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Krissanaprasit A, Key CM, Pontula S, LaBean TH. Self-Assembling Nucleic Acid Nanostructures Functionalized with Aptamers. Chem Rev 2021; 121:13797-13868. [PMID: 34157230 DOI: 10.1021/acs.chemrev.0c01332] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Researchers have worked for many decades to master the rules of biomolecular design that would allow artificial biopolymer complexes to self-assemble and function similarly to the diverse biochemical constructs displayed in natural biological systems. The rules of nucleic acid assembly (dominated by Watson-Crick base-pairing) have been less difficult to understand and manipulate than the more complicated rules of protein folding. Therefore, nucleic acid nanotechnology has advanced more quickly than de novo protein design, and recent years have seen amazing progress in DNA and RNA design. By combining structural motifs with aptamers that act as affinity handles and add powerful molecular recognition capabilities, nucleic acid-based self-assemblies represent a diverse toolbox for use by bioengineers to create molecules with potentially revolutionary biological activities. In this review, we focus on the development of self-assembling nucleic acid nanostructures that are functionalized with nucleic acid aptamers and their great potential in wide ranging application areas.
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Affiliation(s)
- Abhichart Krissanaprasit
- Department of Materials Science and Engineering, College of Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Carson M Key
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Sahil Pontula
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Thomas H LaBean
- Department of Materials Science and Engineering, College of Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
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Chemical Modification of Aptamers for Increased Binding Affinity in Diagnostic Applications: Current Status and Future Prospects. Int J Mol Sci 2020; 21:ijms21124522. [PMID: 32630547 PMCID: PMC7350236 DOI: 10.3390/ijms21124522] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 06/19/2020] [Accepted: 06/22/2020] [Indexed: 12/13/2022] Open
Abstract
Aptamers are short single stranded DNA or RNA oligonucleotides that can recognize analytes with extraordinary target selectivity and affinity. Despite their promising properties and diagnostic potential, the number of commercial applications remains scarce. In order to endow them with novel recognition motifs and enhanced properties, chemical modification of aptamers has been pursued. This review focuses on chemical modifications, aimed at increasing the binding affinity for the aptamer's target either in a non-covalent or covalent fashion, hereby improving their application potential in a diagnostic context. An overview of current methodologies will be given, thereby distinguishing between pre- and post-SELEX (Systematic Evolution of Ligands by Exponential Enrichment) modifications.
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Wang M, Wu H, Duan M, Yang Y, Wang G, Che F, Liu B, He W, Li Q, Zhang L. SS30, a novel thioaptamer targeting CD123, inhibits the growth of acute myeloid leukemia cells. Life Sci 2019; 232:116663. [PMID: 31323275 DOI: 10.1016/j.lfs.2019.116663] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/12/2019] [Accepted: 07/15/2019] [Indexed: 01/08/2023]
Abstract
AIMS CD123 represents an important acute myeloid leukemia (AML) therapeutic target. CD123 aptamers may potentially serve as tumor-homing ligands with excellent affinity and specificity for AML targeted therapy, but their complexity, laborious preparation and nuclease digestion limited pharmacological application. The aim of this study was to develop the first CD123 thioaptamer to overcome these obstacles. MAIN METHODS Flow cytometry was utilized to assess the binding specificity, affinity and anti-nuclease ability of thioaptamer. CCK8, Annexin-V/DAPI, and colony forming assays were used to evaluate the anti-cancer ability of thioaptamer in vitro. The tumor volume, weights, survival rate, H&E staining of organs, and serum level of organ damage biomarkers of animal model were applied to investigate the anti-cancer ability of thioaptamer in vivo. Furthermore, we explored the binding mechanism between thioaptamer and CD123. KEY FINDINGS CD123 thioaptamer SS30 was able to bind to CD123 structure with high specificity in complex nuclease environment, the dissociation constant of 39.1 nM for CD123 peptide and 287.6 nM for CD123+ AML cells, while exhibiting minimal cross-reactivity to albumin. Furthermore, SS30 inhibited the proliferation and survival of AML cell lines and human AML blasts selectively in vitro (P < 0.01). In addition, SS30 prolonged the survival and inhibited tumor growth in a mouse xenograft tumor model in vivo. Of note, SS30 blocked the interaction between IL-3 and CD123, and decreased expression of p-STAT5 and p-AKT. SIGNIFICANCE The proliferation inhibition and nuclease resistance ability of SS30 made it as a more promising functional molecule for AML targeted therapy.
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Affiliation(s)
- Meng Wang
- Department of Orthopaedics, No. 946 Hospital of the PLA, YiNing, XinJiang 0086-835000, PR China
| | - Haibin Wu
- Shaanxi Institute of Pediatric Diseases, Xi'an Children's Hospital, Xi'an, Shaanxi 0086-710003, PR China
| | - Mingyue Duan
- Shaanxi Institute of Pediatric Diseases, Xi'an Children's Hospital, Xi'an, Shaanxi 0086-710003, PR China
| | - Ying Yang
- Shaanxi Institute of Pediatric Diseases, Xi'an Children's Hospital, Xi'an, Shaanxi 0086-710003, PR China
| | - Guoxia Wang
- Shaanxi Institute of Pediatric Diseases, Xi'an Children's Hospital, Xi'an, Shaanxi 0086-710003, PR China
| | - Fengyu Che
- Shaanxi Institute of Pediatric Diseases, Xi'an Children's Hospital, Xi'an, Shaanxi 0086-710003, PR China
| | - Bailing Liu
- Department of Ultrasonography, Xi'an Children's Hospital, PR China
| | - Wei He
- Shaanxi Institute of Pediatric Diseases, Xi'an Children's Hospital, Xi'an, Shaanxi 0086-710003, PR China
| | - Qiao Li
- Clinical Laboratory, Xi'an Children's Hospital, Xi'an, Shaanxi 0086-710003, PR China.
| | - Liyu Zhang
- Shaanxi Institute of Pediatric Diseases, Xi'an Children's Hospital, Xi'an, Shaanxi 0086-710003, PR China; Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 0086-710061, PR China.
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Morita Y, Leslie M, Kameyama H, Volk DE, Tanaka T. Aptamer Therapeutics in Cancer: Current and Future. Cancers (Basel) 2018; 10:cancers10030080. [PMID: 29562664 PMCID: PMC5876655 DOI: 10.3390/cancers10030080] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 03/13/2018] [Accepted: 03/15/2018] [Indexed: 12/14/2022] Open
Abstract
Aptamer-related technologies represent a revolutionary advancement in the capacity to rapidly develop new classes of targeting ligands. Structurally distinct RNA and DNA oligonucleotides, aptamers mimic small, protein-binding molecules and exhibit high binding affinity and selectivity. Although their molecular weight is relatively small—approximately one-tenth that of monoclonal antibodies—their complex tertiary folded structures create sufficient recognition surface area for tight interaction with target molecules. Additionally, unlike antibodies, aptamers can be readily chemically synthesized and modified. In addition, aptamers’ long storage period and low immunogenicity are favorable properties for clinical utility. Due to their flexibility of chemical modification, aptamers are conjugated to other chemical entities including chemotherapeutic agents, siRNA, nanoparticles, and solid phase surfaces for therapeutic and diagnostic applications. However, as relatively small sized oligonucleotides, aptamers present several challenges for successful clinical translation. Their short plasma half-lives due to nuclease degradation and rapid renal excretion necessitate further structural modification of aptamers for clinical application. Since the US Food and Drug Administration (FDA) approval of the first aptamer drug, Macugen® (pegaptanib), which treats wet-age-related macular degeneration, several aptamer therapeutics for oncology have followed and shown promise in pre-clinical models as well as clinical trials. This review discusses the advantages and challenges of aptamers and introduces therapeutic aptamers under investigation and in clinical trials for cancer treatments.
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Affiliation(s)
- Yoshihiro Morita
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, 975 NE 10th, BRC-W, Rm 1415, Oklahoma City, OK 73104, USA.
| | - Macall Leslie
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, 975 NE 10th, BRC-W, Rm 1415, Oklahoma City, OK 73104, USA.
| | - Hiroyasu Kameyama
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, 975 NE 10th, BRC-W, Rm 1415, Oklahoma City, OK 73104, USA.
| | - David E Volk
- McGovern Medical School, Institute of Molecular Medicine, University of Texas Health Science Center at Houston, 1825 Hermann Pressler, Houston, TX 77030, USA.
| | - Takemi Tanaka
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, 975 NE 10th, BRC-W, Rm 1415, Oklahoma City, OK 73104, USA.
- Department of Pathology, College of Medicine, University of Oklahoma Health Sciences Center, 940 SL Young Blvd, Oklahoma City, OK 73104, USA.
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Morph-X-Select: Morphology-based tissue aptamer selection for ovarian cancer biomarker discovery. Biotechniques 2016; 61:249-259. [PMID: 27839510 DOI: 10.2144/000114473] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Accepted: 09/09/2016] [Indexed: 12/28/2022] Open
Abstract
High affinity aptamer-based biomarker discovery has the advantage of simultaneously discovering an aptamer affinity reagent and its target biomarker protein. Here, we demonstrate a morphology-based tissue aptamer selection method that enables us to use tissue sections from individual patients and identify high-affinity aptamers and their associated target proteins in a systematic and accurate way. We created a combinatorial DNA aptamer library that has been modified with thiophosphate substitutions of the phosphate ester backbone at selected 5´dA positions for enhanced nuclease resistance and targeting. Based on morphological assessment, we used image-directed laser microdissection (LMD) to dissect regions of interest bound with the thioaptamer (TA) library and further identified target proteins for the selected TAs. We have successfully identified and characterized the lead candidate TA, V5, as a vimentin-specific sequence that has shown specific binding to tumor vasculature of human ovarian tissue and human microvascular endothelial cells. This new Morph-X-Select method allows us to select high-affinity aptamers and their associated target proteins in a specific and accurate way, and could be used for personalized biomarker discovery to improve medical decision-making and to facilitate the development of targeted therapies to achieve more favorable outcomes.
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Thiviyanathan V, Gorenstein DG. Aptamers and the next generation of diagnostic reagents. Proteomics Clin Appl 2014; 6:563-73. [PMID: 23090891 DOI: 10.1002/prca.201200042] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 09/17/2012] [Accepted: 09/20/2012] [Indexed: 01/06/2023]
Abstract
Antibodies have been extensively used as capture and detection reagents in diagnostic applications of proteomics-based technologies. Proteomic assays need high sensitivity and specificity, a wide dynamic range for detection, and accurate, reproducible quantification with small confidence values. However, several inherent limitations of monoclonal antibodies in meeting the emerging challenges of proteomics led to the development of a new class of oligonucleotide-based reagents. Natural and derivatized nucleic acid aptamers are emerging as promising alternatives to monoclonal antibodies. Aptamers can be effectively used to simultaneously detect thousands of proteins in multiplex discovery platforms, where antibodies often fail due to cross-reactivity problems. Through chemical modification, vast range of additional functional groups can be added at any desired position in the oligonucleotide sequence, therefore the best features of small molecule drugs, proteins, and antibodies can be brought together into aptamers, making aptamers the most versatile reagent in proteomics. In this review, we discuss the recent developments in aptamer technology, including new selection methods and the aptamers' application in proteomics.
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Affiliation(s)
- Varatharasa Thiviyanathan
- Centers for Proteomics & Systems Biology, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, TX, USA
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Radom F, Jurek PM, Mazurek MP, Otlewski J, Jeleń F. Aptamers: molecules of great potential. Biotechnol Adv 2013; 31:1260-74. [PMID: 23632375 DOI: 10.1016/j.biotechadv.2013.04.007] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 03/27/2013] [Accepted: 04/19/2013] [Indexed: 01/08/2023]
Abstract
Aptamers emerged over 20 years ago as a class of nucleic acids able to recognize specific targets. Today, aptamer-related studies constitute a large and important field of biotechnology. Functional oligonucleotides have proved to be a versatile tool in biomedical research due to the ease of synthesis, a wide range of potentially recognized molecular targets and the simplicity of selection. Similarly to antibodies, aptamers can be used to detect or isolate specific molecules, as well as to act as targeting and therapeutic agents. In this review we present different approaches to aptamer application in nanobiotechnology, diagnostics and medicine.
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Affiliation(s)
- Filip Radom
- Department of Protein Engineering, Faculty of Biotechnology, University of Wroclaw, Tamka 2, 50-137 Wroclaw, Poland
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Investigating the antiproliferative activity of high affinity DNA aptamer on cancer cells. PLoS One 2013; 8:e50964. [PMID: 23341879 PMCID: PMC3547035 DOI: 10.1371/journal.pone.0050964] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 10/29/2012] [Indexed: 12/02/2022] Open
Abstract
Vascular endothelial growth factor (VEGF) is an angiogenic mitogen involved in promoting tumor angiogenesis inside the body. VEGF is a key protein required for progression of tumor from benign to malignant phenotype. In this study, we investigated the binding affinity of a previously selected 26-mer DNA aptamer sequence (SL2-B) against heparin binding domain (HBD) of VEGF165 protein. The SL2-B was first chemically modified by introduction of phosphorothioate linkages (PS-linkages). Subsequently, surface plasmon resonance (SPR) spectroscopy and circular dichroism (CD) were used to determine the binding affinity, specificity and to deduce the conformation of PS-modified SL2-B sequence. Finally, antiproliferative activity of the modified SL2-B sequence on Hep G2 cancer cells was investigated. Our results demonstrate a marked enhancement in the biostability of the SL2-B sequence after PS modification. The modified SL2-B sequence also exhibits enhanced antiproliferative activity against Hep G2 cancer cells in hypoxia conditions. In addition, modified SL2-B sequence inhibits the expression of Jagged-1 protein, which is one of the ligands to VEGF linked delta/jagged-notch signaling pathway.
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Serda RE, Godin B, Blanco E, Chiappini C, Ferrari M. Multi-stage delivery nano-particle systems for therapeutic applications. BIOCHIMICA ET BIOPHYSICA ACTA 2011; 1810:317-29. [PMID: 20493927 PMCID: PMC2948075 DOI: 10.1016/j.bbagen.2010.05.004] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2009] [Revised: 04/27/2010] [Accepted: 05/05/2010] [Indexed: 02/06/2023]
Abstract
BACKGROUND The daunting task for drug molecules to reach pathological lesions has fueled rapid advances in Nanomedicine. The progressive evolution of nanovectors has led to the development of multi-stage delivery systems aimed at overcoming the numerous obstacles encountered by nanovectors on their journey to the target site. SCOPE OF REVIEW This review summarizes major findings with respect to silicon-based drug delivery vectors for cancer therapeutics and imaging. Based on rational design, well-established silicon technologies have been adapted for the fabrication of nanovectors with specific shapes, sizes, and porosities. These vectors are part of a multi-stage delivery system that contains multiple nano-components, each designed to achieve a specific task with the common goal of site-directed delivery of therapeutics. MAJOR CONCLUSIONS Quasi-hemispherical and discoidal silicon microparticles are superior to spherical particles with respect to margination in the blood, with particles of different shapes and sizes having unique distributions in vivo. Cellular adhesion and internalization of silicon microparticles is influenced by microparticle shape and surface charge, with the latter dictating binding of serum opsonins. Based on in vitro cell studies, the internalization of porous silicon microparticles by endothelial cells and macrophages is compatible with cellular morphology, intracellular trafficking, mitosis, cell cycle progression, cytokine release, and cell viability. In vivo studies support superior therapeutic efficacy of liposomal encapsulated siRNA when delivered in multi-stage systems compared to free nanoparticles. This article is part of a Special Issue entitled Nanotechnologies - Emerging Applications in Biomedicine.
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Affiliation(s)
- Rita E. Serda
- University of Texas Health Science Center, Department of NanoMedicine and Biomedical Engineering, 1825 Pressler, Suite 537, Houston, TX 77030, USA
| | - Biana Godin
- University of Texas Health Science Center, Department of NanoMedicine and Biomedical Engineering, 1825 Pressler, Suite 537, Houston, TX 77030, USA
| | - Elvin Blanco
- University of Texas Health Science Center, Department of NanoMedicine and Biomedical Engineering, 1825 Pressler, Suite 537, Houston, TX 77030, USA
| | - Ciro Chiappini
- University of Texas at Austin, Department of Biomedical Engineering, 1 University Station, C0400, Austin, TX 78712
| | - Mauro Ferrari
- University of Texas Health Science Center, Department of NanoMedicine and Biomedical Engineering, 1825 Pressler, Suite 537, Houston, TX 77030, USA
- University of Texas at Austin, Department of Biomedical Engineering, 1 University Station, C0400, Austin, TX 78712
- University of Texas MD Anderson Cancer Center, Department of Experimental Therapeutics, Unit 422, 1515 Holcombe Blvd., Houston, TX 77030, USA
- Rice University, Department of Bioengineering, Houston, TX 77005, USA
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Somasunderam A, Thiviyanathan V, Tanaka T, Li X, Neerathilingam M, Lokesh GLR, Mann A, Peng Y, Ferrari M, Klostergaard J, Gorenstein DG. Combinatorial selection of DNA thioaptamers targeted to the HA binding domain of human CD44. Biochemistry 2010; 49:9106-12. [PMID: 20843027 DOI: 10.1021/bi1009503] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
CD44, the primary receptor for hyaluronic acid, plays an important role in tumor growth and metastasis. CD44-hyaluronic acid interactions can be exploited for targeted delivery of anticancer agents specifically to cancer cells. Although various splicing variants of CD44 are expressed on the plasma membrane of cancer cells, the hyaluronic acid binding domain (HABD) is highly conserved among the CD44 splicing variants. Using a novel two-step process, we have identified monothiophosphate-modified aptamers (thioaptamers) that specifically bind to the CD44's HABD with high affinities. Binding affinities of the selected thioaptamers for the HABD were in the range of 180-295 nM, an affinity significantly higher than that of hyaluronic acid (K(d) above the micromolar range). The selected thioaptamers bound to CD44 positive human ovarian cancer cell lines (SKOV3, IGROV, and A2780) but failed to bind the CD44 negative NIH3T3 cell line. Our results indicated that thio substitution at specific positions of the DNA phosphate backbone results in specific and high-affinity binding of thioaptamers to CD44. The selected thioaptamers will be of great interest for further development as a targeting or imaging agent for the delivery of therapeutic payloads for cancer tissues.
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Affiliation(s)
- Anoma Somasunderam
- Institute of Molecular Medicine, University of Texas Health ScienceCenter, Houston, Texas 77030, United States
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