1
|
Gubu A, Zhang X, Lu A, Zhang B, Ma Y, Zhang G. Nucleic acid amphiphiles: Synthesis, properties, and applications. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:144-163. [PMID: 37456777 PMCID: PMC10345231 DOI: 10.1016/j.omtn.2023.05.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Nucleic acid amphiphiles, referring to nucleic acids modified with large hydrophobic groups, have been widely used in programmable bioengineering. Since nucleic acids are intrinsically hydrophilic, the hydrophobic groups endow nucleic acid amphiphiles with unique properties, such as self-assembling, interactions with artificial or biological membranes, and transmembrane transport. Importantly, the hybridization or target binding capability of oligonucleotide itself supplies nucleic acid amphiphiles with excellent programmability. As a result, this type of molecule has attracted considerable attention in academic studies and has enormous potential for further applications. For a comprehensive understanding of nucleic acid amphiphiles, we review the reported research on nucleic acid amphiphiles from their molecular design to final applications, in which we summarize the synthetic strategies for nucleic acid amphiphiles and draw much attention to their unique properties in different contexts. Finally, a summary of the applications of nucleic acid amphiphiles in drug development, bioengineering, and bioanalysis are critically discussed.
Collapse
Affiliation(s)
- Amu Gubu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
- Aptacure Therapeutics Limited, Kowloon, Hong Kong SAR, China
| | - Xueli Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences and Chemical Biology Center, Peking University, No. 38 Xueyuan Road, Beijing, China
| | - Aiping Lu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong 999077, China
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU Institute for Research and Continuing Education, Shenzhen 518000, China
| | - Baoting Zhang
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yuan Ma
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong 999077, China
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU Institute for Research and Continuing Education, Shenzhen 518000, China
| | - Ge Zhang
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong 999077, China
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU Institute for Research and Continuing Education, Shenzhen 518000, China
| |
Collapse
|
2
|
Löffler PMG, Risgaard NA, Svendsen BL, Jepsen KA, Rabe A, Vogel S. Label-free observation of DNA-encoded liposome fusion by surface plasmon resonance. Chem Commun (Camb) 2023; 59:10548-10551. [PMID: 37566388 DOI: 10.1039/d3cc02793g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Assembly and fusion between different populations of lipid nanoparticles was mediated by membrane-anchored lipidated nucleic acid (LiNA) strands and observed using surface plasmon resonance (SPR) as a label-free real-time assay. Irreversible membrane fusion was distinguished from reversible assembly by enzymatical cleavage of dsDNA tethers in situ. The assay enables user-friendly monitoring and application of membrane fusion in the context of liposomal drug delivery or synthetic biology.
Collapse
Affiliation(s)
- Philipp M G Löffler
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense 5230, Denmark.
| | - Nikolaj A Risgaard
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense 5230, Denmark.
| | - Bettina L Svendsen
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense 5230, Denmark.
| | - Katrine A Jepsen
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense 5230, Denmark.
| | - Alexander Rabe
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense 5230, Denmark.
| | - Stefan Vogel
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense 5230, Denmark.
| |
Collapse
|
3
|
Jakobsen U, Rosholm KR, Vogel S. Design, synthesis and membrane anchoring strength of lipidated polyaza crown ether DNA-conjugates (LiNAs) studied by DNA-controlled assembly of liposomes. Org Biomol Chem 2022; 20:9460-9468. [PMID: 36408737 DOI: 10.1039/d2ob01517j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Hybridization-controlled assays for assembly or fusion of liposomes are versatile for detection of both DNA and RNA targets and useful for the evaluation of membrane anchoring strength of LiNAs with applications in the context of liposome assembly, liposome fusion and lipid nanoparticle formulation of therapeutic LiNAs. Herein, we report the synthesis of lipid phosphoramidite building blocks for automated LiNA synthesis and a study on design requirements for efficient lipid membrane anchoring and liposome assembly dependent on lipid membrane anchor length (C10-C20) and structure, the effect of internal linkers and locked nucleic acids (LNA) building blocks on the lipid membrane anchoring strength of LiNAs.
Collapse
Affiliation(s)
- Ulla Jakobsen
- University of Southern Denmark, Department of Physics, Chemistry and Pharmacy, Campusvej 55, 5230 Odense M, Denmark.
| | - Kadla Røskva Rosholm
- University of Southern Denmark, Department of Physics, Chemistry and Pharmacy, Campusvej 55, 5230 Odense M, Denmark.
| | - Stefan Vogel
- University of Southern Denmark, Department of Physics, Chemistry and Pharmacy, Campusvej 55, 5230 Odense M, Denmark.
| |
Collapse
|
4
|
Belkilani M, Farre C, Chevalier Y, Minot S, Bessueille F, Abdelghani A, Jaffrezic-Renault N, Chaix C. Mechanisms of Influenza Virus HA2 Peptide Interaction with Liposomes Studied by Dual-Wavelength MP-SPR. ACS APPLIED MATERIALS & INTERFACES 2022; 14:32970-32981. [PMID: 35834580 DOI: 10.1021/acsami.2c09039] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A phospholipid-based liposome layer was used as an effective biomimetic membrane model to study the binding of the pH-dependent fusogenic peptide (E4-GGYC) from the influenza virus hemagglutinin HA2 subunit. To this end, a multiparameter surface plasmon resonance approach (MP-SPR) was used for monitoring peptide-liposome interactions at two pH values (4.5 and 8) by means of recording sensorgrams in real time without the need for labeling. Biotinylated liposomes were first immobilized as a monolayer onto the surface of an SPR gold chip coated with a streptavidin layer. Multiple sets of sensorgrams with different HA2 peptide concentrations were generated at both pHs. Dual-wavelength Fresnel layer modeling was applied to calculate the thickness (d) and the refractive index (n) of the liposome layer to monitor the change in its optical parameters upon interaction with the peptide. At acidic pH, the peptide, in its α helix form, entered the lipid bilayer of liposomes, inducing vesicle swelling and increasing membrane robustness. Conversely, a contraction of liposomes was observed at pH 8, associated with noninsertion of the peptide in the double layer of phospholipids. The equilibrium dissociation constant KD = 4.7 × 10-7 M of the peptide/liposome interaction at pH 4.5 was determined by fitting the "OneToOne" model to the experimental sensorgrams using Trace Drawer software. Our experimental approach showed that the HA2 peptide at a concentration up to 100 μM produced no disruption of liposomes at pH 4.5.
Collapse
Affiliation(s)
- Meryem Belkilani
- Institute of Analytical Sciences, University of Lyon, CNRS, Claude Bernard Lyon 1 University, 5 rue de la Doua, F-69100 Villeurbanne, France
- University of Tunis, ENSIT, av. Taha Hussein, Montfleury, 1008 Tunis, Tunisia
- INSAT, Research Unit of Nanobiotechnology and Valorisation of Medicinal Plants, University of Carthage, 1080 Charguia Cedex, Tunisia
| | - Carole Farre
- Institute of Analytical Sciences, University of Lyon, CNRS, Claude Bernard Lyon 1 University, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Yves Chevalier
- University of Lyon, CNRS, Claude Bernard Lyon 1 University, LAGEPP, 43 bd 11 Novembre, F-69622 Villeurbanne, France
| | - Sylvain Minot
- Institute of Analytical Sciences, University of Lyon, CNRS, Claude Bernard Lyon 1 University, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - François Bessueille
- Institute of Analytical Sciences, University of Lyon, CNRS, Claude Bernard Lyon 1 University, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Adnane Abdelghani
- INSAT, Research Unit of Nanobiotechnology and Valorisation of Medicinal Plants, University of Carthage, 1080 Charguia Cedex, Tunisia
| | - Nicole Jaffrezic-Renault
- Institute of Analytical Sciences, University of Lyon, CNRS, Claude Bernard Lyon 1 University, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Carole Chaix
- Institute of Analytical Sciences, University of Lyon, CNRS, Claude Bernard Lyon 1 University, 5 rue de la Doua, F-69100 Villeurbanne, France
| |
Collapse
|
5
|
Bakowski K, Vogel S. Evolution of complexity in non-viral oligonucleotide delivery systems: from gymnotic delivery through bioconjugates to biomimetic nanoparticles. RNA Biol 2022; 19:1256-1275. [PMID: 36411594 PMCID: PMC9683052 DOI: 10.1080/15476286.2022.2147278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
From the early days of research on RNA biology and biochemistry, there was an interest to utilize this knowledge and RNA itself for therapeutic applications. Today, we have a series of oligonucleotide therapeutics on the market and many more in clinical trials. These drugs - exploit different chemistries of oligonucleotides, such as modified DNAs and RNAs, peptide nucleic acids (PNAs) or phosphorodiamidate morpholino oligomers (PMOs), and different mechanisms of action, such as RNA interference (RNAi), targeted RNA degradation, splicing modulation, gene expression and modification. Despite major successes e.g. mRNA vaccines developed against SARS-CoV-2 to control COVID-19 pandemic, development of therapies for other diseases is still limited by inefficient delivery of oligonucleotides to specific tissues and organs and often prohibitive costs for the final drug. This is even more critical when targeting multifactorial disorders and patient-specific biological variations. In this review, we will present the evolution of complexity of oligonucleotide delivery methods with focus on increasing complexity of formulations from gymnotic delivery to bioconjugates and to lipid nanoparticles in respect to developments that will enable application of therapeutic oligonucleotides as drugs in personalized therapies.
Collapse
Affiliation(s)
- Kamil Bakowski
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Stefan Vogel
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark,CONTACT Stefan Vogel Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230Odense, Denmark
| |
Collapse
|
6
|
Löffler PMG, Ries O, Vogel S. DNA-Mediated Liposome Fusion Observed by Fluorescence Spectrometry. Methods Mol Biol 2019; 2063:101-118. [PMID: 31667766 DOI: 10.1007/978-1-0716-0138-9_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
DNA-programmed and controlled fusion of lipid membranes have recently been optimized to reliably mix the contents between two populations of liposomes, each functionalized with complementary lipidated DNA (LiNA) oligomer. In this chapter we describe a procedure for DNA-controlled fusion of liposomes mediated by LiNAs that are designed to force bilayers into close proximity. Using a self-quenching fluorescent dye (Sulforhodamine B) to monitor both the mixing of the internal volumes and leakage of the dye into the outer volume we measure the efficiency of content mixing in the bulk population, allowing for direct comparison between different LiNA designs. By generating samples for calibration corresponding to different amounts of content mixing, the average number of fusion events per labeled liposome can be estimated.
Collapse
Affiliation(s)
- Philipp M G Löffler
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
| | - Oliver Ries
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
| | - Stefan Vogel
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark.
| |
Collapse
|
7
|
Löffler PMG, Hansen AH, Ries O, Jakobsen U, Rabe A, Sørensen KT, Glud K, Vogel S. Lipidated Polyaza Crown Ethers as Membrane Anchors for DNA-Controlled Content Mixing between Liposomes. Sci Rep 2019; 9:13856. [PMID: 31554826 PMCID: PMC6761097 DOI: 10.1038/s41598-019-49862-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 08/23/2019] [Indexed: 01/21/2023] Open
Abstract
The ability to manipulate and fuse nano-compartmentalized volumes addresses a demand for spatiotemporal control in the field of synthetic biology, for example in the bottom-up construction of (bio)chemical nanoreactors and for the interrogation of enzymatic reactions in confined space. Herein, we mix entrapped sub-attoliter volumes of liposomes (~135 nm diameter) via lipid bilayer fusion, facilitated by the hybridization of membrane-anchored lipidated oligonucleotides. We report on an improved synthesis of the membrane-anchor phosphoramidites that allows for a flexible choice of lipophilic moiety. Lipid-nucleic acid conjugates (LiNAs) with and without triethylene glycol spacers between anchor and the 17 nt binding sequence were synthesized and their fusogenic potential evaluated. A fluorescence-based content mixing assay was employed for kinetic monitoring of fusion of the bulk liposome populations at different temperatures. Data obtained at 50 °C indicated a quantitative conversion of the limiting liposome population into fused liposomes and an unprecedently high initial fusion rate was observed. For most conditions and designs only low leakage during fusion was observed. These results consolidate LiNA-mediated membrane fusion as a robust platform for programming compartmentalized chemical and enzymatic reactions.
Collapse
Affiliation(s)
- Philipp M G Löffler
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark University of Southern Denmark, Odense M, Denmark
| | - Anders Højgaard Hansen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark University of Southern Denmark, Odense M, Denmark
| | - Oliver Ries
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark University of Southern Denmark, Odense M, Denmark
| | - Ulla Jakobsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark University of Southern Denmark, Odense M, Denmark.,PET & Cyclotron Unit, Department of Nuclear Medicine, Odense University Hospital, Sdr. Boulevard 29, 5000, Odense C, Denmark
| | - Alexander Rabe
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark University of Southern Denmark, Odense M, Denmark
| | - Kristian T Sørensen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark University of Southern Denmark, Odense M, Denmark
| | - Kasper Glud
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark University of Southern Denmark, Odense M, Denmark
| | - Stefan Vogel
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark University of Southern Denmark, Odense M, Denmark.
| |
Collapse
|
8
|
Zhang J, Han J, Ye A, Liu W, Tian M, Lu Y, Wu K, Liu J, Lou MP. Influence of Phospholipids Structure on the Physicochemical Properties and In Vitro Digestibility of Lactoferrin-Loaded Liposomes. FOOD BIOPHYS 2019. [DOI: 10.1007/s11483-019-09581-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
9
|
Ferino A, Miglietta G, Picco R, Vogel S, Wengel J, Xodo LE. MicroRNA therapeutics: design of single-stranded miR-216b mimics to target KRAS in pancreatic cancer cells. RNA Biol 2018; 15:1273-1285. [PMID: 30306823 PMCID: PMC6284578 DOI: 10.1080/15476286.2018.1526536] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Datasets reporting microRNA expression profiles in normal and cancer cells show that miR-216b is aberrantly downregulated in pancreatic ductal adenocarcinoma (PDAC). We found that KRAS, whose mutant G12D allele drives the pathogenesis of PDAC, is a target of miR-216b. To suppress oncogenic KRAS in PDAC cells, we designed single-stranded (ss) miR-216b mimics with unlocked nucleic acid (UNA) modifications to enhance their nuclease resistance. We prepared variants of ss-miR-216b mimics with and without a 5ʹ phosphate group. Both variants strongly suppressed oncogenic KRAS in PDAC cells and inhibited colony formation in pancreatic cancer cells. We observed that the designed ss-miR-216b mimics engaged AGO2 to promote the silencing of KRAS. We also tested a new delivery strategy based on the use of palmityl-oleyl-phosphatidylcholine (POPC) liposomes functionalized with ss-miR-216b conjugated with two palmityl chains and a lipid-modified cell penetrating peptide (TAT). These versatile nanoparticles suppressed oncogenic KRAS in PDAC cells.
Collapse
Affiliation(s)
- Annalisa Ferino
- a Department of Medicine, Laboratory of Biochemistry , University of Udine , Italy
| | - Giulia Miglietta
- a Department of Medicine, Laboratory of Biochemistry , University of Udine , Italy
| | - Raffaella Picco
- a Department of Medicine, Laboratory of Biochemistry , University of Udine , Italy
| | - Stefan Vogel
- b Nucleic Acids Centre , University of Southern Denmark , Odense , Denmark
| | - Jesper Wengel
- b Nucleic Acids Centre , University of Southern Denmark , Odense , Denmark
| | - Luigi E Xodo
- a Department of Medicine, Laboratory of Biochemistry , University of Udine , Italy
| |
Collapse
|
10
|
Comparative performances of lactoferrin-loaded liposomes under in vitro adult and infant digestion models. Food Chem 2018; 258:366-373. [PMID: 29655747 DOI: 10.1016/j.foodchem.2018.03.070] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 02/24/2018] [Accepted: 03/17/2018] [Indexed: 11/22/2022]
Abstract
There remain gaps in our understanding of the fate of liposomes in the infant gastrointestinal tract, especially regarding essential proteins such as lactoferrin. Models in vitro that mirrored digestion in the stomach and intestine of infants and adults were used to explore the behaviour of lactoferrin-loaded liposomes. The liposomes behaved differently in these environments, with less hydrolysis of encapsulated lactoferrin under infant model conditions. Compared to the adult model (1000 ± 66 μM mL-1), fewer free fatty acids were released (500 ± 43 μM mL-1) from liposomal bilayers and there was less alteration in functional groups of phospholipids membranes, based on pH and FTIR after infant model digestion. Particle tracking analysis and TEM supported the reduced damage of particle structure under infant model conditions. This work provides information on the stability of functional protein-loaded liposomes during digestion, and shows the potential of liposomes to be nutrient carriers in infant foods.
Collapse
|
11
|
Löffler PMG, Ries O, Rabe A, Okholm AH, Thomsen RP, Kjems J, Vogel S. A DNA-Programmed Liposome Fusion Cascade. Angew Chem Int Ed Engl 2017; 56:13228-13231. [DOI: 10.1002/anie.201703243] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 05/23/2017] [Indexed: 01/30/2023]
Affiliation(s)
- Philipp M. G. Löffler
- Department of Physics, Chemistry and Pharmacy; University of Southern Denmark; Campusvej 55 5230 Odense Denmark
| | - Oliver Ries
- Department of Physics, Chemistry and Pharmacy; University of Southern Denmark; Campusvej 55 5230 Odense Denmark
| | - Alexander Rabe
- Department of Physics, Chemistry and Pharmacy; University of Southern Denmark; Campusvej 55 5230 Odense Denmark
| | - Anders H. Okholm
- Nanoscience Center, iNANO; University of Aarhus; Gustav Wieds Vej 14 8000 Aarhus C Denmark
| | - Rasmus P. Thomsen
- Nanoscience Center, iNANO; University of Aarhus; Gustav Wieds Vej 14 8000 Aarhus C Denmark
| | - Jørgen Kjems
- Nanoscience Center, iNANO; University of Aarhus; Gustav Wieds Vej 14 8000 Aarhus C Denmark
| | - Stefan Vogel
- Department of Physics, Chemistry and Pharmacy; University of Southern Denmark; Campusvej 55 5230 Odense Denmark
| |
Collapse
|
12
|
Löffler PMG, Ries O, Rabe A, Okholm AH, Thomsen RP, Kjems J, Vogel S. Fusion von Liposomen in einer DNA-programmierten Kaskade. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201703243] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Philipp M. G. Löffler
- Department of Physics, Chemistry and Pharmacy; University of Southern Denmark; Campusvej 55 5230 Odense Dänemark
| | - Oliver Ries
- Department of Physics, Chemistry and Pharmacy; University of Southern Denmark; Campusvej 55 5230 Odense Dänemark
| | - Alexander Rabe
- Department of Physics, Chemistry and Pharmacy; University of Southern Denmark; Campusvej 55 5230 Odense Dänemark
| | - Anders H. Okholm
- Nanoscience Center, iNANO; University of Aarhus; Gustav Wieds Vej 14 8000 Aarhus C Dänemark
| | - Rasmus P. Thomsen
- Nanoscience Center, iNANO; University of Aarhus; Gustav Wieds Vej 14 8000 Aarhus C Dänemark
| | - Jørgen Kjems
- Nanoscience Center, iNANO; University of Aarhus; Gustav Wieds Vej 14 8000 Aarhus C Dänemark
| | - Stefan Vogel
- Department of Physics, Chemistry and Pharmacy; University of Southern Denmark; Campusvej 55 5230 Odense Dänemark
| |
Collapse
|
13
|
Lipid-modified G4-decoy oligonucleotide anchored to nanoparticles: delivery and bioactivity in pancreatic cancer cells. Sci Rep 2016; 6:38468. [PMID: 27929127 PMCID: PMC5144097 DOI: 10.1038/srep38468] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 11/10/2016] [Indexed: 12/28/2022] Open
Abstract
KRAS is mutated in >90% of pancreatic ductal adenocarcinomas. As its inactivation leads to tumour regression, mutant KRAS is considered an attractive target for anticancer drugs. In this study we report a new delivery strategy for a G4-decoy oligonucleotide that sequesters MAZ, a transcription factor essential for KRAS transcription. It is based on the use of palmitoyl-oleyl-phosphatidylcholine (POPC) liposomes functionalized with lipid-modified G4-decoy oligonucleotides and a lipid-modified cell penetrating TAT peptide. The potency of the strategy in pancreatic cancer cells is demonstrated by cell cytometry, confocal microscopy, clonogenic and qRT-PCR assays.
Collapse
|
14
|
Hernández-Ainsa S, Ricci M, Hilton L, Aviñó A, Eritja R, Keyser UF. Controlling the Reversible Assembly of Liposomes through a Multistimuli Responsive Anchored DNA. NANO LETTERS 2016; 16:4462-6. [PMID: 27367802 PMCID: PMC4956241 DOI: 10.1021/acs.nanolett.6b01618] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 06/23/2016] [Indexed: 05/21/2023]
Abstract
We present a novel approach to reversibly control the assembly of liposomes through an anchored multistimuli responsive DNA oligonucleotide decorated with an azobenzene moiety (AZO-ON1). We show that liposomes assembly can be simultaneously controlled by three external stimuli: light, Mg(2+), and temperature. (i) Light alters the interaction of AZO-ON1 with liposomes, which influences DNA coating and consequently liposomes assembly. (ii) Mg(2+) induces the assembly, hence variation in its concentration enables for reversibility. (iii) Double-stranded AZO-ON1 is more efficient than single-stranded AZO-ON1 in triggering the assembly of liposomes and temperature has been used for controllable assembly through DNA thermal denaturation. Our multiresponsive AZO-ON1 represents a unique example in which multiple stimuli can be simultaneously applied to regulate the reversible assembly of liposomes.
Collapse
Affiliation(s)
- Silvia Hernández-Ainsa
- Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
| | - Maria Ricci
- Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
| | - Lloyd Hilton
- Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
| | - Anna Aviñó
- IQAC−CSIC, CIBER-BBN Networking Centre on Bioengineering,
Biomaterials and Nanomedicine, c/Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Ramon Eritja
- IQAC−CSIC, CIBER-BBN Networking Centre on Bioengineering,
Biomaterials and Nanomedicine, c/Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Ulrich F. Keyser
- Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
| |
Collapse
|
15
|
Jakobsen U, Vogel S. Mismatch discrimination of lipidated DNA and LNA-probes (LiNAs) in hybridization-controlled liposome assembly. Org Biomol Chem 2016; 14:6985-95. [PMID: 27356098 DOI: 10.1039/c6ob01120a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Assays for mismatch discrimination and detection of single nucleotide variations by hybridization-controlled assembly of liposomes, which do not require tedious surface chemistry, are versatile for both DNA and RNA targets. We report herein a comprehensive study on different DNA and LNA (locked nucleic acids) probe designs, including membrane-anchoring requirements, studies on different probes and target lengths (including overhangs), DNA and RNA targets (including sequences associated with pathogens) for lipidated nucleic acids (LiNAs). Advantages and limitations of the liposome assembly based assay in the context of mismatch discrimination and SNP detection are presented. The advantages of membrane-anchored LiNA-probes compared to chemically attached probes on solid nanoparticles (e.g. gold nanoparticles) are described. Key functionalities such as non-covalent attachment of LiNA probes without the need for long spacers and the inherent mobility of membrane-anchored probes in lipid-bilayer membranes will be described for several different probe designs.
Collapse
Affiliation(s)
- Ulla Jakobsen
- University of Southern Denmark, Department of Physics, Chemistry and Pharmacy, Campusvej 55, 5230 Odense M, Denmark.
| | | |
Collapse
|
16
|
Ries O, Löffler PMG, Vogel S. Convenient synthesis and application of versatile nucleic acid lipid membrane anchors in the assembly and fusion of liposomes. Org Biomol Chem 2016; 13:9673-80. [PMID: 26264076 DOI: 10.1039/c5ob01207d] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Hydrophobic moieties like lipid membrane anchors are highly demanded modifications for nucleic acid oligomers. Membrane-anchor modified oligonucleotides are applicable in biomedicine leading to new delivery strategies as well as in biophysical investigations towards the assembly and fusion of liposomes or the construction of DNA origami structures. We present herein the synthesis and applications of versatile lipid membrane anchor building blocks suitable for solid-supported oligonucleotide synthesis. These are readily synthesized in bulk in five to seven steps from commercially available precursors and can be incorporated at any position within an oligonucleotide without significantly altering the duplex stability and structure as was proven by thermal denaturation experiments and circular dichroism. Furthermore, their applicability could be demonstrated by the assembly and fusion of liposomes mediated by lipid-modified oligonucleotides.
Collapse
Affiliation(s)
- Oliver Ries
- University of Southern Denmark, Department of Physics, Chemistry and Pharmacy, Campusvej 55, 5230 Odense M, Denmark.
| | | | | |
Collapse
|
17
|
Tao Y, Li M, Ren J, Qu X. Metal nanoclusters: novel probes for diagnostic and therapeutic applications. Chem Soc Rev 2016; 44:8636-63. [PMID: 26400655 DOI: 10.1039/c5cs00607d] [Citation(s) in RCA: 481] [Impact Index Per Article: 60.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Metal nanoclusters, composed of several to a few hundred metal atoms, have received worldwide attention due to their extraordinary physical and chemical characteristics. Recently, great efforts have been devoted to the exploration of the potential diagnostic and therapeutic applications of metal nanoclusters. Here we focus on the recent advances and new horizons in this area, and introduce the rising progress on the use of metal nanoclusters for biological analysis, biological imaging, therapeutic applications, DNA assembly and logic gate construction, enzyme mimic catalysis, as well as thermometers and pH meters. Furthermore, the future challenges in the construction of biofunctional metal nanoclusters for diagnostic and therapeutic applications are also discussed. We expect that the rapidly growing interest in metal nanocluster-based theranostic applications will certainly not only fuel the excitement and stimulate research in this highly active field, but also inspire broader concerns across various disciplines.
Collapse
Affiliation(s)
- Yu Tao
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Changchun, Jilin 130022, China. and University of Chinese Academy of Sciences, Beijing 100039, China
| | - Mingqiang Li
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Changchun, Jilin 130022, China.
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Changchun, Jilin 130022, China.
| |
Collapse
|
18
|
Goldsmith G, Rathinavelan T, Yathindra N. Selective Preference of Parallel DNA Triplexes Is Due to the Disruption of Hoogsteen Hydrogen Bonds Caused by the Severe Nonisostericity between the G*GC and T*AT Triplets. PLoS One 2016; 11:e0152102. [PMID: 27010368 PMCID: PMC4807104 DOI: 10.1371/journal.pone.0152102] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 03/08/2016] [Indexed: 12/14/2022] Open
Abstract
Implications of DNA, RNA and RNA.DNA hybrid triplexes in diverse biological functions, diseases and therapeutic applications call for a thorough understanding of their structure-function relationships. Despite exhaustive studies mechanistic rationale for the discriminatory preference of parallel DNA triplexes with G*GC & T*AT triplets still remains elusive. Here, we show that the highest nonisostericity between the G*GC & T*AT triplets imposes extensive stereochemical rearrangements contributing to context dependent triplex destabilisation through selective disruption of Hoogsteen scheme of hydrogen bonds. MD simulations of nineteen DNA triplexes with an assortment of sequence milieu reveal for the first time fresh insights into the nature and extent of destabilization from a single (non-overlapping), double (overlapping) and multiple pairs of nonisosteric base triplets (NIBTs). It is found that a solitary pair of NIBTs, feasible either at a G*GC/T*AT or T*AT/G*GC triplex junction, does not impinge significantly on triplex stability. But two overlapping pairs of NIBTs resulting from either a T*AT or a G*GC interruption disrupt Hoogsteen pair to a noncanonical mismatch destabilizing the triplex by ~10 to 14 kcal/mol, implying that their frequent incidence in multiples, especially, in short sequences could even hinder triplex formation. The results provide (i) an unambiguous and generalised mechanistic rationale for the discriminatory trait of parallel triplexes, including those studied experimentally (ii) clarity for the prevalence of antiparallel triplexes and (iii) comprehensive perspectives on the sequence dependent influence of nonisosteric base triplets useful in the rational design of TFO's against potential triplex target sites.
Collapse
Affiliation(s)
- Gunaseelan Goldsmith
- Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronics City Phase I, Bangalore, India
- Manipal University, Manipal, India
| | | | - Narayanarao Yathindra
- Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronics City Phase I, Bangalore, India
| |
Collapse
|
19
|
Dobrovolskaia MA, McNeil SE. Strategy for selecting nanotechnology carriers to overcome immunological and hematological toxicities challenging clinical translation of nucleic acid-based therapeutics. Expert Opin Drug Deliv 2015; 12:1163-75. [PMID: 25994601 DOI: 10.1517/17425247.2015.1042857] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Clinical translation of nucleic acid-based therapeutics (NATs) is hampered by assorted challenges in immunotoxicity, hematotoxicity, pharmacokinetics, toxicology and formulation. Nanotechnology-based platforms are being considered to help address some of these challenges due to the nanoparticles' ability to change drug biodistribution, stability, circulation half-life, route of administration and dosage. Addressing toxicology and pharmacology concerns by various means including NATs reformulation using nanotechnology-based carriers has been reviewed before. However, little attention was given to the immunological and hematological issues associated with nanotechnology reformulation. AREAS COVERED This review focuses on application of nanotechnology carriers for delivery of various types of NATs, and how reformulation using nanoparticles affects immunological and hematological toxicities of this promising class of therapeutic agents. EXPERT OPINION NATs share several immunological and hematological toxicities with common nanotechnology carriers. In order to avoid synergy or exaggeration of undesirable immunological and hematological effects of NATs by a nanocarrier, it is critical to consider the immunological compatibility of the nanotechnology platform and its components. Since receptors sensing nucleic acids are located essentially in all cellular compartments, a strategy for developing a nanoformulation with reduced immunotoxicity should first focus on precise delivery to the target site/cells and then on optimizing intracellular distribution.
Collapse
Affiliation(s)
- Marina A Dobrovolskaia
- Principal Scientist, Immunology Section Head,Nanotechnology Characterization Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research , P .O. Box B, Frederick, MD 21702 , USA +1 301 8466939 ; +1 301 846 6399 ;
| | | |
Collapse
|
20
|
Schade M, Berti D, Huster D, Herrmann A, Arbuzova A. Lipophilic nucleic acids--a flexible construction kit for organization and functionalization of surfaces. Adv Colloid Interface Sci 2014; 208:235-51. [PMID: 24650567 DOI: 10.1016/j.cis.2014.02.019] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 02/26/2014] [Accepted: 02/26/2014] [Indexed: 11/19/2022]
Abstract
Lipophilic nucleic acids have become a versatile tool for structuring and functionalization of lipid bilayers and biological membranes as well as cargo vehicles to transport and deliver bioactive compounds, like interference RNA, into cells by taking advantage of reversible hybridization with complementary strands. This contribution reviews the different types of conjugates of lipophilic nucleic acids, and their physicochemical and self-assembly properties. Strategies for choosing a nucleic acid, lipophilic modification, and linker are discussed. Interaction with lipid membranes and its stability, dynamic structure and assembly of lipophilic nucleic acids upon embedding into biological membranes are specific points of the review. A large diversity of conjugates including lipophilic peptide nucleic acid and siRNA provides tailored solutions for specific applications in bio- and nanotechnology as well as in cell biology and medicine, as illustrated through some selected examples.
Collapse
Affiliation(s)
- Matthias Schade
- Humboldt-Universität zu Berlin, Institut für Biologie, Invalidenstr. 42, 10115 Berlin, Germany
| | - Debora Berti
- Dipartimento di Chimica, Universita' di Firenze & CSGI, Via della Lastruccia 3, 50019 Sesto Fiorentino, Firenze, Italy
| | - Daniel Huster
- Universität Leipzig, Institut für Medizinische Physik und Biophysik, Härtelstr. 16-18, 04107 Leipzig, Germany
| | - Andreas Herrmann
- Humboldt-Universität zu Berlin, Institut für Biologie, Invalidenstr. 42, 10115 Berlin, Germany
| | - Anna Arbuzova
- Humboldt-Universität zu Berlin, Institut für Biologie, Invalidenstr. 42, 10115 Berlin, Germany.
| |
Collapse
|
21
|
Serien D, Grimm C, Liebscher J, Herrmann A, Arbuzova A. DNA-controlled aggregation of virus like particles – mimicking a tetherin-like mechanism. NEW J CHEM 2014. [DOI: 10.1039/c4nj00724g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Lipophilic DNA with two α-tocopherol anchors, mimicking tetherin, a cell protein reducing spreading of viruses, induces aggregation of virus-like particles.
Collapse
Affiliation(s)
- Daniela Serien
- Humboldt-Universität zu Berlin
- Institut für Biologie
- 10115 Berlin, Germany
- The University of Tokyo
- Institute of Industrial Science
| | - Christiane Grimm
- Humboldt-Universität zu Berlin
- Institut für Biologie
- 10115 Berlin, Germany
| | - Jürgen Liebscher
- Humboldt-Universität zu Berlin
- Institut für Chemie
- 12489 Berlin, Germany
- National Institute of Research and Development for Isotopic and Molecular Technologies
- Cluj-Napoca, Romania
| | - Andreas Herrmann
- Humboldt-Universität zu Berlin
- Institut für Biologie
- 10115 Berlin, Germany
| | - Anna Arbuzova
- Humboldt-Universität zu Berlin
- Institut für Biologie
- 10115 Berlin, Germany
| |
Collapse
|