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Lee H, Kim H, Lee SY. Self-Assembling Peptidic Bolaamphiphiles for Biomimetic Applications. ACS Biomater Sci Eng 2021; 7:3545-3572. [PMID: 34309378 DOI: 10.1021/acsbiomaterials.1c00576] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Bolaamphiphile, which is a class of amphiphilic molecules, has a unique structure of two hydrophilic head groups at the ends of the hydrophobic center. Peptidic bolaamphiphiles that employ peptides or amino acids as their hydrophilic groups exhibit unique biochemical activities when they self-organize into supramolecular structures, which are not observed in a single molecule. The self-assembled peptidic bolaamphiphiles hold considerable promise for imitating proteins with biochemical activities, such as specific affinity toward heterogeneous substances, a catalytic activity similar to a metalloenzyme, physicochemical activity from harmonized amino acid segments, and the capability to encapsulate genes like a viral vector. These diverse activities give rise to large research interest in biomaterials engineering, along with the synthesis and characterization of the assembled structures. This review aims to address the recent progress in the applications of peptidic bolaamphiphile assemblies whose densely packed peptide motifs on their surface and their stacked hydrophobic centers exhibit unique protein-like activity and designer functionality, respectively.
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Affiliation(s)
- Hyesung Lee
- Department of Chemical and Biomolecular Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Hanbee Kim
- Department of Chemical and Biomolecular Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Sang-Yup Lee
- Department of Chemical and Biomolecular Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
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2
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Johnson MB, Chandler M, Afonin KA. Nucleic acid nanoparticles (NANPs) as molecular tools to direct desirable and avoid undesirable immunological effects. Adv Drug Deliv Rev 2021; 173:427-438. [PMID: 33857556 PMCID: PMC8178219 DOI: 10.1016/j.addr.2021.04.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/05/2021] [Accepted: 04/08/2021] [Indexed: 12/12/2022]
Abstract
Nucleic acid nanoparticles (NANPs) represent a highly versatile molecular platform for the targeted delivery of various therapeutics. However, despite their promise, further clinical translation of this innovative technology can be hindered by immunological off-target effects. All human cells are equipped with an arsenal of receptors that recognize molecular patterns specific to foreign nucleic acids and understanding the rules that guide this recognition offer the key rationale for the development of therapeutic NANPs with tunable immune stimulation. Numerous recent studies have provided increasing evidence that in addition to NANPs' physicochemical properties and therapeutic effects, their interactions with cells of the immune system can be regulated through multiple independently programmable architectural parameters. The results further suggest that defined immunomodulation by NANPs can either support their immunoquiescent delivery or be used for conditional stimulation of beneficial immunological responses.
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Affiliation(s)
- M Brittany Johnson
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Morgan Chandler
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
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3
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Dhandapani RK, Gurusamy D, Palli SR. Development of Catechin, Poly-l-lysine, and Double-Stranded RNA Nanoparticles. ACS APPLIED BIO MATERIALS 2021; 4:4310-4318. [PMID: 35006843 DOI: 10.1021/acsabm.1c00109] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Developing strategies to optimize double-stranded RNA (dsRNA) delivery remains a significant challenge in improving RNA interference (RNAi) in insects. Nanoformulations may provide an avenue for the safe and effective delivery of dsRNA. We investigated nanoparticle-mediated gene silencing using biodegradable polymers, poly-l-lysine (PLL), and polyphenol (-)-epigallocatechin gallate (EGCG) for dsRNA delivery into Spodoptera frugiperda (Sf9) cells. Negatively charged cores were formed by EGCG and dsRNA complexes, and PLL was used to encapsulate the cores. The nanoparticles were characterized by dynamic light scattering (DLS), transmission electron microscopy (TEM), scanning transmission electron microscopy (STEM), and energy-dispersive spectrometry (EDS) analysis. The stability of the nanoparticles was assessed by incubating them in nuclease-containing Sf9 cell conditioned media. The effectiveness of the nanoparticles was investigated in Sf9 cells stably expressing the luciferase gene. The results revealed that the nanoparticles formed were small and spherical. The PLL/EGCG/dsRNA nanoparticles exhibited better stability compared to that of PLL/dsRNA or naked dsRNA. Nanoparticles prepared with dsRNA targeting the luciferase gene induced an efficient knockdown (66.7%) of the target gene. In Sf9 cells, nanoparticles prepared with Cy3- or CyPHer-5E-labeled dsRNA showed higher cellular uptake and endosomal escape, respectively, than the naked dsRNA. The improvement in uptake and cytosolic delivery may have helped to increase the knockdown efficiency. In Sf9 cells, the nanoparticles prepared with dsRNA targeting the inhibitor of apoptosis gene induced apoptosis by knocking down its expression. In conclusion, we demonstrate that PLL/EGCG/dsRNA nanoparticles are stable, highly efficient, and effective in dsRNA delivery and knockdown of the target gene.
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Affiliation(s)
- Ramesh Kumar Dhandapani
- Department of Entomology, University of Kentucky, S-225 Agricultural Science Center North, Lexington, Kentucky 40546-0091, United States
| | - Dhandapani Gurusamy
- Department of Entomology, University of Kentucky, S-225 Agricultural Science Center North, Lexington, Kentucky 40546-0091, United States
| | - Subba Reddy Palli
- Department of Entomology, University of Kentucky, S-225 Agricultural Science Center North, Lexington, Kentucky 40546-0091, United States
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4
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Hughes JR, Miller AS, Wallace CE, Vemuri GN, Iovine PM. Biomedically Relevant Applications of Bolaamphiphiles and Bolaamphiphile-Containing Materials. Front Chem 2021; 8:604151. [PMID: 33553103 PMCID: PMC7855593 DOI: 10.3389/fchem.2020.604151] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/15/2020] [Indexed: 12/28/2022] Open
Abstract
Bolaamphiphiles (BAs) are structurally segmented molecules with rich assembly characteristics and diverse physical properties. Interest in BAs as standalone active agents or as constituents of more complex therapeutic formulations has increased substantially in recent years. The preorganized amphiphilicity of BAs allows for a range of biological activities including applications that rely on multivalency. This review summarizes BA-related research in biomedically relevant areas. In particular, we review BA-related literature in four areas: gene delivery, antimicrobial materials, hydrogels, and prodrugs. We also discuss several distinguishing characteristics of BAs that impact their utility as biomedically relevant compounds.
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Affiliation(s)
| | | | | | | | - Peter M. Iovine
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, CA, United States
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5
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Dobrovolskaia MA, Bathe M. Opportunities and challenges for the clinical translation of structured DNA assemblies as gene therapeutic delivery and vaccine vectors. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2021; 13:e1657. [PMID: 32672007 PMCID: PMC7736207 DOI: 10.1002/wnan.1657] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 05/27/2020] [Accepted: 05/29/2020] [Indexed: 12/12/2022]
Abstract
Gene therapeutics including siRNAs, anti-sense oligos, messenger RNAs, and CRISPR ribonucleoprotein complexes offer unmet potential to treat over 7,000 known genetic diseases, as well as cancer, through targeted in vivo modulation of aberrant gene expression and immune cell activation. Compared with viral vectors, nonviral delivery vectors offer controlled immunogenicity and low manufacturing cost, yet suffer from limitations in toxicity, targeting, and transduction efficiency. Structured DNA assemblies fabricated using the principle of scaffolded DNA origami offer a new nonviral delivery vector with intrinsic, yet controllable immunostimulatory properties and virus-like spatial presentation of ligands and immunogens for cell-specific targeting, activation, and control over intracellular trafficking, in addition to low manufacturing cost. However, the relative utilities and limitations of these vectors must clearly be demonstrated in preclinical studies for their clinical potential to be realized. Here, we review the major capabilities, opportunities, and challenges we foresee in translating these next-generation delivery and vaccine vectors to the clinic. This article is categorized under: Therapeutic Approaches and Drug Discovery > Emerging Technologies Biology-Inspired Nanomaterials > Nucleic Acid-Based Structures Therapeutic Approaches and Drug Discovery > Nanomedicine for Oncologic Disease.
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Affiliation(s)
- Marina A. Dobrovolskaia
- Nanotechnology Characterization Laboratory, Cancer Research Technology ProgramFrederick National Laboratory for Cancer Research sponsored by National Cancer InstituteFrederickMaryland
| | - Mark Bathe
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMassachusetts
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6
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Mahdavi M, Fattahi A, Nouranian S. Doxorubicin Stability and Retention on PEGylated Graphene Oxide Nanocarriers Adjacent to Human Serum Albumin. ACS APPLIED BIO MATERIALS 2020; 3:7646-7653. [DOI: 10.1021/acsabm.0c00843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Mina Mahdavi
- Department of Chemical Engineering, The University of Mississippi, University, Mississippi 38677, United States
| | - Ali Fattahi
- Center for Applied NanoBioscience and Medicine, College of Medicine−Phoenix, The University of Arizona, Phoenix, Arizona 85004, United States
- Whitespace Enterprises, 1305 W Auto Drive, Tempe, Arizona 85284, United States
| | - Sasan Nouranian
- Department of Chemical Engineering, The University of Mississippi, University, Mississippi 38677, United States
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Kim T, Viard M, Afonin KA, Gupta K, Popov M, Salotti J, Johnson PF, Linder C, Heldman E, Shapiro BA. Characterization of Cationic Bolaamphiphile Vesicles for siRNA Delivery into Tumors and Brain. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 20:359-372. [PMID: 32200271 PMCID: PMC7090283 DOI: 10.1016/j.omtn.2020.02.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 12/19/2019] [Accepted: 02/23/2020] [Indexed: 12/27/2022]
Abstract
Small interfering RNAs (siRNAs) are potential therapeutic substances due to their gene silencing capability as exemplified by the recent approval by the US Food and Drug Administration (FDA) of the first siRNA therapeutic agent (patisiran). However, the delivery of naked siRNAs is challenging because of their short plasma half-lives and poor cell penetrability. In this study, we used vesicles made from bolaamphiphiles (bolas), GLH-19 and GLH-20, to investigate their ability to protect siRNA from degradation by nucleases while delivering it to target cells, including cells in the brain. Based on computational and experimental studies, we found that GLH-19 vesicles have better delivery characteristics than do GLH-20 vesicles in terms of stability, binding affinity, protection against nucleases, and transfection efficiency, while GLH-20 vesicles contribute to efficient release of the delivered siRNAs, which become available for silencing. Our studies with vesicles made from a mixture of the two bolas (GLH-19 and GLH-20) show that they were able to deliver siRNAs into cultured cancer cells, into a flank tumor and into the brain. The vesicles penetrate cell membranes and the blood-brain barrier (BBB) by endocytosis and transcytosis, respectively, mainly through the caveolae-dependent pathway. These results suggest that GLH-19 strengthens vesicle stability, provides protection against nucleases, and enhances transfection efficiency, while GLH-20 makes the siRNA available for gene silencing.
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Affiliation(s)
- Taejin Kim
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Mathias Viard
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA; The Center for Biomedical Engineering and Science, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Kshitij Gupta
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Mary Popov
- Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Jacqueline Salotti
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Peter F Johnson
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | | | | | - Bruce A Shapiro
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
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Chandler M, Panigaj M, Rolband LA, Afonin KA. Challenges to optimizing RNA nanostructures for large scale production and controlled therapeutic properties. Nanomedicine (Lond) 2020; 15:1331-1340. [PMID: 32452262 PMCID: PMC7304434 DOI: 10.2217/nnm-2020-0034] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 03/16/2020] [Indexed: 02/06/2023] Open
Abstract
Nucleic acids have been utilized to construct an expansive collection of nanoarchitectures varying in design, physicochemical properties, cellular processing and biomedical applications. However, the broader therapeutic adaptation of nucleic acid nanoassemblies in general, and RNA-based nanoparticles in particular, have faced several challenges in moving towards (pre)clinical settings. For one, the large-batch synthesis of nucleic acids is still under development, with multi-stranded and chemically modified assemblies requiring greater production capacity while maintaining consistent medical-grade outputs. Furthermore, the unknown immunostimulation by these nanomaterials poses additional challenges, necessary to be overcome for optimizing future development of clinically approved RNA nanoparticles.
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Affiliation(s)
- Morgan Chandler
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Martin Panigaj
- Institute of Biology & Ecology, Faculty of Science, Pavol Jozef Safarik University in Kosice, Kosice, Slovak Republic
| | - Lewis A Rolband
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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Dobrovolskaia MA. Nucleic Acid Nanoparticles at a Crossroads of Vaccines and Immunotherapies. Molecules 2019; 24:molecules24244620. [PMID: 31861154 PMCID: PMC6943637 DOI: 10.3390/molecules24244620] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/13/2019] [Accepted: 12/13/2019] [Indexed: 02/06/2023] Open
Abstract
Vaccines and immunotherapies involve a variety of technologies and act through different mechanisms to achieve a common goal, which is to optimize the immune response against an antigen. The antigen could be a molecule expressed on a pathogen (e.g., a disease-causing bacterium, a virus or another microorganism), abnormal or damaged host cells (e.g., cancer cells), environmental agent (e.g., nicotine from a tobacco smoke), or an allergen (e.g., pollen or food protein). Immunogenic vaccines and therapies optimize the immune response to improve the eradication of the pathogen or damaged cells. In contrast, tolerogenic vaccines and therapies retrain or blunt the immune response to antigens, which are recognized by the immune system as harmful to the host. To optimize the immune response to either improve the immunogenicity or induce tolerance, researchers employ different routes of administration, antigen-delivery systems, and adjuvants. Nanocarriers and adjuvants are of particular interest to the fields of vaccines and immunotherapy as they allow for targeted delivery of the antigens and direct the immune response against these antigens in desirable direction (i.e., to either enhance immunogenicity or induce tolerance). Recently, nanoparticles gained particular attention as antigen carriers and adjuvants. This review focuses on a particular subclass of nanoparticles, which are made of nucleic acids, so-called nucleic acid nanoparticles or NANPs. Immunological properties of these novel materials and considerations for their clinical translation are discussed.
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Affiliation(s)
- Marina A Dobrovolskaia
- Nanotechnology Characterization Lab, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21702, USA
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10
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Saw PE, Yao H, Lin C, Tao W, Farokhzad OC, Xu X. Stimuli-Responsive Polymer-Prodrug Hybrid Nanoplatform for Multistage siRNA Delivery and Combination Cancer Therapy. NANO LETTERS 2019; 19:5967-5974. [PMID: 31381852 DOI: 10.1021/acs.nanolett.9b01660] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Nanoparticles (NPs) formulated with cationic lipids and/or polymers have shown substantial potential for systemic delivery of RNA therapeutics such as small interfering RNA (siRNA) for the treatment of cancer and other diseases. While both cationic lipids and polymers have demonstrated the promise to facilitate siRNA encapsulation and endosomal escape, they could also hamper cytosolic siRNA release due to charge interaction and induce potential toxicities. Herein, a unique polymer-prodrug hybrid NP platform was developed for multistage siRNA delivery and combination cancer therapy. This NP system is composed of (i) a hydrophilic polyethylene glycol (PEG) shell, (ii) a hydrophobic NP core made with a tumor microenvironment (TME) pH-responsive polymer, and (iii) charge-mediated complexes of siRNA and amphiphilic cationic mitoxantrone (MTO)-based prodrug that are encapsulated in the NP core. After intravenous administration, the long-circulating NPs accumulate in tumor tissues and then rapidly release the siRNA-prodrug complexes via TME pH-mediated NP disassociation for subsequent tissue penetration and cytosolic transport. With the overexpressed esterase in tumor cells to hydrolyze the amphiphilic structure of the prodrug and thereby induce destabilization of the siRNA-prodrug complexes, the therapeutic siRNA and anticancer drug MTO can be efficiently released in the cytoplasm, ultimately leading to the combinational inhibition of tumor growth via concurrent RNAi-mediated gene silencing and MTO-mediated chemotherapy.
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Affiliation(s)
- Phei Er Saw
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital , Sun Yat-Sen University , Guangzhou 510120 , P. R. China
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital , Sun Yat-Sen University , Guangzhou 510120 , P. R. China
| | - Herui Yao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital , Sun Yat-Sen University , Guangzhou 510120 , P. R. China
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital , Sun Yat-Sen University , Guangzhou 510120 , P. R. China
| | - Chunhao Lin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital , Sun Yat-Sen University , Guangzhou 510120 , P. R. China
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital , Sun Yat-Sen University , Guangzhou 510120 , P. R. China
| | - Wei Tao
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Omid C Farokhzad
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Xiaoding Xu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital , Sun Yat-Sen University , Guangzhou 510120 , P. R. China
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital , Sun Yat-Sen University , Guangzhou 510120 , P. R. China
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Ayat NR, Sun Z, Sun D, Yin M, Hall RC, Vaidya AM, Liu X, Schilb AL, Scheidt JH, Lu ZR. Formulation of Biocompatible Targeted ECO/siRNA Nanoparticles with Long-Term Stability for Clinical Translation of RNAi. Nucleic Acid Ther 2019; 29:195-207. [PMID: 31140918 PMCID: PMC6686697 DOI: 10.1089/nat.2019.0784] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 03/29/2019] [Indexed: 12/22/2022] Open
Abstract
Nanoparticle based siRNA formulations often suffer from aggregation and loss of function during storage. We in this study report a frozen targeted RGD-polyethylene glycol (PEG)-ECO/siβ3 nanoparticle formulation with a prolonged shelf life and preserved nanoparticle functionality. The targeted RGD-PEG-ECO/siβ3 nanoparticles are formed by step-wised self-assembly of RGD-PEG-maleimide, ECO, and siRNA. The nanoparticles have a diameter of 224.5 ± 9.41 nm and a zeta potential to 45.96 ± 3.67 mV in water and a size of 234.34 ± 3.01 nm and a near neutral zeta potential in saline solution. The addition of sucrose does not affect their size and zeta potential and substantially preserves the integrity and biological activities of frozen and lyophilized formulations of the targeted nanoparticles. The frozen formulation with as low as 5% sucrose retains nanoparticle integrity (90% siRNA encapsulation), size distribution (polydispersity index [PDI] ≤20%), and functionality (at least 75% silencing efficiency) at -80°C for at least 1 year. The frozen RGD-PEG-ECO/siβ3 nanoparticle formulation exhibits excellent biocompatibility, with no adverse effects on hemocompatibility and minimal immunogenicity. As RNAi holds the promise in treating the previously untreatable diseases, the frozen nanoparticle formulation with the low sucrose concentration has the potential to be a delivery platform for clinical translation of RNAi therapeutics.
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Affiliation(s)
- Nadia R. Ayat
- Department of Biomedical Engineering, School of Engineering, Case Western Reserve University, Cleveland, Ohio
| | - Zhanhu Sun
- Department of Biomedical Engineering, School of Engineering, Case Western Reserve University, Cleveland, Ohio
| | - Da Sun
- Department of Biomedical Engineering, School of Engineering, Case Western Reserve University, Cleveland, Ohio
| | - Michelle Yin
- Department of Biomedical Engineering, School of Engineering, Case Western Reserve University, Cleveland, Ohio
| | - Ryan C. Hall
- Department of Biomedical Engineering, School of Engineering, Case Western Reserve University, Cleveland, Ohio
| | - Amita M. Vaidya
- Department of Biomedical Engineering, School of Engineering, Case Western Reserve University, Cleveland, Ohio
| | - Xujie Liu
- Department of Biomedical Engineering, School of Engineering, Case Western Reserve University, Cleveland, Ohio
| | - Andrew L. Schilb
- Department of Biomedical Engineering, School of Engineering, Case Western Reserve University, Cleveland, Ohio
| | - Josef H. Scheidt
- Department of Biomedical Engineering, School of Engineering, Case Western Reserve University, Cleveland, Ohio
| | - Zheng-Rong Lu
- Department of Biomedical Engineering, School of Engineering, Case Western Reserve University, Cleveland, Ohio
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12
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Oliver RC, Rolband LA, Hutchinson-Lundy AM, Afonin KA, Krueger JK. Small-Angle Scattering as a Structural Probe for Nucleic Acid Nanoparticles (NANPs) in a Dynamic Solution Environment. NANOMATERIALS (BASEL, SWITZERLAND) 2019; 9:E681. [PMID: 31052508 PMCID: PMC6566709 DOI: 10.3390/nano9050681] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 04/16/2019] [Accepted: 04/19/2019] [Indexed: 12/23/2022]
Abstract
Nucleic acid-based technologies are an emerging research focus area for pharmacological and biological studies because they are biocompatible and can be designed to produce a variety of scaffolds at the nanometer scale. The use of nucleic acids (ribonucleic acid (RNA) and/or deoxyribonucleic acid (DNA)) as building materials in programming the assemblies and their further functionalization has recently established a new exciting field of RNA and DNA nanotechnology, which have both already produced a variety of different functional nanostructures and nanodevices. It is evident that the resultant architectures require detailed structural and functional characterization and that a variety of technical approaches must be employed to promote the development of the emerging fields. Small-angle X-ray and neutron scattering (SAS) are structural characterization techniques that are well placed to determine the conformation of nucleic acid nanoparticles (NANPs) under varying solution conditions, thus allowing for the optimization of their design. SAS experiments provide information on the overall shapes and particle dimensions of macromolecules and are ideal for following conformational changes of the molecular ensemble as it behaves in solution. In addition, the inherent differences in the neutron scattering of nucleic acids, lipids, and proteins, as well as the different neutron scattering properties of the isotopes of hydrogen, combined with the ability to uniformly label biological macromolecules with deuterium, allow one to characterize the conformations and relative dispositions of the individual components within an assembly of biomolecules. This article will review the application of SAS methods and provide a summary of their successful utilization in the emerging field of NANP technology to date, as well as share our vision on its use in complementing a broad suite of structural characterization tools with some simulated results that have never been shared before.
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Affiliation(s)
- Ryan C Oliver
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA.
| | - Lewis A Rolband
- UNC Charlotte Chemistry Department, Charlotte, NC 28223, USA.
| | | | - Kirill A Afonin
- UNC Charlotte Chemistry Department, Charlotte, NC 28223, USA.
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Chandler M, Afonin KA. Smart-Responsive Nucleic Acid Nanoparticles (NANPs) with the Potential to Modulate Immune Behavior. NANOMATERIALS (BASEL, SWITZERLAND) 2019; 9:E611. [PMID: 31013847 PMCID: PMC6523571 DOI: 10.3390/nano9040611] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 03/29/2019] [Accepted: 04/08/2019] [Indexed: 12/24/2022]
Abstract
Nucleic acids are programmable and biocompatible polymers that have beneficial uses in nanotechnology with broad applications in biosensing and therapeutics. In some cases, however, the development of the latter has been impeded by the unknown immunostimulatory properties of nucleic acid-based materials, as well as a lack of functional dynamicity due to stagnant structural design. Recent research advancements have explored these obstacles in tandem via the assembly of three-dimensional, planar, and fibrous cognate nucleic acid-based nanoparticles, called NANPs, for the conditional activation of embedded and otherwise quiescent functions. Furthermore, a library of the most representative NANPs was extensively analyzed in human peripheral blood mononuclear cells (PBMCs), and the links between the programmable architectural and physicochemical parameters of NANPs and their immunomodulatory properties have been established. This overview will cover the recent development of design principles that allow for fine-tuning of both the physicochemical and immunostimulatory properties of dynamic NANPs and discuss the potential impacts of these novel strategies.
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Affiliation(s)
- Morgan Chandler
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
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14
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Orabi AS, Abou El-Nour KM, Ahmed SA, El-Falouji AI. Novel gold and silver-Sarcophine complexes as antitumor agents against MCF7 and HepG2 cells: Synthesis, characterization, in Silico, in Vitro and docking studies. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2018.10.058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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15
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16
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Narayanan K, Khan M, Gopalan B, Antony J, Das T, Yang YY, Wan ACA. Sensitization of Cancer Cells via Non-Viral Delivery of Apoptosis Inducing Proteins Using a Cationic Bolaamphiphile. Biotechnol J 2018; 14:e1800020. [PMID: 29802765 DOI: 10.1002/biot.201800020] [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: 01/04/2018] [Revised: 05/18/2018] [Indexed: 01/10/2023]
Abstract
Cationic bolaamphiphile polymers had been previously studied as efficient delivery system for the delivery of proteins with relatively low toxicity. Here, the authors investigate the use of a protein delivery system based on a cationic bolaamphiphile to sensitize cancer cells toward apoptosis-inducing drugs as a novel approach for cancer therapy. The authors demonstrates the efficacy of the system by two strategies. The first strategy involves delivery of a survivin antibody to inhibit survivin activity. Sensitization of MCF-7 cells to doxorubicin is observed by survivin inhibition by antibodies. The IC50 of doxorubicin is reduced ≈2.5-fold after delivery of survivin antibodies to breast cancer cells and induction of apoptosis is shown by Western blotting with apoptosis specific antibodies. In a second approach, functional wild type p53 is delivered into p53-null liver cancer (Hep3B) cells, sensitizing the cells toward the p53 pathway drug, Nutlin. Nutlin reduced the viability of Hep3B cells by ≈42% at 15 μM concentration, demonstrating the effectiveness of p53 delivery. The expression of p21, a downstream target of p53 further confirmed the functional status of the delivered protein. In conclusion. The successful delivery of apoptosis inducing proteins and sensitization of cancer cells via cationic bolaamphiphile polymer represents a promising system for cancer therapeutics.
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Affiliation(s)
| | - Majad Khan
- Department of Chemistry, King Fahd University of Petroleum and Minerals, Dhahran, 34463, Kingdom of Saudi Arabia
| | - Began Gopalan
- Institute of Bioengineering and Nanotechnology, The NanosSingapore, 138669, Singapore
| | - Jane Antony
- Institute of Bioengineering and Nanotechnology, The NanosSingapore, 138669, Singapore
| | - Tultul Das
- Institute of Bioengineering and Nanotechnology, The NanosSingapore, 138669, Singapore
| | - Yi Yan Yang
- Institute of Bioengineering and Nanotechnology, The NanosSingapore, 138669, Singapore
| | - Andrew C A Wan
- Institute of Bioengineering and Nanotechnology, The NanosSingapore, 138669, Singapore
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17
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Dendritic peptide bolaamphiphiles for siRNA delivery to primary adipocytes. Biomaterials 2018; 178:458-466. [PMID: 29705001 DOI: 10.1016/j.biomaterials.2018.04.024] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 04/11/2018] [Accepted: 04/13/2018] [Indexed: 12/31/2022]
Abstract
Obesity is a major risk factor for diabetes, heart disease and other health problems. Adipose tissue plays a central role in the development of obesity and obesity-associated diseases. Gene therapy targeting adipose tissue may provide a promising strategy for obesity treatment. However, nucleic acid delivery to adipose tissue or even cultured adipocytes is challenging due to low delivery efficacy and high toxicity of the current cationic lipid based delivery systems, or monoamphiphiles. Herein, we report using dendritic peptide bolaamphiphiles (bolas) to deliver siRNA to primary adipocytes and hepatocytes. The bola consists of two l-Lysine dendrons connected to a fluorocarbon core through disulfide linkages. The Lysine dendrons are functionalized with l-histidine and l-tryptophan to promote endosomal escape and cellular uptake. The bola exhibited over 70% knockdown of GAPDH gene in both primary adipocytes and hepatocytes. Importantly, different from Lipofectamine that significantly reduced genes involved in lipolysis, lipogenesis, fatty acid oxidation and ketogenesis, the bolas had little to no effect on these genes. These results demonstrate the bola as a promising new vector for clinical and experimental applications for delivery of siRNA to metabolic organs.
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18
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Falsini S, Di Cola E, In M, Giordani M, Borocci S, Ristori S. Complexation of short ds RNA/DNA oligonucleotides with Gemini micelles: a time resolved SAXS and computational study. Phys Chem Chem Phys 2018; 19:3046-3055. [PMID: 28079203 DOI: 10.1039/c6cp06475b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Gene therapy is based on nucleic acid delivery to pathogenic cells in order to modulate their gene expression. The most used non viral vectors are lipid-based nanoaggregates, which are safer than viral carriers and have been shown to assemble easily with both DNA and RNA. However, the transfection efficiency of non viral carriers still needs to be improved before intensive practise in clinical trials can be implemented. For this purpose, the in depth characterization of the complexes formed by nucleic acids and their transporters is of great relevance. In particular, information on the structure and assembly mechanism can be useful to improve our general knowledge of these artificial transfection agents. In this paper, the complexation mechanism of short interfering RNA and DNA molecules (siRNA and siDNA, respectively) with cationic micelles is investigated by combining small angle X-ray scattering experiments and molecular dynamics simulations. Micelles were obtained by Gemini surfactants with different spacer lengths (12-3-12, 12-6-12). The siRNA and siDNA used were double strand molecules characterized by the same length and homologous sequence, in order to perform a close comparison. We showed that complexes appear in solution immediately after mixing and, therefore, the investigation of complex formation requires fast experimental techniques, such as time resolved synchrotron SAXS (Tr-SAXS). The obtained systems had internal arrangement constituted by layers of squeezed micelles alternating the nucleic acids. Both SAXS and MD analyses allowed us to evaluate the mean size of complexes in the range of a few nanometers, with looser and less ordered stacking for the DNA containing aggregates.
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Affiliation(s)
- Sara Falsini
- Department of Chemistry "Ugo Shiff" & CSGI, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, FI, Italy
| | - Emanuela Di Cola
- European Synchrotron Radiation Facility (ESRF), 71 Avenue des martyrs 38000, Grenoble, France
| | - Martin In
- Laboratoire Charles Coloumb, UMR, 5221 CNRS-UM, Place Eugène Bataillon, F-34095 Montpellier Cedex 05, France
| | - Maria Giordani
- CNR-Istituto di Metodologie Chimiche, Area della Ricerca di Roma 1, Via Salaria km 29300, 00015 Monterotondo RM, Italy
| | - Stefano Borocci
- CNR-Istituto di Metodologie Chimiche, Area della Ricerca di Roma 1, Via Salaria km 29300, 00015 Monterotondo RM, Italy and Dipartimento per la Innovazione nei Sistemi Biologici, Agroalimentari e Forestali (DIBAF), Università degli Studi della Tuscia, Largo dell'Università, snc 01100, Viterbo, Italy
| | - Sandra Ristori
- Dipartimento di Scienze della Terra, Università di Firenze, Via La Pira 4, 50121, Firenze, Italy
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19
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Martínez-Negro M, Guerrero-Martínez A, García-Río L, Domènech Ò, Aicart E, Tros de Ilarduya C, Junquera E. Multidisciplinary Approach to the Transfection of Plasmid DNA by a Nonviral Nanocarrier Based on a Gemini-Bolaamphiphilic Hybrid Lipid. ACS OMEGA 2018; 3:208-217. [PMID: 30023772 PMCID: PMC6044976 DOI: 10.1021/acsomega.7b01657] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 12/26/2017] [Indexed: 06/08/2023]
Abstract
A multidisciplinary strategy, including both biochemical and biophysical studies, was proposed here to evaluate the potential of lipid nanoaggregates consisting of a mixture of a gemini-bolaamphiphilic lipid (C6C22C6) and the well-known helper lipid 1,2-dioleoyl-sn-glycero-3-phosphatidylethanolamine (DOPE) to transfect plasmid DNA into living cells in an efficient and safe way. For that purpose, several experimental techniques were employed, such as zeta potential (phase analysis light scattering methodology), agarose gel electrophoresis (pDNA compaction and pDNA protection assays), small-angle X-ray scattering, cryo-transmission electron microscopy, atomic force microscopy, fluorescence-assisted cell sorting, luminometry, and cytotoxicity assays. The results revealed that the cationic lipid and plasmid offer only 70 and 30% of their nominal positive () and negative charges (), respectively. Upon mixing with DOPE, they form lipoplexes that self-aggregate in typical multilamellar Lα lyotropic liquid-crystal nanostructures with sizes in the range of 100-200 nm and low polydispersities, very suitably fitted to remain in the bloodstream and cross the cell membrane. Interestingly, these nanoaggregates were able to compact, protect (from the degrading effect of DNase I), and transfect two DNA plasmids (pEGFP-C3, encoding the green fluorescent protein, and pCMV-Luc, encoding luciferase) into COS-7 cells, with an efficiency equal or even superior to that of the universal control Lipo2000*, as long as the effective +/- charge ratio was maintained higher than 1 but reasonably close to electroneutrality. Moreover, this transfection process was not cytotoxic because the viability of COS-7 cells remained at high levels, greater than 80%. All of these features make the C6C22C6/DOPE nanosystem an optimal nonviral gene nanocarrier in vitro and a potentially interesting candidate for future in vivo experiments.
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Affiliation(s)
- María Martínez-Negro
- Departamento
de Química Física I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Andrés Guerrero-Martínez
- Departamento
de Química Física I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Luis García-Río
- Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CIQUS) and Departamento de Química
Física, Universidade de Santiago, 15782 Santiago, Spain
| | - Òscar Domènech
- Departamento
de Farmacia, Tecnología Farmacéutica y Fisicoquímica,
Facultad de Farmacia y Ciencia de Los Alimentos, Universitat de Barcelona, and Institut de Nanociència i Nanotecnologia
IN2UB, Barcelona, Catalonia 08028, Spain
| | - Emilio Aicart
- Departamento
de Química Física I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Conchita Tros de Ilarduya
- Departamento
de Farmacia y Tecnología Farmacéutica, Facultad de Farmacia, Universidad de Navarra, Instituto de Investigación
Sanitaria de Navarra, 31008 Pamplona, Spain
| | - Elena Junquera
- Departamento
de Química Física I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
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20
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Johnson MB, Halman JR, Satterwhite E, Zakharov AV, Bui MN, Benkato K, Goldsworthy V, Kim T, Hong E, Dobrovolskaia MA, Khisamutdinov EF, Marriott I, Afonin KA. Programmable Nucleic Acid Based Polygons with Controlled Neuroimmunomodulatory Properties for Predictive QSAR Modeling. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:10.1002/smll.201701255. [PMID: 28922553 PMCID: PMC6258062 DOI: 10.1002/smll.201701255] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/14/2017] [Indexed: 05/13/2023]
Abstract
In the past few years, the study of therapeutic RNA nanotechnology has expanded tremendously to encompass a large group of interdisciplinary sciences. It is now evident that rationally designed programmable RNA nanostructures offer unique advantages in addressing contemporary therapeutic challenges such as distinguishing target cell types and ameliorating disease. However, to maximize the therapeutic benefit of these nanostructures, it is essential to understand the immunostimulatory aptitude of such tools and identify potential complications. This paper presents a set of 16 nanoparticle platforms that are highly configurable. These novel nucleic acid based polygonal platforms are programmed for controllable self-assembly from RNA and/or DNA strands via canonical Watson-Crick interactions. It is demonstrated that the immunostimulatory properties of these particular designs can be tuned to elicit the desired immune response or lack thereof. To advance the current understanding of the nanoparticle properties that contribute to the observed immunomodulatory activity and establish corresponding designing principles, quantitative structure-activity relationship modeling is conducted. The results demonstrate that molecular weight, together with melting temperature and half-life, strongly predicts the observed immunomodulatory activity. This framework provides the fundamental guidelines necessary for the development of a new library of nanoparticles with predictable immunomodulatory activity.
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Affiliation(s)
- M. Brittany Johnson
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, NC 28223, USA
| | - Justin R. Halman
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Emily Satterwhite
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Alexey V. Zakharov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - My N. Bui
- Department of Chemistry, Ball State University, Muncie, IN 47306, USA
| | - Kheiria Benkato
- Department of Chemistry, Ball State University, Muncie, IN 47306, USA
| | | | - Taejin Kim
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Enping Hong
- Nanotechnology Characterization Lab, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Marina A. Dobrovolskaia
- Nanotechnology Characterization Lab, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | | | - Ian Marriott
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, NC 28223, USA
| | - Kirill A. Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
- The Center for Biomedical Engineering and Science, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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21
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Li X, Omotere O, Qian L, Dougherty ER. Review of stochastic hybrid systems with applications in biological systems modeling and analysis. EURASIP JOURNAL ON BIOINFORMATICS & SYSTEMS BIOLOGY 2017; 2017:8. [PMID: 28667450 PMCID: PMC5493609 DOI: 10.1186/s13637-017-0061-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Accepted: 06/05/2017] [Indexed: 11/10/2022]
Abstract
Stochastic hybrid systems (SHS) have attracted a lot of research interests in recent years. In this paper, we review some of the recent applications of SHS to biological systems modeling and analysis. Due to the nature of molecular interactions, many biological processes can be conveniently described as a mixture of continuous and discrete phenomena employing SHS models. With the advancement of SHS theory, it is expected that insights can be obtained about biological processes such as drug effects on gene regulation. Furthermore, combining with advanced experimental methods, in silico simulations using SHS modeling techniques can be carried out for massive and rapid verification or falsification of biological hypotheses. The hope is to substitute costly and time-consuming in vitro or in vivo experiments or provide guidance for those experiments and generate better hypotheses.
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Affiliation(s)
- Xiangfang Li
- Department of Electrical and Computer Engineering, Prairie View A&M University, Prairie View, 77446, TX, USA.
| | - Oluwaseyi Omotere
- Department of Electrical and Computer Engineering, Prairie View A&M University, Prairie View, 77446, TX, USA
| | - Lijun Qian
- Department of Electrical and Computer Engineering, Prairie View A&M University, Prairie View, 77446, TX, USA
| | - Edward R Dougherty
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, 77843, TX, USA
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22
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Xu X, Wu J, Liu Y, Saw PE, Tao W, Yu M, Zope H, Si M, Victorious A, Rasmussen J, Ayyash D, Farokhzad OC, Shi J. Multifunctional Envelope-Type siRNA Delivery Nanoparticle Platform for Prostate Cancer Therapy. ACS NANO 2017; 11:2618-2627. [PMID: 28240870 PMCID: PMC5626580 DOI: 10.1021/acsnano.6b07195] [Citation(s) in RCA: 154] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
With the capability of specific silencing of target gene expression, RNA interference (RNAi) technology is emerging as a promising therapeutic modality for the treatment of cancer and other diseases. One key challenge for the clinical applications of RNAi is the safe and effective delivery of RNAi agents such as small interfering RNA (siRNA) to a particular nonliver diseased tissue (e.g., tumor) and cell type with sufficient cytosolic transport. In this work, we proposed a multifunctional envelope-type nanoparticle (NP) platform for prostate cancer (PCa)-specific in vivo siRNA delivery. A library of oligoarginine-functionalized and sharp pH-responsive polymers was synthesized and used for self-assembly with siRNA into NPs with the features of long blood circulation and pH-triggered oligoarginine-mediated endosomal membrane penetration. By further modification with ACUPA, a small molecular ligand specifically recognizing prostate-specific membrane antigen (PSMA) receptor, this envelope-type nanoplatform with multifunctional properties can efficiently target PSMA-expressing PCa cells and silence target gene expression. Systemic delivery of the siRNA NPs can efficiently silence the expression of prohibitin 1 (PHB1), which is upregulated in PCa and other cancers, and significantly inhibit PCa tumor growth. These results suggest that this multifunctional envelope-type nanoplatform could become an effective tool for PCa-specific therapy.
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Affiliation(s)
- Xiaoding Xu
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Jun Wu
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Yanlan Liu
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Phei Er Saw
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Wei Tao
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Mikyung Yu
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Harshal Zope
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Michelle Si
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Amanda Victorious
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Jonathan Rasmussen
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Dana Ayyash
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Omid C. Farokhzad
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Jinjun Shi
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
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23
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Hu B, Yuan Y, Yan Y, Zhou X, Li Y, Kan Q, Li S. Preparation and evaluation of a novel anticancer drug delivery carrier for 5-Fluorouracil using synthetic bola-amphiphile based on lysine as polar heads. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2017; 75:637-645. [PMID: 28415509 DOI: 10.1016/j.msec.2017.02.106] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 02/20/2017] [Accepted: 02/21/2017] [Indexed: 01/05/2023]
Abstract
A novel bolaamphiphile surfactant N,N'-(dodecane-1, 12-diyl) bis (2,6-diaminohexanamide) (DADL) was designed and synthesized using l-lysine and 1,12-diaminododecane as the hydrophilic and hydrophobic part, respectively. After separation and purification, the structure of the synthetic bolaamphiphile surfactant was verified by FTIR, MS and 1H NMR. The synthetic bolaamphiphile was able to self-assemble to form vesicles. After formulation screening, vesicles loaded with 5-Fluorouracil (5-Fu) were prepared with Tween 60 and DADL by sonication and were examined by dynamic light scattering and transmission electron microscopy. Micro-FTIR was applied to investigate the conformation of the bola molecules within the vesicle membrane. The release profile of the vesicles showed a pH-sensitive and sustained release. No significant toxicity was observed in an in vitro cell viability assay. The antitumor efficacy of the 5-Fu-loaded vesicles on H22 tumor-bearing mice was remarkably high due to the EPR effects. These results show that our novel bolaamphiphile derived from lysine has excellent potential as a pH-sensitive drug carrier.
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Affiliation(s)
- Beibei Hu
- School of Pharmacy, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang 110016, China
| | - Yue Yuan
- School of Pharmacy, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang 110016, China.
| | - Yun Yan
- College of Chemistry and Molecular Engineering, Peking University, 202 Chenfu Road, Beijing 100871, China
| | - Xiaoping Zhou
- School of Pharmacy, Jilin University, 1266 Fujin Road, Changchun 130021, China
| | - Yue Li
- School of Pharmacy, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang 110016, China
| | - Qiming Kan
- School of Pharmacy, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang 110016, China
| | - Sanming Li
- School of Pharmacy, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang 110016, China.
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24
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Abstract
Molecular dynamics (MD) simulations have been used as one of the main research tools to study a wide range of biological systems and bridge the gap between X-ray crystallography or NMR structures and biological mechanism. In the field of RNA nanostructures, MD simulations have been used to fix steric clashes in computationally designed RNA nanostructures, characterize the dynamics, and investigate the interaction between RNA and other biomolecules such as delivery agents and membranes.In this chapter we present examples of computational protocols for molecular dynamics simulations in explicit and implicit solvent using the Amber Molecular Dynamics Package. We also show examples of post-simulation analysis steps and briefly mention selected tools beyond the Amber package. Limitations of the methods, tools, and protocols are also discussed. Most of the examples are illustrated for a small RNA duplex (helix), but the protocols are applicable to any nucleic acid structure, subject only to the computational speed and memory limitations of the hardware available to the user.
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Affiliation(s)
- Taejin Kim
- Department of Chemistry, New York University, 10th Floor Silver Center, 100 Washington Square East, New York, NY, 10003, USA
| | - Wojciech K Kasprzak
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Bruce A Shapiro
- RNA Structure and Design Section, RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA.
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25
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Cooper BM, Putnam D. Polymers for siRNA Delivery: A Critical Assessment of Current Technology Prospects for Clinical Application. ACS Biomater Sci Eng 2016; 2:1837-1850. [PMID: 33440520 DOI: 10.1021/acsbiomaterials.6b00363] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The number of polymer-based vectors for siRNA delivery in clinical trials lags behind other delivery strategies; however, the molecular architectures and chemical compositions available to polymers make them attractive candidates for further exploration. Polymer vectors are extensively investigated in academic laboratories worldwide with fundamental progress having recently been made in the areas of high-throughput screening, synthetic methods, cellular internalization, endosomal escape and computational prediction and analysis. This review assesses recent advances within the field and highlights relevant developments from within the complementary fields of nanotechnology and protein chemistry with the intent to propose future work that addresses key gaps within the current body of knowledge, potentially advancing the development of the next generation of polymeric vectors.
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Affiliation(s)
- Bailey M Cooper
- Meinig School of Biomedical Engineering and ‡Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - David Putnam
- Meinig School of Biomedical Engineering and Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
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26
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Parlea L, Puri A, Kasprzak W, Bindewald E, Zakrevsky P, Satterwhite E, Joseph K, Afonin KA, Shapiro BA. Cellular Delivery of RNA Nanoparticles. ACS COMBINATORIAL SCIENCE 2016; 18:527-47. [PMID: 27509068 PMCID: PMC6345529 DOI: 10.1021/acscombsci.6b00073] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
RNA nanostructures can be programmed to exhibit defined sizes, shapes and stoichiometries from naturally occurring or de novo designed RNA motifs. These constructs can be used as scaffolds to attach functional moieties, such as ligand binding motifs or gene expression regulators, for nanobiology applications. This review is focused on four areas of importance to RNA nanotechnology: the types of RNAs of particular interest for nanobiology, the assembly of RNA nanoconstructs, the challenges of cellular delivery of RNAs in vivo, and the delivery carriers that aid in the matter. The available strategies for the design of nucleic acid nanostructures, as well as for formulation of their carriers, make RNA nanotechnology an important tool in both basic research and applied biomedical science.
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Affiliation(s)
- Lorena Parlea
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Anu Puri
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Wojciech Kasprzak
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Eckart Bindewald
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Paul Zakrevsky
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Emily Satterwhite
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Kenya Joseph
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Kirill A. Afonin
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- Nanoscale Science Program, University of North Carolina at Charlotte, Charlotte North Carolina 28223, United States
- The Center for Biomedical Engineering and Science, University of North Carolina at Charlotte, Charlotte North Carolina 28223, United States
| | - Bruce A. Shapiro
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
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27
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Afonin KA, Viard M, Tedbury P, Bindewald E, Parlea L, Howington M, Valdman M, Johns-Boehme A, Brainerd C, Freed EO, Shapiro BA. The Use of Minimal RNA Toeholds to Trigger the Activation of Multiple Functionalities. NANO LETTERS 2016; 16:1746-53. [PMID: 26926382 PMCID: PMC6345527 DOI: 10.1021/acs.nanolett.5b04676] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Current work reports the use of single-stranded RNA toeholds of different lengths to promote the reassociation of various RNA-DNA hybrids, which results in activation of multiple split functionalities inside human cells. The process of reassociation is analyzed and followed with a novel computational multistrand secondary structure prediction algorithm and various experiments. All of our previously designed RNA/DNA nanoparticles employed single-stranded DNA toeholds to initiate reassociation. The use of RNA toeholds is advantageous because of the simpler design rules, the shorter toeholds, and the smaller size of the resulting nanoparticles (by up to 120 nucleotides per particle) compared to the same hybrid nanoparticles with single-stranded DNA toeholds. Moreover, the cotranscriptional assemblies result in higher yields for hybrid nanoparticles with ssRNA toeholds.
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Affiliation(s)
- Kirill A. Afonin
- Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
- Department of Chemistry, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, North Carolina 28223, United States
| | - Mathias Viard
- Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
- Basic Science Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Philip Tedbury
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Eckart Bindewald
- Basic Science Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Lorena Parlea
- Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Marshall Howington
- Department of Chemistry, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, North Carolina 28223, United States
| | - Melissa Valdman
- Department of Chemistry, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, North Carolina 28223, United States
| | - Alizah Johns-Boehme
- Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Cara Brainerd
- Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Eric O. Freed
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Bruce A. Shapiro
- Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
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Huang Z, Zhang YM, Cheng Q, Zhang J, Liu YH, Wang B, Yu XQ. Structure–activity relationship studies of symmetrical cationic bolasomes as non-viral gene vectors. J Mater Chem B 2016; 4:5575-5584. [DOI: 10.1039/c6tb00870d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Bolalipids based on lysine or cyclen headgroups were synthesized and their structure–activity relationship as gene delivery vectors was studied.
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Affiliation(s)
- Zheng Huang
- Key Laboratory of Green Chemistry & Technology (Ministry of Education)
- College of Chemistry
- Sichuan University
- Chengdu 610064
- P. R. China
| | - Yi-Mei Zhang
- Key Laboratory of Green Chemistry & Technology (Ministry of Education)
- College of Chemistry
- Sichuan University
- Chengdu 610064
- P. R. China
| | - Qian Cheng
- Key Laboratory of Green Chemistry & Technology (Ministry of Education)
- College of Chemistry
- Sichuan University
- Chengdu 610064
- P. R. China
| | - Ji Zhang
- Key Laboratory of Green Chemistry & Technology (Ministry of Education)
- College of Chemistry
- Sichuan University
- Chengdu 610064
- P. R. China
| | - Yan-Hong Liu
- Key Laboratory of Green Chemistry & Technology (Ministry of Education)
- College of Chemistry
- Sichuan University
- Chengdu 610064
- P. R. China
| | - Bing Wang
- Key Laboratory of Green Chemistry & Technology (Ministry of Education)
- College of Chemistry
- Sichuan University
- Chengdu 610064
- P. R. China
| | - Xiao-Qi Yu
- Key Laboratory of Green Chemistry & Technology (Ministry of Education)
- College of Chemistry
- Sichuan University
- Chengdu 610064
- P. R. China
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29
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Zeng H, Johnson ME, Oldenhuis N, Tiambeng TN, Guan Z. Structure-Based Design of Dendritic Peptide Bolaamphiphiles for siRNA Delivery. ACS CENTRAL SCIENCE 2015; 1:303-312. [PMID: 26436138 PMCID: PMC4582325 DOI: 10.1021/acscentsci.5b00233] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Indexed: 05/21/2023]
Abstract
Development of safe and effective delivery vectors is a critical challenge for the application of RNA interference (RNAi)-based biotechnologies. In this study we show the rational design of a series of novel dendritic peptide bolaamphiphile vectors that demonstrate high efficiency for the delivery of small interfering RNA (siRNA) while exhibiting low cytotoxicity and hemolytic activity. Systematic investigation into structure-property relationships revealed an important correlation between molecular design, self-assembled nanostructure, and biological activity. The unique bolaamphiphile architecture proved a key factor for improved complex stability and transfection efficiency. The optimal vector contains a fluorocarbon core and exhibited enhanced delivery efficiency to a variety of cell lines and improved serum resistance when compared to hydrocarbon analogues and lipofectamine RNAiMAX. In addition to introducing a promising new vector system for siRNA delivery, the structure-property relationships and "fluorocarbon effect" revealed herein offer critical insight for further development of novel materials for nucleic acid delivery and other biomaterial applications.
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30
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Gupta K, Afonin KA, Viard M, Herrero V, Kasprzak W, Kagiampakis I, Kim T, Koyfman AY, Puri A, Stepler M, Sappe A, KewalRamani VN, Grinberg S, Linder C, Heldman E, Blumenthal R, Shapiro BA. Bolaamphiphiles as carriers for siRNA delivery: From chemical syntheses to practical applications. J Control Release 2015; 213:142-151. [PMID: 26151705 PMCID: PMC4699870 DOI: 10.1016/j.jconrel.2015.06.041] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 06/01/2015] [Accepted: 06/29/2015] [Indexed: 12/15/2022]
Abstract
In this study we have investigated a new class of cationic lipids--"bolaamphiphiles" or "bolas"--for their ability to efficiently deliver small interfering RNAs (siRNAs) to cancer cells. The bolas of this study consist of a hydrophobic chain with one or more positively charged head groups at each end. Recently, we reported that micelles of the bolas GLH-19 and GLH-20 (derived from vernonia oil) efficiently deliver siRNAs, while having relatively low toxicities in vitro and in vivo. Our previous studies validated that; bolaamphiphiles can be designed to vary the magnitude of siRNA shielding, its delivery, and its subsequent release. To further understand the structural features of bolas critical for siRNAs delivery, new structurally related bolas (GLH-58 and GLH-60) were designed and synthesized from jojoba oil. Both bolas have similar hydrophobic domains and contain either one, in GLH-58, or two, in GLH-60 positively charged head groups at each end of the hydrophobic core. We have computationally predicted and experimentally validated that GLH-58 formed more stable nano sized micelles than GLH-60 and performed significantly better in comparison to GLH-60 for siRNA delivery. GLH-58/siRNA complexes demonstrated better efficiency in silencing the expression of the GFP gene in human breast cancer cells at concentrations of 5μg/mL, well below the toxic dose. Moreover, delivery of multiple different siRNAs targeting the HIV genome demonstrated further inhibition of virus production.
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Affiliation(s)
- Kshitij Gupta
- Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Kirill A Afonin
- Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; Department of Chemistry, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, NC 28223, USA
| | - Mathias Viard
- Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; Basic Science Program, Leidos Biomedical Research Inc., Frederick National Laboratory, Frederick, MD 21702, USA
| | - Virginia Herrero
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Wojciech Kasprzak
- Basic Science Program, Leidos Biomedical Research Inc., Frederick National Laboratory, Frederick, MD 21702, USA
| | - Ioannis Kagiampakis
- HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Taejin Kim
- Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Alexey Y Koyfman
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anu Puri
- Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Marissa Stepler
- Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Alison Sappe
- Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Vineet N KewalRamani
- Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Sarina Grinberg
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Charles Linder
- Department of Biotechnology, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Eliahu Heldman
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Robert Blumenthal
- Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Bruce A Shapiro
- Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
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31
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Williford JM, Santos JL, Shyam R, Mao HQ. Shape Control in Engineering of Polymeric Nanoparticles for Therapeutic Delivery. Biomater Sci 2015; 3:894-907. [PMID: 26146550 PMCID: PMC4486355 DOI: 10.1039/c5bm00006h] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Nanoparticle-mediated delivery of therapeutics holds great potential for the diagnosis and treatment of a wide range of diseases. Significant advances have been made in the design of new polymeric nanoparticle carriers through modulation of their physical and chemical structures and biophysical properties. Nanoparticle shape has been increasingly proposed as an important attribute dictating their transport properties in biological milieu. In this review, we highlight three major methods for preparing polymeric nanoparticles that allow for exquisite control of particle shape. Special attention is given to various approaches to controlling nanoparticle shape by tuning copolymer structural parameters and assembly conditions. This review also provides comparisons of these methods in terms of their unique capabilities, materials choices, and specific delivery cargos, and summarizes the biological effects of nanoparticle shape on transport properties at the tissue and cellular levels.
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Affiliation(s)
- John-Michael Williford
- Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, Maryland 21205
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218
- Translational Tissue Engineering Center, Johns Hopkins School of Medicine, Baltimore, MD 21287
| | - Jose Luis Santos
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218
- Translational Tissue Engineering Center, Johns Hopkins School of Medicine, Baltimore, MD 21287
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218
| | - Rishab Shyam
- Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, Maryland 21205
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218
- Translational Tissue Engineering Center, Johns Hopkins School of Medicine, Baltimore, MD 21287
| | - Hai-Quan Mao
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218
- Translational Tissue Engineering Center, Johns Hopkins School of Medicine, Baltimore, MD 21287
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD 21218
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32
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Gupta K, Mattingly SJ, Knipp RJ, Afonin KA, Viard M, Bergman JT, Stepler M, Nantz MH, Puri A, Shapiro BA. Oxime ether lipids containing hydroxylated head groups are more superior siRNA delivery agents than their nonhydroxylated counterparts. Nanomedicine (Lond) 2015; 10:2805-18. [PMID: 26107486 PMCID: PMC4636123 DOI: 10.2217/nnm.15.105] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
AIM To evaluate the structure-activity relationship of oxime ether lipids (OELs) containing modifications in the hydrophobic domains (chain length, degree of unsaturation) and hydrophilic head groups (polar domain hydroxyl groups) toward complex formation with siRNA molecules and siRNA delivery efficiency of resulting complexes to a human breast cancer cell line (MDA-MB-231). MATERIALS & METHODS Ability of lipoplex formation between oxime ether lipids with nucleic acids were examined using biophysical techniques. The potential of OELs to deliver nucleic acids and silence green fluorescent protein (GFP) gene was analyzed using MDA-MB-231 and MDA-MB-231/GFP cells, respectively. RESULTS & CONCLUSION Introduction of hydroxyl groups to the polar domain of the OELs and unsaturation into the hydrophobic domain favor higher transfection and gene silencing in a cell culture system.
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Affiliation(s)
- Kshitij Gupta
- Gene Regulation & Chromosome Biology Lab, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | | | - Ralph J Knipp
- Department of Chemistry, University of Louisville, Louisville, KY 40292, USA
| | - Kirill A Afonin
- Gene Regulation & Chromosome Biology Lab, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
- Department of Chemistry, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, NC 28223, USA
| | - Mathias Viard
- Basic Research Lab, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
- Basic Science Program, Leidos Biomedical Research, Inc., National Cancer Institute, Center for Cancer Research, Frederick National Laboratory for Cancer Research, Frederick, MD 21702-1201, USA
| | - Joseph T Bergman
- Gene Regulation & Chromosome Biology Lab, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Marissa Stepler
- Gene Regulation & Chromosome Biology Lab, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Michael H Nantz
- Department of Chemistry, University of Louisville, Louisville, KY 40292, USA
| | - Anu Puri
- Gene Regulation & Chromosome Biology Lab, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Bruce A Shapiro
- Gene Regulation & Chromosome Biology Lab, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
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33
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Afonin KA, Viard M, Kagiampakis I, Case CL, Dobrovolskaia MA, Hofmann J, Vrzak A, Kireeva M, Kasprzak WK, KewalRamani VN, Shapiro BA. Triggering of RNA interference with RNA-RNA, RNA-DNA, and DNA-RNA nanoparticles. ACS NANO 2015; 9:251-9. [PMID: 25521794 PMCID: PMC4310632 DOI: 10.1021/nn504508s] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 12/11/2014] [Indexed: 05/08/2023]
Abstract
Control over cellular delivery of different functionalities and their synchronized activation is a challenging task. We report several RNA and RNA/DNA-based nanoparticles designed to conditionally activate the RNA interference in various human cells. These nanoparticles allow precise control over their formulation, stability in blood serum, and activation of multiple functionalities. Importantly, interferon and pro-inflammatory cytokine activation assays indicate the significantly lower responses for DNA nanoparticles compared to the RNA counterparts, suggesting greater potential of these molecules for therapeutic use.
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Affiliation(s)
- Kirill A. Afonin
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Mathias Viard
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
- Basic Science Program, Leidos Biomedical Research, Inc., NCI Center for Cancer Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Ioannis Kagiampakis
- HIV Drug Resistance Program, NCI, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Christopher L. Case
- HIV Drug Resistance Program, NCI, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Marina A. Dobrovolskaia
- Nanotechnology Characterization Lab, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Jen Hofmann
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Ashlee Vrzak
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Maria Kireeva
- Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, NCI, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Wojciech K. Kasprzak
- Basic Science Program, Leidos Biomedical Research, Inc., NCI Center for Cancer Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Vineet N. KewalRamani
- HIV Drug Resistance Program, NCI, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Bruce A. Shapiro
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
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Abstract
Ribozymes are structured RNA molecules that act as catalysts in different biological reactions. From simple genome cleaving activities in satellite RNAs to more complex functions in cellular protein synthesis and gene regulation, ribozymes play important roles in all forms of life. Several naturally existing ribozymes have been modified for use as therapeutics in different conditions, with HIV-1 infection being one of the most studied. This chapter summarizes data from different preclinical and clinical studies conducted to evaluate the potential of ribozymes to be used in HIV-1 therapies. The different ribozyme motifs that have been modified, as well as their target sites and expression strategies, are described. RNA conjugations used to enhance the antiviral effect of ribozymes are also presented and the results from clinical trials conducted to date are summarized. Studies on anti-HIV-1 ribozymes have provided valuable information on the optimal expression strategies and clinical protocols for RNA gene therapy and remain competitive candidates for future therapy.
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Fariya M, Jain A, Dhawan V, Shah S, Nagarsenker MS. Bolaamphiphiles: a pharmaceutical review. Adv Pharm Bull 2014; 4:483-91. [PMID: 25671179 PMCID: PMC4312395 DOI: 10.5681/apb.2014.072] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Revised: 08/04/2014] [Accepted: 10/19/2014] [Indexed: 01/10/2023] Open
Abstract
The field of drug discovery is ever growing and excipients play a major role in it. A novel class of amphiphiles has been discussed in the review. The review focuses on natural as well as synthetic bolaamphiphiles, their chemical structures and importantly, their ability to self assemble rendering them of great use to pharmaceutical industry. Recent reports on their ability to be used in fabrication of suitable nanosized carriers for drug as well as genes to target site, has been discussed substantially to understand the potential of bolaamphiphiles in field of drug delivery.
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Affiliation(s)
- Mayur Fariya
- Department of Pharmaceutics, Bombay College of Pharmacy, Kalina, Santacruz (E), Mumbai – 400098, India
| | - Ankitkumar Jain
- Department of Pharmaceutics, Bombay College of Pharmacy, Kalina, Santacruz (E), Mumbai – 400098, India
| | - Vivek Dhawan
- Department of Pharmaceutics, Bombay College of Pharmacy, Kalina, Santacruz (E), Mumbai – 400098, India
| | - Sanket Shah
- Department of Pharmaceutics, Bombay College of Pharmacy, Kalina, Santacruz (E), Mumbai – 400098, India
| | - Mangal S. Nagarsenker
- Department of Pharmaceutics, Bombay College of Pharmacy, Kalina, Santacruz (E), Mumbai – 400098, India
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36
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Afonin K, Viard M, Koyfman AY, Martins AN, Kasprzak WK, Panigaj M, Desai R, Santhanam A, Grabow WW, Jaeger L, Heldman E, Reiser J, Chiu W, Freed EO, Shapiro BA. Multifunctional RNA nanoparticles. NANO LETTERS 2014; 14:5662-71. [PMID: 25267559 PMCID: PMC4189619 DOI: 10.1021/nl502385k] [Citation(s) in RCA: 156] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 08/27/2014] [Indexed: 05/06/2023]
Abstract
Our recent advancements in RNA nanotechnology introduced novel nanoscaffolds (nanorings); however, the potential of their use for biomedical applications was never fully revealed. As presented here, besides functionalization with multiple different short interfering RNAs for combinatorial RNA interference (e.g., against multiple HIV-1 genes), nanorings also allow simultaneous embedment of assorted RNA aptamers, fluorescent dyes, proteins, as well as recently developed RNA-DNA hybrids aimed to conditionally activate multiple split functionalities inside cells.
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Affiliation(s)
- Kirill
A. Afonin
- Basic
Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Mathias Viard
- Basic
Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
- Basic
Science Program, Leidos Biomedical Research,
Inc., NCI Center for Cancer Research, Frederick National Laboratory
for Cancer Research, Frederick, Maryland 21702, United States
| | - Alexey Y. Koyfman
- National
Center for Macromolecular Imaging, Verna and Marrs McLean Department
of Biochemistry and Molecular Biology, Baylor
College of Medicine, Houston, Texas 77030, United States
| | - Angelica N. Martins
- HIV
Drug Resistance Program, National Cancer
Institute, Frederick, Maryland 21702, United
States
| | - Wojciech K. Kasprzak
- Basic
Science Program, Leidos Biomedical Research,
Inc., NCI Center for Cancer Research, Frederick National Laboratory
for Cancer Research, Frederick, Maryland 21702, United States
| | - Martin Panigaj
- Food
and Drug Administration, Center for Biologics Evaluation and Research,
Office of Cellular, Tissue and Gene Therapies, Silver Spring, Maryland 20993, United States
| | - Ravi Desai
- Basic
Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Arti Santhanam
- Basic
Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Wade W. Grabow
- Department
of Chemistry, Seattle Pacific University, Seattle, Washington 98119, United States
| | - Luc Jaeger
- Department
of Chemistry and Biochemistry, Biomolecular Science and Engineering
Program, University of California, Santa Barbara, California 93106-9510, United States
| | - Eliahu Heldman
- Basic
Science Program, Leidos Biomedical Research,
Inc., NCI Center for Cancer Research, Frederick National Laboratory
for Cancer Research, Frederick, Maryland 21702, United States
| | - Jakob Reiser
- Food
and Drug Administration, Center for Biologics Evaluation and Research,
Office of Cellular, Tissue and Gene Therapies, Silver Spring, Maryland 20993, United States
| | - Wah Chiu
- National
Center for Macromolecular Imaging, Verna and Marrs McLean Department
of Biochemistry and Molecular Biology, Baylor
College of Medicine, Houston, Texas 77030, United States
| | - Eric O. Freed
- HIV
Drug Resistance Program, National Cancer
Institute, Frederick, Maryland 21702, United
States
| | - Bruce A. Shapiro
- Basic
Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
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Afonin K, Kasprzak WK, Bindewald E, Kireeva M, Viard M, Kashlev M, Shapiro BA. In silico design and enzymatic synthesis of functional RNA nanoparticles. Acc Chem Res 2014; 47:1731-41. [PMID: 24758371 PMCID: PMC4066900 DOI: 10.1021/ar400329z] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Indexed: 12/25/2022]
Abstract
CONSPECTUS: The use of RNAs as scaffolds for biomedical applications has several advantages compared with other existing nanomaterials. These include (i) programmability, (ii) precise control over folding and self-assembly, (iii) natural functionalities as exemplified by ribozymes, riboswitches, RNAi, editing, splicing, and inherent translation and transcription control mechanisms, (iv) biocompatibility, (v) relatively low immune response, and (vi) relatively low cost and ease of production. We have tapped into several of these properties and functionalities to construct RNA-based functional nanoparticles (RNA NPs). In several cases, the structural core and the functional components of the NPs are inherent in the same construct. This permits control over the spatial disposition of the components, intracellular availability, and precise stoichiometry. To enable the generation of RNA NPs, a pipeline is being developed. On one end, it encompasses the rational design and various computational schemes that promote design of the RNA-based nanoconstructs, ultimately producing a set of sequences consisting of RNA or RNA-DNA hybrids, which can assemble into the designed construct. On the other end of the pipeline is an experimental component, which takes the produced sequences and uses them to initialize and characterize their proper assembly and then test the resulting RNA NPs for their function and delivery in cell culture and animal models. An important aspect of this pipeline is the feedback that constantly occurs between the computational and the experimental parts, which synergizes the refinement of both the algorithmic methodologies and the experimental protocols. The utility of this approach is depicted by the several examples described in this Account (nanocubes, nanorings, and RNA-DNA hybrids). Of particular interest, from the computational viewpoint, is that in most cases, first a three-dimensional representation of the assembly is produced, and only then are algorithms applied to generate the sequences that will assemble into the designated three-dimensional construct. This is opposite to the usual practice of predicting RNA structures from a given sequence, that is, the RNA folding problem. To be considered is the generation of sequences that upon assembly have the proper intra- or interstrand interactions (or both). Of particular interest from the experimental point of view is the determination and characterization of the proper thermodynamic, kinetic, functionality, and delivery protocols. Assembly of RNA NPs from individual single-stranded RNAs can be accomplished by one-pot techniques under the proper thermal and buffer conditions or, potentially more interestingly, by the use of various RNA polymerases that can promote the formation of RNA NPs cotransciptionally from specifically designed DNA templates. Also of importance is the delivery of the RNA NPs to the cells of interest in vitro or in vivo. Nonmodified RNAs rapidly degrade in blood serum and have difficulties crossing biological membranes due to their negative charge. These problems can be overcome by using, for example, polycationic lipid-based carriers. Our work involves the use of bolaamphiphiles, which are amphipathic compounds with positively charged hydrophilic head groups at each end connected by a hydrophobic chain. We have correlated results from molecular dynamics computations with various experiments to understand the characteristics of such delivery agents.
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Affiliation(s)
- Kirill
A. Afonin
- Basic
Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Wojciech K. Kasprzak
- Basic
Science Program, Leidos Biomedical Research,
Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Eckart Bindewald
- Basic
Science Program, Leidos Biomedical Research,
Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Maria Kireeva
- Gene
Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Mathias Viard
- Basic
Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
- Basic
Science Program, Leidos Biomedical Research,
Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Mikhail Kashlev
- Gene
Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Bruce A. Shapiro
- Basic
Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
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38
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Afonin KA, Kasprzak W, Bindewald E, Puppala PS, Diehl AR, Hall KT, Kim TJ, Zimmermann MT, Jernigan RL, Jaeger L, Shapiro BA. Computational and experimental characterization of RNA cubic nanoscaffolds. Methods 2014; 67:256-65. [PMID: 24189588 PMCID: PMC4007386 DOI: 10.1016/j.ymeth.2013.10.013] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 10/11/2013] [Accepted: 10/16/2013] [Indexed: 01/03/2023] Open
Abstract
The fast-developing field of RNA nanotechnology requires the adoption and development of novel and faster computational approaches to modeling and characterization of RNA-based nano-objects. We report the first application of Elastic Network Modeling (ENM), a structure-based dynamics model, to RNA nanotechnology. With the use of an Anisotropic Network Model (ANM), a type of ENM, we characterize the dynamic behavior of non-compact, multi-stranded RNA-based nanocubes that can be used as nano-scale scaffolds carrying different functionalities. Modeling the nanocubes with our tool NanoTiler and exploring the dynamic characteristics of the models with ANM suggested relatively minor but important structural modifications that enhanced the assembly properties and thermodynamic stabilities. In silico and in vitro, we compared nanocubes having different numbers of base pairs per side, showing with both methods that the 10 bp-long helix design leads to more efficient assembly, as predicted computationally. We also explored the impact of different numbers of single-stranded nucleotide stretches at each of the cube corners and showed that cube flexibility simulations help explain the differences in the experimental assembly yields, as well as the measured nanomolecule sizes and melting temperatures. This original work paves the way for detailed computational analysis of the dynamic behavior of artificially designed multi-stranded RNA nanoparticles.
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Affiliation(s)
- Kirill A Afonin
- Center for Cancer Research Nanobiology Program, National Cancer Institute, Frederick, MD 21702, USA
| | - Wojciech Kasprzak
- Basic Science Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Eckart Bindewald
- Basic Science Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Praneet S Puppala
- Center for Cancer Research Nanobiology Program, National Cancer Institute, Frederick, MD 21702, USA
| | - Alex R Diehl
- Center for Cancer Research Nanobiology Program, National Cancer Institute, Frederick, MD 21702, USA
| | - Kenneth T Hall
- Center for Cancer Research Nanobiology Program, National Cancer Institute, Frederick, MD 21702, USA
| | - Tae Jin Kim
- Center for Cancer Research Nanobiology Program, National Cancer Institute, Frederick, MD 21702, USA
| | - Michael T Zimmermann
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Robert L Jernigan
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Luc Jaeger
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA.
| | - Bruce A Shapiro
- Center for Cancer Research Nanobiology Program, National Cancer Institute, Frederick, MD 21702, USA.
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Afonin KA, Desai R, Viard M, Kireeva ML, Bindewald E, Case CL, Maciag AE, Kasprzak WK, Kim T, Sappe A, Stepler M, KewalRamani VN, Kashlev M, Blumenthal R, Shapiro BA. Co-transcriptional production of RNA-DNA hybrids for simultaneous release of multiple split functionalities. Nucleic Acids Res 2014; 42:2085-97. [PMID: 24194608 PMCID: PMC3919563 DOI: 10.1093/nar/gkt1001] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 09/30/2013] [Accepted: 10/04/2013] [Indexed: 12/12/2022] Open
Abstract
Control over the simultaneous delivery of different functionalities and their synchronized intracellular activation can greatly benefit the fields of RNA and DNA biomedical nanotechnologies and allow for the production of nanoparticles and various switching devices with controllable functions. We present a system of multiple split functionalities embedded in the cognate pairs of RNA-DNA hybrids which are programmed to recognize each other, re-associate and form a DNA duplex while also releasing the split RNA fragments which upon association regain their original functions. Simultaneous activation of three different functionalities (RNAi, Förster resonance energy transfer and RNA aptamer) confirmed by multiple in vitro and cell culture experiments prove the concept. To automate the design process, a novel computational tool that differentiates between the thermodynamic stabilities of RNA-RNA, RNA-DNA and DNA-DNA duplexes was developed. Moreover, here we demonstrate that besides being easily produced by annealing synthetic RNAs and DNAs, the individual hybrids carrying longer RNAs can be produced by RNA polymerase II-dependent transcription of single-stranded DNA templates.
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Affiliation(s)
- Kirill A. Afonin
- Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA, Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, HIV Drug Resistance Program, NCI-Frederick, Frederick, MD 21702, USA and Chemical Biology Laboratory, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Ravi Desai
- Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA, Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, HIV Drug Resistance Program, NCI-Frederick, Frederick, MD 21702, USA and Chemical Biology Laboratory, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Mathias Viard
- Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA, Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, HIV Drug Resistance Program, NCI-Frederick, Frederick, MD 21702, USA and Chemical Biology Laboratory, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Maria L. Kireeva
- Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA, Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, HIV Drug Resistance Program, NCI-Frederick, Frederick, MD 21702, USA and Chemical Biology Laboratory, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Eckart Bindewald
- Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA, Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, HIV Drug Resistance Program, NCI-Frederick, Frederick, MD 21702, USA and Chemical Biology Laboratory, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Christopher L. Case
- Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA, Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, HIV Drug Resistance Program, NCI-Frederick, Frederick, MD 21702, USA and Chemical Biology Laboratory, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Anna E. Maciag
- Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA, Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, HIV Drug Resistance Program, NCI-Frederick, Frederick, MD 21702, USA and Chemical Biology Laboratory, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Wojciech K. Kasprzak
- Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA, Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, HIV Drug Resistance Program, NCI-Frederick, Frederick, MD 21702, USA and Chemical Biology Laboratory, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Taejin Kim
- Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA, Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, HIV Drug Resistance Program, NCI-Frederick, Frederick, MD 21702, USA and Chemical Biology Laboratory, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Alison Sappe
- Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA, Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, HIV Drug Resistance Program, NCI-Frederick, Frederick, MD 21702, USA and Chemical Biology Laboratory, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Marissa Stepler
- Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA, Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, HIV Drug Resistance Program, NCI-Frederick, Frederick, MD 21702, USA and Chemical Biology Laboratory, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Vineet N. KewalRamani
- Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA, Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, HIV Drug Resistance Program, NCI-Frederick, Frederick, MD 21702, USA and Chemical Biology Laboratory, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Mikhail Kashlev
- Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA, Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, HIV Drug Resistance Program, NCI-Frederick, Frederick, MD 21702, USA and Chemical Biology Laboratory, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Robert Blumenthal
- Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA, Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, HIV Drug Resistance Program, NCI-Frederick, Frederick, MD 21702, USA and Chemical Biology Laboratory, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Bruce A. Shapiro
- Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA, Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, HIV Drug Resistance Program, NCI-Frederick, Frederick, MD 21702, USA and Chemical Biology Laboratory, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
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40
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Chou ST, Hom K, Zhang D, Leng Q, Tricoli LJ, Hustedt JM, Lee A, Shapiro MJ, Seog J, Kahn JD, Mixson AJ. Enhanced silencing and stabilization of siRNA polyplexes by histidine-mediated hydrogen bonds. Biomaterials 2013; 35:846-55. [PMID: 24161165 DOI: 10.1016/j.biomaterials.2013.10.019] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 10/04/2013] [Indexed: 01/27/2023]
Abstract
Branched peptides containing histidines and lysines (HK) have been shown to be effective carriers for DNA and siRNA. We anticipate that elucidation of the binding mechanism of HK with siRNA will provide greater insight into the self-assembly and delivery of the HK:siRNA polyplex. Non-covalent bonds between histidine residues and nucleic acids may enhance the stability of siRNA polyplexes. We first compared the polyplex biophysical properties of a branched HK with those of branched asparagine-lysine peptide (NK). Consistent with siRNA silencing experiments, gel electrophoresis demonstrated that the HK siRNA polyplex maintained its integrity with prolonged incubation in serum, whereas siRNA in complex with NK was degraded in a time-dependent manner. Isothermal titration calorimetry of various peptides binding to siRNA at pH 7.3 showed that branched polylysine, interacted with siRNA was initially endothermic, whereas branched HK exhibited an exothermic reaction at initial binding. The exothermic interaction indicates formation of non-ionic bonds between histidines and siRNA; purely electrostatic interaction is entropy-driven and endothermic. To investigate the type of non-ionic bond, we studied the protonation state of imidazole rings of a selectively (15)N labeled branched HK by heteronuclear single quantum coherence NMR. The peak of Nδ1-H tautomers of imidazole shifted downfield (in the direction of deprotonation) by 0.5-1.0 ppm with addition of siRNA, providing direct evidence that histidines formed hydrogen bonds with siRNA at physiological pH. These results establish that histidine-rich peptides form hydrogen bonds with siRNA, thereby enhancing the stability and biological activity of the polyplex in vitro and in vivo.
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Affiliation(s)
- Szu-Ting Chou
- Department of Pathology, University of Maryland Baltimore, MSTF Building, 10 South Pine Street, Baltimore, MD 21201, United States; Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742, United States.
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41
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Afonin KA, Viard M, Martins AN, Lockett SJ, Maciag AE, Freed EO, Heldman E, Jaeger L, Blumenthal R, Shapiro BA. Activation of different split functionalities on re-association of RNA-DNA hybrids. NATURE NANOTECHNOLOGY 2013; 8:296-304. [PMID: 23542902 PMCID: PMC3618561 DOI: 10.1038/nnano.2013.44] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 02/26/2013] [Indexed: 05/12/2023]
Abstract
Split-protein systems, an approach that relies on fragmentation of proteins with their further conditional re-association to form functional complexes, are increasingly used for various biomedical applications. This approach offers tight control of protein functions and improved detection sensitivity. Here we report a similar technique based on a pair of RNA-DNA hybrids that can be used generally for triggering different split functionalities. Individually, each hybrid is inactive but when two cognate hybrids re-associate, different functionalities are triggered inside mammalian cells. As a proof of concept, this work mainly focuses on the activation of RNA interference. However, the release of other functionalities (such as resonance energy transfer and RNA aptamer) is also shown. Furthermore, in vivo studies demonstrate a significant uptake of the hybrids by tumours together with specific gene silencing. This split-functionality approach presents a new route in the development of 'smart' nucleic acid-based nanoparticles and switches for various biomedical applications.
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Affiliation(s)
- Kirill A. Afonin
- Center for Cancer Research Nanobiology Program, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Mathias Viard
- Center for Cancer Research Nanobiology Program, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
- Basic Science Program, SAIC-Frederick, Inc., NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Angelica N. Martins
- HIV Drug Resistance Program, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Stephen J. Lockett
- Advanced Technology Program, SAIC-Frederick, Inc., NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Anna E. Maciag
- Basic Science Program, SAIC-Frederick, Inc., NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
- Chemical Biology Laboratory, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Eric O. Freed
- HIV Drug Resistance Program, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Eliahu Heldman
- Basic Science Program, SAIC-Frederick, Inc., NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Luc Jaeger
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA
| | - Robert Blumenthal
- Center for Cancer Research Nanobiology Program, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Bruce A. Shapiro
- Center for Cancer Research Nanobiology Program, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
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