Structural similarity, molecular docking, and molecular dynamics (MD) were utilized to screen aptamers and characterize the detailed interactions between the selected aptamers and the S protein. We identified two mutated aptamers, namely, RBD-1CM1 and RBD-1CM2, which presented better docking results against the S protein compared with the RBD-1C aptamer. Through the MD simulation, we further confirmed that the RBD-1CM1 aptamer can form the most stable complex with the S protein based on the number of hydrogen bonds formed between the two biomolecules. Based on the experimental data of quartz crystal microbalance (QCM), the RBD-1CM1 aptamer could produce larger signals in mass change and exhibit an improved binding affinity to the S protein. Therefore, the RBD-1CM1 aptamer, which was selected from 1431 mutants, was the best potential candidate for the detection of SARS-CoV-2. The RBD-1CM1 aptamer can be an alternative biological element for the development of SARS-CoV-2 diagnostic testing.
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Affiliation(s)
- Yu-Chao Lin
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, China Medical University Hospital, Taichung 404333, Taiwan;
- School of Medicine, China Medical University, Taichung 404333, Taiwan
| | - Wen-Yih Chen
- Department of Chemical and Materials Engineering, National Central University, Jhong-Li 32001, Taiwan;
| | - En-Te Hwu
- Department of Health Technology, Technical University of Denmark, 2800 Lyngby, Denmark;
| | - Wen-Pin Hu
- Department of Bioinformatics and Medical Engineering, Asia University, Taichung 41354, Taiwan
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung 40447, Taiwan
- Correspondence:
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Optimization of Short RNA Aptamers for TNBC Cell Targeting. Int J Mol Sci 2022; 23:ijms23073511. [PMID: 35408872 PMCID: PMC8998535 DOI: 10.3390/ijms23073511] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 02/07/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is an aggressive cancer with limited targeted therapies. RNA aptamers, suitably chemically modified, work for therapeutic purposes in the same way as antibodies. We recently generated 2′Fluoro-pyrimidines RNA-aptamers that act as effective recognition elements for functional surface signatures of TNBC cells. Here, we optimized three of them by shortening and proved the truncated aptamers as optimal candidates to enable active targeting to TNBC. By using prediction of secondary structure to guide truncation, we identified structural regions that account for the binding motifs of the full-length aptamers. Their chemical synthesis led to short aptamers with superb nuclease resistance, which specifically bind to TNBC target cells and rapidly internalize into acidic compartments. They interfere with the growth of TNBC cells as mammospheres, thus confirming their potential as anti-tumor agents. We propose sTN145, sTN58 and sTN29 aptamers as valuable tools for selective TNBC targeting and promising candidates for effective treatments, including therapeutic agents and targeted delivery nanovectors.
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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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In silico structural analysis of truncated 2’ fluoro-RNA aptamer: Elucidating EGF-1 and EGF-2 binding domains on factor IX protein. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.10.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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13
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Study on the binding mode of aptamer to ampicillin and its electrochemical response behavior in two different reaction media. Anal Bioanal Chem 2021; 413:6877-6887. [PMID: 34595555 DOI: 10.1007/s00216-021-03646-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/30/2021] [Accepted: 09/01/2021] [Indexed: 10/20/2022]
Abstract
A study was carried out to investigate the binding mode of aptamer to ampicillin (AMP) and its electrochemical response behavior. The binding mode was confirmed using the molecular dynamics (MD) simulation method to obtain the corresponding binding dynamic change process. Following the confirmed binding mode, a qualitative elucidation was provided on the electrochemical response characteristics of a single-probe aptamer-based folding sensor. The results show that there exist two different binding modes in two different solution systems, Phys2 and H2O (0.1 M NaCl). These two binding modes can respectively induce two different contraction changes, thereby driving the methylene blue (MB)-modified aptamer probe to show a "close-to-interface" convergence behavior with different degrees on the actual electrode surface, which validates two apparently different electrochemical response behavior characteristics of "signal-on" for the sensor. By contrast, H2O (0.1 M NaCl) as the reaction medium is more conducive to the formation of a stable aptamer/AMP complex and the development of a high-sensitivity analytical method with a low detection limit of 0.033 μM. The simulation results effectively support the experimental results, which is helpful in gaining a deeper understanding of the relationship between the signaling mechanism and practical analytical performance for aptamer-based folding sensors at the molecular level.
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14
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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: 2] [Impact Index Per Article: 0.7] [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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Kuroiwa S, Hayashi H, Toyama R, Kaneko N, Horii K, Ohashi K, Momma T, Osaka T. Potassium-regulated Immobilization of Cortisol Aptamer for Field-effect Transistor Biosensor to Detect Changes in Charge Distribution with Aptamer Transformation. CHEM LETT 2021. [DOI: 10.1246/cl.200876] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Shigeki Kuroiwa
- Research Organization for Nano & Life Innovation, Waseda University, 513 Waseda-tsurumaki-cho, Shinjuku, Tokyo 162-0041, Japan
| | - Hiroki Hayashi
- Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan
| | - Ryo Toyama
- Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan
| | - Naoto Kaneko
- NEC Solution Innovators, Ltd., 1-18-7 Shinkiba, Koto-ku, Tokyo 136-8627, Japan
| | - Katsunori Horii
- NEC Solution Innovators, Ltd., 1-18-7 Shinkiba, Koto-ku, Tokyo 136-8627, Japan
| | - Keishi Ohashi
- Research Organization for Nano & Life Innovation, Waseda University, 513 Waseda-tsurumaki-cho, Shinjuku, Tokyo 162-0041, Japan
| | - Toshiyuki Momma
- Research Organization for Nano & Life Innovation, Waseda University, 513 Waseda-tsurumaki-cho, Shinjuku, Tokyo 162-0041, Japan
- Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan
| | - Tetsuya Osaka
- Research Organization for Nano & Life Innovation, Waseda University, 513 Waseda-tsurumaki-cho, Shinjuku, Tokyo 162-0041, Japan
- Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan
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16
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Abstract
The COVID-19 coronavirus is a new strain of coronavirus that had not been previously detected in humans. As its severe pathogenicity is concerned, it is important to study it thoroughly to aid in the discovery of a cure. In this study, the microRNAs (miRNAs) of COVID-19 were annotated to provide a powerful tool for the study of this novel coronavirus. We obtained 16 novel coronavirus genome sequences and the mature sequences of all viruses in the microRNA database (miRbase), and then used the miRNA mature sequences of the virus to perform the Basic Local Alignment Search Tool (BLAST) analysis in the coronavirus genome, extending the matched regions of approximately 20 bp to two segments by 200 bp. Six sequences were obtained after deleting redundant sequences. Then, the hairpin structures of the mature miRNAs were determined using RNAfold. The mature sequence on one hairpin arm was selected into a total of 4 sequences, and finally the relevant miRNA precursor prediction tools were used to verify whether the selected sequences are miRNA precursor sequences of the novel coronavirus. The miRNAs of the novel coronavirus were annotated by our newly developed method, which will lay the foundation for further study of this virus.
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17
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Wang C, Liu S, Wu Q, Cheng Y, Feng T, Song J, Yang R, Geng H, Lu G, Wang S, Hao L. Porcine IGF-1R synonymous mutations in the intracellular domain affect cell proliferation and alter kinase activity. Int J Biol Macromol 2020; 152:147-153. [PMID: 32109480 DOI: 10.1016/j.ijbiomac.2020.02.281] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 02/23/2020] [Accepted: 02/24/2020] [Indexed: 01/04/2023]
Abstract
Miniature pigs are regarded as ideal organ donors for xenotransplantation into humans. Elucidating the formation mechanism of miniature pigs is important. The insulin-like growth factor 1 receptor (IGF-1R) is crucial in the regulation of cell proliferation and organismal growth. According to our previous research, the IGF-1R expression levels between large and miniature pigs showed different profiles in liver and muscle tissues. Here, five synonymous mutations of IGF-1R in the coding sequence (CDS) of intracellular domain (ICD) between large and miniature pigs were analysed by constructing expression vectors of two haplotypes and named pcDNA3.1-LP (with the CDS of IGF-1R ICD of Large White pigs, LP group) and pcDNA3.1-BM (with the CDS of IGF-1R ICD of Bama Xiang pigs, BM group). The IGF-1R of the BM group was expressed lower than that of the LP group in transcription, translation and autophosphorylation levels. The IGF-1R of the BM group also down-regulated the protein levels of p-AKT/p-ERK than that of the LP group. PK-15 and C2C12 cell proliferation were detected to further understand the function of the haplotype. Results showed that the proliferation viability of PK-15 and C2C12 cells weakened in the BM group. Moreover, the mRNA and protein stabilities of the BM group were higher than those of the LP group. Our data indicated that two haplotypes of IGF-1R CDS in ICD between large and miniature pigs altered IGF-1R expression and down-regulated AKT and ERK signalling pathways at translation levels, resulting in an inhibitory effect on PK-15 and C2C12 cell proliferation.
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Affiliation(s)
- Chunli Wang
- College of Animal Science, Jilin University, 5333 Xi'an Road, Changchun, Jilin 130062, China
| | - Songcai Liu
- College of Animal Science, Jilin University, 5333 Xi'an Road, Changchun, Jilin 130062, China; Five-Star Animal Health Pharmaceutical Factory of Jilin Province, 5333 Xi'an Road, Changchun, Jilin 130062, China
| | - Qingyan Wu
- College of Animal Science, Jilin University, 5333 Xi'an Road, Changchun, Jilin 130062, China
| | - Yunyun Cheng
- Guangdong Provincial Key Laboratory of Animal Nutritional Regulation, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China
| | - Tianqi Feng
- College of Animal Science, Jilin University, 5333 Xi'an Road, Changchun, Jilin 130062, China
| | - Jie Song
- College of Animal Science, Jilin University, 5333 Xi'an Road, Changchun, Jilin 130062, China
| | - Rui Yang
- College of Animal Science, Jilin University, 5333 Xi'an Road, Changchun, Jilin 130062, China
| | - Hongwei Geng
- College of Animal Science, Jilin University, 5333 Xi'an Road, Changchun, Jilin 130062, China
| | - Guanhong Lu
- College of Animal Science, Jilin University, 5333 Xi'an Road, Changchun, Jilin 130062, China
| | - Siyao Wang
- College of Animal Science, Jilin University, 5333 Xi'an Road, Changchun, Jilin 130062, China
| | - Linlin Hao
- College of Animal Science, Jilin University, 5333 Xi'an Road, Changchun, Jilin 130062, China.
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