1
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Stransky F, Kostrz D, Follenfant M, Pomplun S, Meyners C, Strick T, Hausch F, Gosse C. Use of DNA forceps to measure receptor-ligand dissociation equilibrium constants in a single-molecule competition assay. Methods Enzymol 2024; 694:51-82. [PMID: 38492958 DOI: 10.1016/bs.mie.2024.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2024]
Abstract
The ability of biophysicists to decipher the behavior of individual biomolecules has steadily improved over the past thirty years. However, it still remains unclear how an ensemble of data acquired at the single-molecule level compares with the data acquired on an ensemble of the same molecules. We here propose an assay to tackle this question in the context of dissociation equilibrium constant measurements. A sensor is built by engrafting a receptor and a ligand onto a flexible dsDNA scaffold and mounting this assembly on magnetic tweezers. This way, looking at the position of the magnetic bead enables one to determine in real-time if the two molecular partners are associated or not. Next, to quantify the affinity of the scrutinized single-receptor for a given competitor, various amounts of the latter molecule are introduced in solution and the equilibrium response of the sensor is monitored throughout the titration protocol. Proofs of concept are established for the binding of three rapamycin analogs to the FKBP12 cis-trans prolyl isomerase. For each of these drugs the mean affinity constant obtained on a ten of individual receptors agrees with the one previously determined in a bulk assay. Furthermore, experimental contingencies are sufficient to explain the dispersion observed over the single-molecule values.
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Affiliation(s)
- François Stransky
- Institut de Biologie de l'Ecole Normale Supérieure, ENS, CNRS, INSERM, PSL Research University, Paris, France
| | - Dorota Kostrz
- Institut de Biologie de l'Ecole Normale Supérieure, ENS, CNRS, INSERM, PSL Research University, Paris, France
| | - Maryne Follenfant
- Institut de Biologie de l'Ecole Normale Supérieure, ENS, CNRS, INSERM, PSL Research University, Paris, France
| | - Sebastian Pomplun
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Christian Meyners
- Department of Chemistry and Biochemistry, Technical University Darmstadt, Darmstadt, Germany
| | - Terence Strick
- Institut de Biologie de l'Ecole Normale Supérieure, ENS, CNRS, INSERM, PSL Research University, Paris, France
| | - Felix Hausch
- Department of Chemistry and Biochemistry, Technical University Darmstadt, Darmstadt, Germany; Centre for Synthetic Biology, Technical University Darmstadt, Darmstadt, Germany
| | - Charlie Gosse
- Institut de Biologie de l'Ecole Normale Supérieure, ENS, CNRS, INSERM, PSL Research University, Paris, France.
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2
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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.
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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
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3
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Saher O, Zaghloul EM, Umek T, Hagey DW, Mozafari N, Danielsen MB, Gouda AS, Lundin KE, Jørgensen PT, Wengel J, Smith CIE, Zain R. Chemical Modifications and Design Influence the Potency of Huntingtin Anti-Gene Oligonucleotides. Nucleic Acid Ther 2023; 33:117-131. [PMID: 36735581 PMCID: PMC10066784 DOI: 10.1089/nat.2022.0046] [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: 02/04/2023] Open
Abstract
Huntington's disease is a neurodegenerative, trinucleotide repeat (TNR) disorder affecting both males and females. It is caused by an abnormal increase in the length of CAG•CTG TNR in exon 1 of the Huntingtin gene (HTT). The resultant, mutant HTT mRNA and protein cause neuronal toxicity, suggesting that reduction of their levels would constitute a promising therapeutic approach. We previously reported a novel strategy in which chemically modified oligonucleotides (ONs) directly target chromosomal DNA. These anti-gene ONs were able to downregulate both HTT mRNA and protein. In this study, various locked nucleic acid (LNA)/DNA mixmer anti-gene ONs were tested to investigate the effects of varying ON length, LNA content, and fatty acid modification on HTT expression. Altering the length did not significantly influence the ON potency, while LNA content was critical for activity. Utilization of palmitoyl-modified LNA monomers enhanced the ON activity relatively to the corresponding nonmodified LNA under serum starvation conditions. Furthermore, the number of palmitoylated LNA monomers and their positioning greatly affected ON potency. In addition, we performed RNA sequencing analysis, which showed that the anti-gene ONs affect the "immune system process, mRNA processing, and neurogenesis." Furthermore, we observed that for repeat containing genes, there is a higher tendency for antisense off-targeting. Taken together, our findings provide an optimized design of anti-gene ONs that could potentially be developed as DNA-targeting therapeutics for this class of TNR-related diseases.
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Affiliation(s)
- Osama Saher
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-14186 Huddinge, Sweden.,Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Eman M Zaghloul
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-14186 Huddinge, Sweden.,Department of Pharmaceutics, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
| | - Tea Umek
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-14186 Huddinge, Sweden
| | - Daniel W Hagey
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-14186 Huddinge, Sweden
| | - Negin Mozafari
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-14186 Huddinge, Sweden
| | - Mathias B Danielsen
- Department of Physics, Chemistry and Pharmacy, Biomolecular Nanoscale Engineering Center, University of Southern Denmark, Odense, Denmark
| | - Alaa S Gouda
- Department of Physics, Chemistry and Pharmacy, Biomolecular Nanoscale Engineering Center, University of Southern Denmark, Odense, Denmark.,Department of Chemistry, Faculty of Science, Benha University, Benha, Egypt
| | - Karin E Lundin
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-14186 Huddinge, Sweden
| | - Per T Jørgensen
- Department of Physics, Chemistry and Pharmacy, Biomolecular Nanoscale Engineering Center, University of Southern Denmark, Odense, Denmark
| | - Jesper Wengel
- Department of Physics, Chemistry and Pharmacy, Biomolecular Nanoscale Engineering Center, University of Southern Denmark, Odense, Denmark
| | - C I Edvard Smith
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-14186 Huddinge, Sweden
| | - Rula Zain
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-14186 Huddinge, Sweden.,Centre for Rare Diseases, Department of Clinical Genetics, Karolinska University Hospital, SE-17176 Stockholm, Sweden
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4
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Zhang Z, Chen H, Fang L, He H, Mao C, Zuo H. Solution-Phase Synthesis of DNA Amphiphiles for DNA Micellar Assembly. Bioconjug Chem 2023; 34:85-91. [PMID: 36173879 DOI: 10.1021/acs.bioconjchem.2c00325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Hydrophobic moieties of amphiphilic DNAs can help DNAs penetrate cell membranes, but the conjugation of hydrophobic moieties to DNAs in solution phase remains challenging. Herein we report a solution-phase synthesis method to conjugate hydrophobic molecules to DNAs. This method is simple and efficient. The resulted amphiphilic DNAs can spontaneously assemble into micelles, which may serve as nanocarriers for cellular delivery of nucleic acids and water-insoluble drugs.
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Affiliation(s)
- Zhe Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Huaiqing Chen
- Biological Sciences Research Center, State Key laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China
| | - Liang Fang
- Department of Oncology, The Ninth People's Hospital of Chongqing, Chongqing 400700, China
| | - Huawei He
- Biological Sciences Research Center, State Key laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China
| | - Chengde Mao
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China.,Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Hua Zuo
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
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5
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Oka Y. Exclusion of Anchor-Matched Peptide Nucleic Acid from Liquid-Ordered Domains by Hybridization with Complementary Flavin-Labeled DNA. ACS OMEGA 2023; 8:1109-1113. [PMID: 36643542 PMCID: PMC9835180 DOI: 10.1021/acsomega.2c06463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Membrane-anchored proteins and their mimics, such as peptide nucleic acids (PNAs), are known to partition preferentially into either lipid raft/liquid-ordered (lo) domains or into non-raft/liquid-disordered (ld) domains, depending on their lipophilic anchors. Here, anchor-matched PNA was demonstrated to be excluded from the lo microdomains of giant unilamellar vesicles by hybridization with the complementary flavin-labeled DNA. As shown in control experiments using Alexa Fluor 488-labeled DNA, which showed that the preferential partitioning was the lo domain, the domain distribution of PNA was not only dependent on the lipophilic anchor but also on the structure of the hybridized DNA or PNA pair. In such systems, the main factors that influence changes in the domain selectivity of the probes are most likely to also be interactivity (i.e., steric bulkiness), hydrophilicity, and self-assembling ability. These findings may have the potential to contribute to the elucidation of membrane-active peptides, the method of their activation, and their applications in medicine such as antimicrobial use, especially with regard to their actions at the interface between the lo and ld domains in cells.
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6
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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.
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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.
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7
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Dimitrov E, Toncheva-Moncheva N, Bakardzhiev P, Forys A, Doumanov J, Mladenova K, Petrova S, Trzebicka B, Rangelov S. Nucleic acid-based supramolecular structures: vesicular spherical nucleic acids from a non-phospholipid nucleolipid. NANOSCALE ADVANCES 2022; 4:3793-3803. [PMID: 36133345 PMCID: PMC9470030 DOI: 10.1039/d2na00527a] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 08/08/2022] [Indexed: 06/16/2023]
Abstract
Vesicular spherical nucleic acids are dynamic nucleic acid-based supramolecular structures that are held together via non-covalent bonds. They have promising applications as drug and nucleic acid delivery materials, diagnostic and imaging tools and platforms for development of various therapeutic schemes. In this contribution, we report on vesicular spherical nucleic acids, constructed from a non-phospholipid nucleolipid - an original hybrid biomacromolecule, composed of a hydrophobic residue, resembling that of the naturally occurring phospholipids, and a DNA oligonucleotide strand. The nucleolipid was synthesized by coupling of dibenzocyclooctyne-functionalized oligonucleotide and azidated 1,3-dihexadecyloxy-propane-2-ol via an azide-alkyne click reaction. In aqueous solution it spontaneously self-associated into nanosized supramolecular structures, identified as unilamellar vesicles composed of a self-closed interdigitated bilayer. Vesicular structures were also formed upon intercalation of the nucleolipid via its lipid-mimetic residue in the phospholipid bilayer membrane of liposomes prepared from readily available and FDA-approved lipids (1,2-dipalmitoyl-rac-glycero-3-phosphocholine and cholesterol). The vesicular structures are thoroughly investigated by light scattering (dynamic, static, and electrophoretic) and cryogenic TEM and the physical characteristics, in particular, number of strands per particle, grafting density, and conformation of the strands, were compared to those of reference spherical nucleic acids. Finally, the vesicular structures were shown to exhibit cellular internalization with no need of transfection agents and enhanced colloidal and nuclease stability.
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Affiliation(s)
- Erik Dimitrov
- Institute of Polymers, Bulgarian Academy of Sciences Akad. G. Bonchev St. 103A 1113 Sofia Bulgaria
| | | | - Pavel Bakardzhiev
- Institute of Polymers, Bulgarian Academy of Sciences Akad. G. Bonchev St. 103A 1113 Sofia Bulgaria
| | - Aleksander Forys
- Centre of Polymer and Carbon Materials, Polish Academy of Sciences M. Curie-Sklodowskiej 34 Zabrze Poland
| | - Jordan Doumanov
- Department of Biochemistry, Faculty of Biology, Sofia University St. Kliment Ohridski Dragan Tsankov Blvd. 8 1164 Sofia Bulgaria
| | - Kirilka Mladenova
- Department of Biochemistry, Faculty of Biology, Sofia University St. Kliment Ohridski Dragan Tsankov Blvd. 8 1164 Sofia Bulgaria
| | - Svetla Petrova
- Department of Biochemistry, Faculty of Biology, Sofia University St. Kliment Ohridski Dragan Tsankov Blvd. 8 1164 Sofia Bulgaria
| | - Barbara Trzebicka
- Centre of Polymer and Carbon Materials, Polish Academy of Sciences M. Curie-Sklodowskiej 34 Zabrze Poland
| | - Stanislav Rangelov
- Institute of Polymers, Bulgarian Academy of Sciences Akad. G. Bonchev St. 103A 1113 Sofia Bulgaria
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8
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Page S, Khan T, Kühl P, Schwach G, Storch K, Chokshi H. Patient Centricity Driving Formulation Innovation: Improvements in Patient Care Facilitated by Novel Therapeutics and Drug Delivery Technologies. Annu Rev Pharmacol Toxicol 2022; 62:341-363. [PMID: 34990203 DOI: 10.1146/annurev-pharmtox-052120-093517] [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: 11/09/2022]
Abstract
Innovative formulation technologies can play a crucial role in transforming a novel molecule to a medicine that significantly enhances patients' lives. Improved mechanistic understanding of diseases has inspired researchers to expand the druggable space using new therapeutic modalities such as interfering RNA, protein degraders, and novel formats of monoclonal antibodies. Sophisticated formulation strategies are needed to deliver the drugs to their sites of action and to achieve patient centricity, exemplified by messenger RNA vaccines and oral peptides. Moreover, access to medical information via digital platforms has resulted in better-informed patient groups that are requesting consideration of their needs during drug development. This request is consistent with health authority efforts to upgrade their regulations to advance age-appropriate product development for patients. This review describes formulation innovations contributingto improvements in patient care: convenience of administration, preferred route of administration, reducing dosing burden, and achieving targeted delivery of new modalities.
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Affiliation(s)
- Susanne Page
- Pharma Technical Development, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland;
| | - Tarik Khan
- Pharma Technical Development, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland;
| | - Peter Kühl
- Pharma Technical Development, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland;
| | - Gregoire Schwach
- Pharma Technical Development, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland;
| | - Kirsten Storch
- Pharma Technical Development, Roche Diagnostics GmbH, 68305 Mannheim, Germany
| | - Hitesh Chokshi
- Pharma Technical Development, Roche TCRC Inc., Little Falls, New Jersey 07424, USA
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9
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Vafaei S, Allabush F, Tabaei SR, Male L, Dafforn TR, Tucker JHR, Mendes PM. Förster Resonance Energy Transfer Nanoplatform Based on Recognition-Induced Fusion/Fission of DNA Mixed Micelles for Nucleic Acid Sensing. ACS NANO 2021; 15:8517-8524. [PMID: 33961404 PMCID: PMC8158853 DOI: 10.1021/acsnano.1c00156] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 04/29/2021] [Indexed: 05/29/2023]
Abstract
The dynamic nature of micellar nanostructures is employed to form a self-assembled Förster resonance energy transfer (FRET) nanoplatform for enhanced sensing of DNA. The platform consists of lipid oligonucleotide FRET probes incorporated into micellar scaffolds, where single recognition events result in fusion and fission of DNA mixed micelles, triggering the fluorescence response of multiple rather than a single FRET pair. In comparison to conventional FRET substrates where a single donor interacts with a single acceptor, the micellar multiplex FRET system showed ∼20- and ∼3-fold enhancements in the limit of detection and FRET efficiency, respectively. This supramolecular signal amplification approach could potentially be used to improve FRET-based diagnostic assays of nucleic acid and non-DNA based targets.
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Affiliation(s)
- Setareh Vafaei
- School
of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Francia Allabush
- School
of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Seyed R. Tabaei
- School
of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Louise Male
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Timothy R. Dafforn
- School
of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - James H. R. Tucker
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Paula M. Mendes
- School
of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
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10
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Wang S, Allen N, Prakash TP, Liang XH, Crooke ST. Lipid Conjugates Enhance Endosomal Release of Antisense Oligonucleotides Into Cells. Nucleic Acid Ther 2019; 29:245-255. [PMID: 31158063 DOI: 10.1089/nat.2019.0794] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Antisense oligonucleotides modified with phosphorothioate linkages (PS-ASOs) can enter cells via endocytic pathways and must escape from membraned organelles to reach target RNAs. We recently found that membrane destabilization induced by different lipid species contributes to PS-ASO release from late endosomes (LEs). In this study, we characterized intracellular uptake, trafficking, and activities of PS-ASOs conjugated with different lipid species. We found that palmitic acid-, tocopherol-, and cholesterol-conjugated PS-ASOs have increased protein binding and enhanced intracellular uptake compared to unconjugated PS-ASOs. Similar to the parental PS-ASO, the lipid-conjugated PS-ASOs traffic from early to LEs without incorporation into lipid droplets. Unlike parental PS-ASOs, the lipid-conjugated PS-ASOs tend to remain associated with plasma or endosomal membranes, and this appears to influence their release from endosomes. The lipid-conjugated PS-ASOs were released more rapidly than parental PS-ASO. These results suggest that lipid conjugation enhances the interactions of PS-ASOs with proteins or membranes, in turn facilitating intracellular trafficking and endosomal release.
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Affiliation(s)
- Shiyu Wang
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California
| | - Nickolas Allen
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California
| | - Thazha P Prakash
- Department of Medicinal Chemistry, Ionis Pharmaceuticals, Inc., Carlsbad, California
| | - Xue-Hai Liang
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California
| | - Stanley T Crooke
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California
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11
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Shu Y, Yin H, Rajabi M, Li H, Vieweger M, Guo S, Shu D, Guo P. RNA-based micelles: A novel platform for paclitaxel loading and delivery. J Control Release 2018; 276:17-29. [PMID: 29454064 PMCID: PMC5964609 DOI: 10.1016/j.jconrel.2018.02.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Revised: 02/08/2018] [Accepted: 02/09/2018] [Indexed: 12/22/2022]
Abstract
RNA can serve as powerful building blocks for bottom-up fabrication of nanostructures for biotechnological and biomedical applications. In addition to current self-assembly strategies utilizing base pairing, motif piling and tertiary interactions, we reported for the first time the formation of RNA based micellar nanoconstruct with a cholesterol molecule conjugated onto one helical end of a branched pRNA three-way junction (3WJ) motif. The resulting amphiphilic RNA micelles consist of a hydrophilic RNA head and a covalently linked hydrophobic lipid tail that can spontaneously assemble in aqueous solution via hydrophobic interaction. Taking advantage of pRNA 3WJ branched structure, the assembled RNA micelles are capable of escorting multiple functional modules. As a proof of concept for delivery for therapeutics, Paclitaxel was loaded into the RNA micelles with significantly improved water solubility. The successful construction of the drug loaded RNA micelles was confirmed and characterized by agarose gel electrophoresis, atomic force microscopy (AFM), dynamic light scattering (DLS), and fluorescence Nile Red encapsulation assay. The estimate critical micelle formation concentration ranges from 39 nM to 78 nM. The Paclitaxel loaded RNA micelles can internalize into cancer cells and inhibit their proliferation. Further studies showed that the Paclitaxel loaded RNA micelles induced cancer cell apoptosis in a Caspase-3 dependent manner but RNA micelles alone exhibited low cytotoxicity. Finally, the Paclitaxel loaded RNA micelles targeted to tumor in vivo without accumulation in healthy tissues and organs. There is also no or very low induction of pro-inflammatory response. Therefore, multivalence, cancer cell permeability, combined with controllable assembly, low or non toxic nature, and tumor targeting are all promising features that make our pRNA micelles a suitable platform for potential drug delivery.
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Affiliation(s)
- Yi Shu
- Nanobiotechnology Center, Markey Cancer Center and Department of Pharmaceutical Sciences/College of Pharmacy, University of Kentucky, Lexington, KY 40536, United States
| | - Hongran Yin
- Center for RNA Nanobiotechnology and Nanomedicine, Division of Pharmaceutics and Pharmaceutical Chemistry/College of Pharmacy, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State Universtiy, Columbus, OH 43210, United States
| | - Mehdi Rajabi
- Nanobiotechnology Center, Markey Cancer Center and Department of Pharmaceutical Sciences/College of Pharmacy, University of Kentucky, Lexington, KY 40536, United States
| | - Hui Li
- Center for RNA Nanobiotechnology and Nanomedicine, Division of Pharmaceutics and Pharmaceutical Chemistry/College of Pharmacy, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State Universtiy, Columbus, OH 43210, United States; Nanobiotechnology Center, Markey Cancer Center and Department of Pharmaceutical Sciences/College of Pharmacy, University of Kentucky, Lexington, KY 40536, United States
| | - Mario Vieweger
- Center for RNA Nanobiotechnology and Nanomedicine, Division of Pharmaceutics and Pharmaceutical Chemistry/College of Pharmacy, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State Universtiy, Columbus, OH 43210, United States
| | - Sijin Guo
- Center for RNA Nanobiotechnology and Nanomedicine, Division of Pharmaceutics and Pharmaceutical Chemistry/College of Pharmacy, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State Universtiy, Columbus, OH 43210, United States
| | - Dan Shu
- Center for RNA Nanobiotechnology and Nanomedicine, Division of Pharmaceutics and Pharmaceutical Chemistry/College of Pharmacy, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State Universtiy, Columbus, OH 43210, United States
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, Division of Pharmaceutics and Pharmaceutical Chemistry/College of Pharmacy, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State Universtiy, Columbus, OH 43210, United States.
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12
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Trinh T, Chidchob P, Bazzi HS, Sleiman HF. DNA micelles as nanoreactors: efficient DNA functionalization with hydrophobic organic molecules. Chem Commun (Camb) 2016; 52:10914-7. [PMID: 27533528 DOI: 10.1039/c6cc04970b] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We report a micelle-templated method to enhance the reactivity of DNA with highly hydrophobic molecules. Lipids, chromophores and polymers can be conjugated to DNA in high yield and under mild conditions. This method expands the range of DNA-templated reactions for DNA-encoded libraries, oligonucleotide and drug delivery, nanopore mimetics and DNA nanotechnology.
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Affiliation(s)
- Tuan Trinh
- Department of Chemistry and Center for Self-Assembled Chemical Structures, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8.
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13
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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.
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Affiliation(s)
- Oliver Ries
- University of Southern Denmark, Department of Physics, Chemistry and Pharmacy, Campusvej 55, 5230 Odense M, Denmark.
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14
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Wu F, Zhang Y, Yang Z. An Overview of Self-Assembly and Morphological Regulation of Amphiphilic DNA Organic Hybrids. CHINESE J CHEM 2015. [DOI: 10.1002/cjoc.201400846] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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15
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Aimé A, Beztsinna N, Patwa A, Pokolenko A, Bestel I, Barthélémy P. Quantum dot lipid oligonucleotide bioconjugates: toward a new anti-microRNA nanoplatform. Bioconjug Chem 2014; 24:1345-55. [PMID: 23888900 DOI: 10.1021/bc400157z] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The construction of new nanotools is presented here using the example of fluorescent semiconductor nanocrystals, quantum dots (QDs). In this study, the implementation of the new lipid oligonucleotide conjugate-functionalized quantum dots (LON-QDs) is realized in four steps: (i) the synthesis of the lipid oligonucleotide conjugates (LONs), (ii) the encapsulation of QDs by nucleolipids and LONs, (iii) the study of the duplex formation of LON-QDs with the complementary ON partners, and (iv) the cellular uptake of the LON-QD platform and hybridization with the target ONs (microRNA and miR-21).
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Borre Hansen M, Krog Andersen N, Raunkjaer M, Trolle Jørgensen P, Wengel J. Functionalization of 2″- C-(Piperazinomethyl)-2′,3′-BcNA (Bicyclic Nucleic Acids) with Pyren-1-ylcarbonyl Units. Helv Chim Acta 2014. [DOI: 10.1002/hlca.201400141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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17
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Waybrant B, Pearce TR, Kokkoli E. Effect of polyethylene glycol, alkyl, and oligonucleotide spacers on the binding, secondary structure, and self-assembly of fractalkine binding FKN-S2 aptamer-amphiphiles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:7465-7474. [PMID: 24849928 DOI: 10.1021/la500403v] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Previously we identified an aptamer, named FKN-S2, which binds the cell surface protein fractalkine with high affinity and specificity. In this paper a hydrophobic dialkyl C16 tail was added to the aptamer to create an aptamer-amphiphile. We investigated how the tail and a spacer molecule of varying length and hydrophobicity, inserted between the tail and the aptamer headgroup, affect the binding, structure, and self-assembly properties of the aptamer-amphiphile. We synthesized aptamer-amphiphiles with no spacer (NoSPR), polyethylene glycol (PEG4, PEG8, PEG24), alkyl (C12 and C24), or oligonucleotide (T10 and T5: 10 and 5 thymine, and A10: 10 adenine) spacers. The addition of the tail reduced the binding affinity of the aptamer-amphiphile over 7.5-fold compared to the free aptamer. The hydrophobic alkyl spacers resulted in the greatest loss of affinity, and the hydrophilic PEG spacers improved amphiphile affinity but did not restore it to that of the free aptamer. Interestingly, oligonucleotide spacers produced the highest affinity amphiphiles. Nucleotide composition did not affect affinity, however, as the T10 and A10 spacers had equal affinity. The oligonucleotide spacer amphiphiles had the highest affinity because the oligonucleotide spacer increased the affinity of free aptamer; the FKN-S2 aptamer plus the oligonucleotide spacer had a higher affinity than the free FKN-S2 aptamer. Circular dichroism (CD) spectroscopy and thermal melting studies indicated the aptamer forms a stem-loop and intramolecular G-quadruplex, and the tail strongly stabilized the formation of the G-quadruplex in a buffer. Cryogenic transmission electron microscopy (cryo-TEM) imaging showed the aptamer-amphiphiles, independent of the spacer used, self-assembled into micelles and nanotapes, flat bilayer structures that were often twisted. Finally, liposomes functionalized with the FKN-S2 amphiphile were incubated with fractalkine expressing cells, and the amount of binding was dependent on the concentration of the amphiphile on the liposome surface.
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Affiliation(s)
- Brett Waybrant
- Department of Chemical Engineering and Materials Science, and ‡Department of Biomedical Engineering, University of Minnesota , Minneapolis, Minnesota 55455, United States
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18
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Glang S, Rieth T, Borchmann D, Fortunati I, Signorini R, Detert H. Arylethynyl-Substituted Tristriazolotriazines: Synthesis, Optical Properties, and Thermotropic Behavior. European J Org Chem 2014. [DOI: 10.1002/ejoc.201400088] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Tanabe K, Ando Y, Hara D, Ito T, Nishimoto SI. Oligonucleotides with consecutive alkylated phosphate units: aggregation characteristics and drug transport into living cells. RSC Adv 2014. [DOI: 10.1039/c3ra47662f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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20
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Jakobsen U, Vogel S. Assembly of liposomes controlled by triple helix formation. Bioconjug Chem 2013; 24:1485-95. [PMID: 23885785 DOI: 10.1021/bc300690m] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Attachment of DNA to the surface of different solid nanoparticles (e.g., gold and silica nanoparticles) is well established, and a number of DNA-modified solid nanoparticle systems have been applied to thermal denaturation analysis of oligonucleotides. We report herein the noncovalent immobilization of oligonucleotides on the surface of soft nanoparticles (i.e., liposomes) and the subsequent controlled assembly by DNA triple helix formation. The noncovalent approach avoids tedious surface chemistry and necessary purification procedures and can simplify and extend the available methodology for the otherwise difficult thermal denaturation analysis of complex triple helical DNA assemblies. The approach is based on lipid modified triplex forming oligonucleotides (TFOs) which control the assembly of liposomes in solution in the presence of single- or double-stranded DNA targets. The thermal denaturation analysis is monitored by ultraviolet spectroscopy at submicromolar concentrations and compared to regular thermal denaturation assays in the absence of liposomes. We report on triplex forming oligonucleotides (TFOs) based on DNA and locked nucleic acid (LNA)/DNA hybrid building blocks and different target sequences (G or C-rich) to explore the applicability of the method for different triple helical assembly modes. We demonstrate advantages and limitations of the approach and show the reversible and reproducible formation of liposome aggregates during thermal denaturation cycles. Nanoparticle tracking analysis (NTA) and dynamic light scattering (DLS) show independently from ultraviolet spectroscopy experiments the formation of liposome aggregates.
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Affiliation(s)
- Ulla Jakobsen
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Campusvej 55, 5230 Odense M, Denmark
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21
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Ugarte-Uribe B, Grijalvo S, Busto JV, Martín C, Eritja R, Goñi FM, Alkorta I. Double-tailed lipid modification as a promising candidate for oligonucleotide delivery in mammalian cells. Biochim Biophys Acta Gen Subj 2013; 1830:4872-84. [PMID: 23800579 DOI: 10.1016/j.bbagen.2013.06.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 05/31/2013] [Accepted: 06/13/2013] [Indexed: 12/17/2022]
Abstract
BACKGROUND The potential use of nucleic acids as therapeutic drugs has triggered the quest for oligonucleotide conjugates with enhanced cellular permeability. To this end, the biophysical aspects of previously reported potential lipid oligodeoxyribonucleotide conjugates were studied including its membrane-binding properties and cellular uptake. METHODS These conjugates were fully characterized by MALDI-TOF mass spectrometry and HPLC chromatography. Their ability to insert into lipid model membrane systems was evaluated by Langmuir balance and confocal microscopy followed by the study of the internalization of a lipid oligodeoxyribonucleotide conjugate bearing a double-tail lipid modification (C28) into different cell lines by confocal microscopy and flow cytometry. This compound was also compared with other lipid containing conjugates and with the classical lipoplex formulation using Transfectin as transfection reagent. RESULTS This double-tail lipid modification showed better incorporation into both lipid model membranes and cell systems. Indeed, this lipid conjugation was capable of inserting the oligodeoxyribonucleotide into both liquid-disordered and liquid-ordered domains of model lipid bilayer systems and produced an enhancement of oligodeoxyribonucleotide uptake in cells, even better than the effect caused by lipoplexes. In addition, in β2 integrin (CR3) expressing cells this receptor was directly involved in the enhanced internalization of this compound. CONCLUSIONS All these features confirm that the dual lipid modification (C28) is an excellent modification for enhancing nucleic acid delivery without altering their binding properties. GENERAL SIGNIFICANCE Compared to the commercial lipoplex approach, oligodeoxyribonucleotide conjugation with C28 dual lipid modification seems to be promising to improve oligonucleotide delivery in mammalian cells.
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Affiliation(s)
- Begoña Ugarte-Uribe
- Department of Biochemistry and Molecular Biology, UPV/EHU and Biophysics Unit, Leioa, Spain
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22
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Pokholenko O, Gissot A, Vialet B, Bathany K, Thiéry A, Barthélémy P. Lipid oligonucleotide conjugates as responsive nanomaterials for drug delivery. J Mater Chem B 2013; 1:5329-5334. [DOI: 10.1039/c3tb20357c] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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23
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Rattanakiat S, Nishikawa M, Takakura Y. Self-assembling CpG DNA nanoparticles for efficient antigen delivery and immunostimulation. Eur J Pharm Sci 2012; 47:352-8. [PMID: 22771546 DOI: 10.1016/j.ejps.2012.06.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 04/25/2012] [Accepted: 06/25/2012] [Indexed: 10/28/2022]
Abstract
DNA containing unmethylated deoxycytidylyl-deoxyguanosine (CpG) dinucleotides (CpG DNA) is a potent stimulator of immune responses through triggering of Toll-like receptor 9 (TLR9). In the present study, we synthesized cholesterol-modified CpG oligodeoxynucleotide (Chol-CpG ODN) and investigated its ability to form nanoparticles by self-assembling, then examined their immunostimulatory activity and potency to deliver antigens to antigen presenting cells (APCs). Chol-CpG ODN spontaneously formed particles in aqueous solutions. Cholesterol modification increased the stability of ODN in serum. Chol-CpG ODN was efficiently taken up by mouse macrophage-like RAW264.7 cells and induced a large amount of tumor necrosis factor-α compared with unmodified CpG ODN. Then, ovalbumin (OVA), a model antigen, was incorporated into Chol-CpG ODN nanoparticles. Cholesterol-modified GpC ODN (Chol-GpC ODN) was used to assess the importance of CpG motif on the antigen-specific immune response. Vaccination of mice with OVA/Chol-CpG ODN induced high level interferon-γ production from splenocytes. Furthermore, a high serum level of OVA-specific immunoglobulin G2a was observed in mice receiving OVA/Chol-CpG ODN. Neither CpG ODN nor Chol-GpC ODN was effective at all. These results indicate that self-assembling nanoparticles of Chol-CpG ODN are effective for inducing antigen-specific immune responses because of the high immunostimulatory activity, ability to incorporate antigens and tropism to APCs.
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Affiliation(s)
- Sakulrat Rattanakiat
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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24
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Liu H, Kwong B, Irvine DJ. Membrane Anchored Immunostimulatory Oligonucleotides for In Vivo Cell Modification and Localized Immunotherapy. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201101266] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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25
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Liu H, Kwong B, Irvine DJ. Membrane anchored immunostimulatory oligonucleotides for in vivo cell modification and localized immunotherapy. Angew Chem Int Ed Engl 2011; 50:7052-5. [PMID: 21688362 PMCID: PMC3166645 DOI: 10.1002/anie.201101266] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2011] [Revised: 04/28/2011] [Indexed: 11/12/2022]
Affiliation(s)
- Haipeng Liu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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26
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Patwa A, Gissot A, Bestel I, Barthélémy P. Hybrid lipid oligonucleotide conjugates: synthesis, self-assemblies and biomedical applications. Chem Soc Rev 2011; 40:5844-54. [PMID: 21611637 DOI: 10.1039/c1cs15038c] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Hybrid lipid oligonucleotide conjugates are finding more and more biotechnological applications. This short critical review highlights their synthesis, supramolecular organization as well as their applications in the field of biotechnology (111 references).
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Affiliation(s)
- Amit Patwa
- Université Bordeaux Segalen, Bordeaux, F-33076, France
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27
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Laing BM, Barrow-Laing L, Harrington M, Long EC, Bergstrom DE. Properties of double-stranded oligonucleotides modified with lipophilic substituents. Bioconjug Chem 2011; 21:1537-44. [PMID: 20672836 DOI: 10.1021/bc100201n] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We have synthesized a series of short, self-complementary oligonucleotide sequences modified at their 5'- and/or 3'- termini with a lipophilic dodecane (C12); these systems serve as models to assess the biophysical properties of double-stranded DNA (dsDNA) equipped with potentially stabilizing lipophilic substituents. Addition of C12 to the 5'-termini of self-complementary 10 nucleotide sequences increased their duplex melting temperatures (T(m)) by approximately 4-8 degrees C over their corresponding unmodified sequences. C12 functionalities added to both the 3'- and 5'-termini increased T(m) values by approximately 10-12 degrees C. The observed increases in T(m) correlated with greater duplex stabilities as determined by the free energy values (DeltaG) derived from T(m) plots. There is a greater degree of stabilization when C12 is positioned with a C.G base pair at the termini, and the stabilizing effect of lipophilic groups far exceeds the effect seen in adding an additional base pair to both ends of DNA. Stable, short dsDNA sequences are of potential interest in the development of transcription factor decoy oligonucleotides as possible therapeutic agents and/or biological tools. These results suggest that the stability of short dsDNA sequences are improved by lipophilic substituents and can be used as the basis for the design of dsDNAs with improved biological stabilities and function under physiological conditions.
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Affiliation(s)
- Brian M Laing
- Department of Medicinal Chemistry and Molecular Pharmacology and Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, USA
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28
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Emond M, Sun J, Grégoire J, Maurin S, Tribet C, Jullien L. Photoinduced pH drops in water. Phys Chem Chem Phys 2011; 13:6493-9. [DOI: 10.1039/c0cp02464c] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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29
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Gambinossi F, Banchelli M, Durand A, Berti D, Brown T, Caminati G, Baglioni P. Modulation of density and orientation of amphiphilic DNA anchored to phospholipid membranes. I. Supported lipid bilayers. J Phys Chem B 2010; 114:7338-47. [PMID: 20446700 DOI: 10.1021/jp100730x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
In the present series of papers, we describe the results of a systematic study on the anchoring of cholesterol-tagged oligonucleotides to phospholipids bilayers followed by membrane-assisted hybridization of the complementary strand in solution. This paper describes the anchoring of novel cholesterol-modified DNA-18mers in supported lipid bilayers (SLB) of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine: we compared the behavior of two anchoring functionalities differing in the number of cholesterol units and in the length of a spacer group. Quartz Crystal Microbalance with impedance monitoring (QCM-Z) measurements showed that both oligonucleotides insert into the bilayer membrane through cholesterol anchoring; however, dramatic differences, in terms of surface organization and thickness, are found as the number of anchoring units increases. In the case of multiple cholesterol units, a peculiar three-regimes concentration dependence was revealed and correlated to the effective size of the adsorbing units. Interestingly, for high oligonucleotide concentration, the adsorption process was rationalized in terms of a compaction model of amphiphilic DNA molecules. QCM-Z temperature cycles of the SLB-anchored double strands provided clear evidence for reversible hybridization at the bilayer interface.
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Affiliation(s)
- Filippo Gambinossi
- Department of Chemistry and CSGI, University of Florence, via della Lastruccia 3-Sesto Fiorentino, 50019 Florence, Italy
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30
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Banchelli M, Gambinossi F, Durand A, Caminati G, Brown T, Berti D, Baglioni P. Modulation of density and orientation of amphiphilic DNA on phospholipid membranes. II. Vesicles. J Phys Chem B 2010; 114:7348-58. [PMID: 20446699 DOI: 10.1021/jp100731c] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
In the present series of papers, we describe the results of a systematic study on the anchoring of cholesterol-tagged oligonucleotides to phospholipid bilayers followed by membrane-assisted hybridization of the complementary strand in solution. This paper compares the behavior of two cholesteryl modified oligonucleotides, differing in the architecture and hydrophobicity of the lipophilic moiety, in the self-aggregation, hybridization, and insertion in phospholipid vesicle membranes. We have focused our attention on a singly substituted derivative (SC-ON(1)) and a multicholesterol (MC-ON(1)) derivative, where the cholesteryl units are inserted at the desired positions along a noncoupling T-sequence. The self-aggregation properties in solution are also explicitly taken into account and evaluated as competitive with respect to the adsorption at fluid or solid interfaces and to hybridization with the complementary ON(2) sequence. By exploring a wide range of ON derivative concentrations, different peculiar scenarios emerge for different hydrophobicity of the amphiphilic DNA guest molecules on the vesicles, in terms of distribution and conformation of the single strand and consequent coupling properties with the complementary strand in solution.
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Affiliation(s)
- Martina Banchelli
- Department of Chemistry and CSGI, University of Florence, via della Lastruccia 3-Sesto Fiorentino, 50019 Florence, Italy
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31
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Liu H, Zhu Z, Kang H, Wu Y, Sefan K, Tan W. DNA-based micelles: synthesis, micellar properties and size-dependent cell permeability. Chemistry 2010; 16:3791-7. [PMID: 20162643 PMCID: PMC3544201 DOI: 10.1002/chem.200901546] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Functional nanomaterials based on molecular self-assembly hold great promise for applications in biomedicine and biotechnology. However, their efficacy could be a problem and can be improved by precisely controlling the size, structure, and functions. This would require a molecular engineering design capable of producing monodispersed functional materials characterized by beneficial changes in size, shape, and chemical structure. To address this challenge, we have designed and constructed a series of amphiphilic oligonucleotide molecules. In aqueous solutions, the amphiphilic oligonucleotide molecules, consisting of a hydrophilic oligonucleotide covalently linked to hydrophobic diacyllipid tails, spontaneously self-assemble into monodispersed, three-dimensional micellar nanostructures with a lipid core and a DNA corona. These hierarchical architectures are results of intermolecular hydrophobic interactions. Experimental testing further showed that these types of micelles have excellent thermal stability and their size can be fine-tuned by changing the length of the DNA sequence. Moreover, in the micelle system, the molecular recognition properties of DNA are intact, thus, our DNA micelles can hybridize with complimentary sequences while retaining their structural integrity. Importantly, when interacting with cell membranes, the highly charged DNA micelles are able to disintegrate themselves and insert into the cell membrane, completing the process of internalization by endocytosis. Interestingly, the fluorescence was found accumulated in confined regions of cytosole. Finally, we show that the kinetics of this internalization process is size-dependent. Therefore, cell permeability, combined with small sizes and natural nontoxicity are all excellent features that make our DNA-micelles highly suitable for a variety of applications in nanobiotechnology, cell biology, and drug delivery systems.
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Affiliation(s)
- Haipeng Liu
- Center for research at the Bio/Nano Interface, Department of Chemistry Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, USA, Fax: (+1) 352-846-2410
| | - Zhi Zhu
- Center for research at the Bio/Nano Interface, Department of Chemistry Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, USA, Fax: (+1) 352-846-2410
| | - Huaizhi Kang
- Center for research at the Bio/Nano Interface, Department of Chemistry Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, USA, Fax: (+1) 352-846-2410
| | - Yanrong Wu
- Center for research at the Bio/Nano Interface, Department of Chemistry Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, USA, Fax: (+1) 352-846-2410
| | - Kwame Sefan
- Center for research at the Bio/Nano Interface, Department of Chemistry Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, USA, Fax: (+1) 352-846-2410
| | - Weihong Tan
- Center for research at the Bio/Nano Interface, Department of Chemistry Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, USA, Fax: (+1) 352-846-2410
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Banchelli M, Bombelli FB, Berti D, Baglioni P. Chapter 13 - Soft hybrid nanostructures composed of phospholipid liposomes decorated with oligonucleotides. Methods Enzymol 2010; 464:249-77. [PMID: 19903559 DOI: 10.1016/s0076-6879(09)64013-1] [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: 04/23/2023]
Abstract
This chapter reports on the design, preparation, and characterization of liposomes decorated with synthetic lipid-oligonucleotide conjugates. Several key parameters should be considered for a successful preparation of these functional nanostructures that can be employed further as building blocks in DNA-directed assembly of nano-objects. These parameters are reviewed explicitly in this report and their contributions are discussed.
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Affiliation(s)
- Martina Banchelli
- Department of Chemistry and CSGI, University of Florence, Sesto Fiorentino, Florence, Italy
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Barilero T, Le Saux T, Gosse C, Jullien L. Fluorescent Thermometers for Dual-Emission-Wavelength Measurements: Molecular Engineering and Application to Thermal Imaging in a Microsystem. Anal Chem 2009; 81:7988-8000. [DOI: 10.1021/ac901027f] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- T. Barilero
- Ecole Normale Supérieure, Département de Chimie, UMR CNRS-ENS-UPMC Paris 6 8640 Pasteur, 24, Rue Lhomond, 75005 Paris, France, and Laboratoire de Photonique et de Nanostructures, LPN-CNRS, Route de Nozay, 91460 Marcoussis, France
| | - T. Le Saux
- Ecole Normale Supérieure, Département de Chimie, UMR CNRS-ENS-UPMC Paris 6 8640 Pasteur, 24, Rue Lhomond, 75005 Paris, France, and Laboratoire de Photonique et de Nanostructures, LPN-CNRS, Route de Nozay, 91460 Marcoussis, France
| | - C. Gosse
- Ecole Normale Supérieure, Département de Chimie, UMR CNRS-ENS-UPMC Paris 6 8640 Pasteur, 24, Rue Lhomond, 75005 Paris, France, and Laboratoire de Photonique et de Nanostructures, LPN-CNRS, Route de Nozay, 91460 Marcoussis, France
| | - L. Jullien
- Ecole Normale Supérieure, Département de Chimie, UMR CNRS-ENS-UPMC Paris 6 8640 Pasteur, 24, Rue Lhomond, 75005 Paris, France, and Laboratoire de Photonique et de Nanostructures, LPN-CNRS, Route de Nozay, 91460 Marcoussis, France
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Gissot A, Di Primo C, Bestel I, Giannone G, Chapuis H, Barthélémy P. Sensitive liposomes encoded with oligonucleotide amphiphiles: a biocompatible switch. Chem Commun (Camb) 2008:5550-2. [PMID: 18997948 DOI: 10.1039/b812398e] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA-tagged liposomes made of DOPC specifically bind to a fluorescently labelled complementary ss-DNA with virtually no influence from the lipid bilayer despite the absence of a linker; depending on an external stimulus, either physical (temperature) or chemical (competitive complementary ON sequences), the liposomes switch between an on and off fluorescent state depending on the location of the probe either at the surface or in the bulk.
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Affiliation(s)
- Arnaud Gissot
- Université de Bordeaux, 33076 Bordeaux Cedex, France
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Stengel G, Simonsson L, Campbell RA, Höök F. Determinants for Membrane Fusion Induced by Cholesterol-Modified DNA Zippers. J Phys Chem B 2008; 112:8264-74. [DOI: 10.1021/jp802005b] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gudrun Stengel
- Department of Solid State Physics, University of Lund, 22100 Lund, Sweden, and Department of Physical Chemistry, Getingevägen 60, Box 124, 22100 Lund, Sweden
| | - Lisa Simonsson
- Department of Solid State Physics, University of Lund, 22100 Lund, Sweden, and Department of Physical Chemistry, Getingevägen 60, Box 124, 22100 Lund, Sweden
| | - Richard A. Campbell
- Department of Solid State Physics, University of Lund, 22100 Lund, Sweden, and Department of Physical Chemistry, Getingevägen 60, Box 124, 22100 Lund, Sweden
| | - Fredrik Höök
- Department of Solid State Physics, University of Lund, 22100 Lund, Sweden, and Department of Physical Chemistry, Getingevägen 60, Box 124, 22100 Lund, Sweden
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36
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Gissot A, Camplo M, Grinstaff MW, Barthélémy P. Nucleoside, nucleotide and oligonucleotide based amphiphiles: a successful marriage of nucleic acids with lipids. Org Biomol Chem 2008; 6:1324-33. [PMID: 18385837 DOI: 10.1039/b719280k] [Citation(s) in RCA: 139] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Amphiphilic molecules based on nucleosides, nucleotides and oligonucleotides are finding more and more biotechnological applications. This Perspective highlights their synthesis, supramolecular organization as well as their applications in the field of biotechnology.
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Affiliation(s)
- Arnaud Gissot
- Université Victor Segalen, Bordeaux, F-33076, France
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Brodersen N, Li J, Kaczmarek O, Bunge A, Löser L, Huster D, Herrmann A, Liebscher J. Nucleosides with 5′-Fixed Lipid Groups - Synthesis and Anchoring in Lipid Membranes. European J Org Chem 2007. [DOI: 10.1002/ejoc.200700521] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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38
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Estévez-Torres A, Gosse C, Le Saux T, Allemand JF, Croquette V, Berthoumieux H, Lemarchand A, Jullien L. Fourier analysis to measure diffusion coefficients and resolve mixtures on a continuous electrophoresis chip. Anal Chem 2007; 79:8222-31. [PMID: 17892271 DOI: 10.1021/ac070532z] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report a method to measure diffusion coefficients of fluorescent solutes in the 10(2)-10(6) Da molecular mass range in a glass-PDMS chip. Upon applying a permanent electric field, the solute is introduced through a narrow channel into a wide analysis chamber where it migrates along the injection axis and diffuses in two dimensions. The diffusion coefficient is extracted after 1D Fourier transform of the resulting stationary concentration pattern. Analysis is straightforward, requiring no numerical integration or velocity field simulation. The diffusion coefficients measured for fluorescein, rhodamine green-labeled oligonucleotides, and YOYO-1-stained dsDNA fragments agree with the literature values and with our own fluorescence correlation spectroscopy measurements. As shown for 151 and 1257 base pair dsDNA mixtures, the present method allows us to rely on diffusion to quantitatively characterize the nature and the composition of binary mixtures. In particular, we implement a DNA hybridization assay to illustrate the efficiency of the proposed protocol for library screening.
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Affiliation(s)
- A Estévez-Torres
- Ecole Normale Supérieure, Département de Chimie, UMR CNRS ENS Université Paris 6, 8640, 24, rue Lhomond, 75005 Paris, France
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Bunge A, Kurz A, Windeck AK, Korte T, Flasche W, Liebscher J, Herrmann A, Huster D. Lipophilic oligonucleotides spontaneously insert into lipid membranes, bind complementary DNA strands, and sequester into lipid-disordered domains. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2007; 23:4455-64. [PMID: 17367171 DOI: 10.1021/la063188u] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
For the development of surface functionalized bilayers, we have synthesized lipophilic oligonucleotides to combine the molecular recognition mechanism of nucleic acids and the self-assembly characteristics of lipids in planar membranes. A lipophilic oligonucleotide consisting of 21 thymidine units and two lipophilic nucleotides with an alpha-tocopherol moiety as a lipophilic anchor was synthesized using solid-phase methods with a phosphoramadite strategy. The interaction of the water soluble lipophilic oligonucleotide with vesicular lipid membranes and its capability to bind complementary DNA strands was studied using complementary methods such as NMR, EPR, DSC, fluorescence spectroscopy, and fluorescence microscopy. This oligonucleotide inserted stably into preformed membranes from the aqueous phase. Thereby, no significant perturbation of the lipid bilayer and its stability was observed. However, the non-lipidated end of the oligonucleotide is exposed to the aqueous environment, is relatively mobile, and is free to interact with complementary DNA strands. Binding of the complementary single-stranded DNA molecules is fast and accomplished by the formation of Watson-Crick base pairs, which was confirmed by 1H NMR chemical shift analysis and fluorescence resonance energy transfer. The molecular structure of the membrane bound DNA double helix is very similar to the free double-stranded DNA. Further, the membrane bound DNA double strands also undergo regular melting. Finally, in raft-like membrane mixtures, the lipophilic oligonucleotide was shown to preferentially sequester into liquid-disordered membrane domains.
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Affiliation(s)
- Andreas Bunge
- Junior Research Group "Structural Biology of Membrane Proteins", Institute of Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3, D-06120 Halle, Germany
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40
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Spinelli N, Edupuganti OP, Defrancq E, Dumy P. New solid support for the synthesis of 3'-oligonucleotide conjugates through glyoxylic oxime bond formation. Org Lett 2007; 9:219-22. [PMID: 17217269 DOI: 10.1021/ol062607b] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A novel solid support 1 was synthesized to incorporate glyoxylic aldehyde functionality at the oligonucleotide 3'-terminus. 6-mer and 11-mer oligonucleotide sequences containing 3'-glyoxylic aldehyde functionality were prepared by using this support. These modified oligonucleotides were coupled to reporters containing an aminooxy group to prepare oligonucleotide 3'-conjugates through glyoxylic oxime bond formation. The hydrolytic stability of a glyoxylic oxime linkage was also investigated. [reaction: see text].
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Affiliation(s)
- Nicolas Spinelli
- Département de Chimie Moléculaire, UMR CNRS 5250, ICMG FR2607, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 9, France
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Rosemeyer H. Nucleolipids: natural occurrence, synthesis, molecular recognition, and supramolecular assemblies as potential precursors of life and bioorganic materials. Chem Biodivers 2007; 2:977-1063. [PMID: 17193189 DOI: 10.1002/cbdv.200590082] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Nucleolipids are hybrid molecules composed of a nucleobase, a nucleoside, a nucleotide or an oligonucleotide (either DNA or RNA), and a lipophilic moiety, which might be either simply a single- or double-chained alkyl (or alkenyl) moiety or a carbocyclic hydrocarbon such as cholesterol, a vitamin, or a bile acid. This review covers all aspects of nucleolipids, namely their natural occurrence, their synthesis, their molecular recognition, as well as aggregation behavior, either in aqueous or non-aqueous solution. Potential future aspects of nucleolipids in material sciences and for the elucidation of biochemical reactions in living cells are discussed.
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Affiliation(s)
- Helmut Rosemeyer
- Katholieke Universiteit Leuven, Dept. Farmaceutische Wetenschappen, Afd. Medicinale Chemie, Minderbroederstraat 10, B-3000 Leuven.
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Aujard I, Benbrahim C, Gouget M, Ruel O, Baudin JB, Neveu P, Jullien L. o-Nitrobenzyl Photolabile Protecting Groups with Red-Shifted Absorption: Syntheses and Uncaging Cross-Sections for One- and Two-Photon Excitation. Chemistry 2006; 12:6865-79. [PMID: 16763952 DOI: 10.1002/chem.200501393] [Citation(s) in RCA: 230] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We evaluated the o-nitrobenzyl platform for designing photolabile protecting groups with red-shifted absorption that could be photolyzed upon one- and two-photon excitation. Several synthetic pathways to build different conjugated o-nitrobenzyl backbones, as well as to vary the benzylic position, are reported. Relative to the reference 4,5-dimethoxy-2-nitrobenzyl group, several o-nitrobenzyl derivatives exhibit a large and red-shifted one-photon absorption within the near-UV range. Uncaging after one-photon excitation was studied by measuring UV-visible absorption and steady-state fluorescence emission on model caged ethers and esters. In the whole series investigated, the caged substrates were released cleanly upon photolysis. Quantum yields of uncaging after one-photon absorption lie within the 0.1-1 % range. We observed that these drop as the maximum wavelength absorption of the o-nitrobenzyl protecting group is increased. A new method based on fluorescence correlation spectroscopy (FCS) after two-photon excitation was used to measure the action uncaging cross section for two-photon excitation. The series of o-nitrobenzyl caged fluorescent coumarins investigated exhibit values within the 0.1-0.01 Goeppert-Mayer (GM) range. Such results are in line with the low quantum yields of uncaging associated with cross-sections of 1-50 GM for two-photon absorption. Although the cross-sections for one- and two-photon absorption of o-nitrobenzyl photolabile protecting groups can be readily improved, we emphasize the difficulty in enlarging the corresponding action uncaging cross-sections in view of the observed trend of their quantum yield of uncaging.
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Affiliation(s)
- Isabelle Aujard
- Département de Chimie (C.N.R.S. U.M.R. 8640), Ecole Normale Supérieure, 24 rue Lhomond, 75231 Paris Cedex 05, France
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Rohr K, Vogel S. Polyaza Crown Ethers as Non-Nucleosidic Building Blocks in DNA Conjugates: Synthesis and Remarkable Stabilization of dsDNA. Chembiochem 2006; 7:463-70. [PMID: 16508997 DOI: 10.1002/cbic.200500392] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The synthesis of amphiphilic polyaza crown ether monomers X (benzyl-substituted), Y (palmityl-substituted) and Z (cholesteryl-substituted) and their incorporation into oligonucleotides are described. Their effects on thermal duplex stability were investigated by UV melting curve analysis in different alkaline metal buffer solutions. Thermal-denaturation experiments showed remarkable stabilization of dsDNA by polyaza crown ether monomers when incorporated in opposite positions. The series of polyaza crown ether monomers (X, Y and Z) with different overall lipophilicities showed a trend of increased stability of the corresponding dsDNA with increasing lipophilicity of the polyaza crown ether monomer. Multiple incorporations of benzyl-substituted polyaza crown ether monomer X as dangling ends on both sides of dsDNA resulted in strongly increased stability of the corresponding duplex.
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Affiliation(s)
- Katja Rohr
- Nucleic Acid Center, Department of Chemistry, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
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Milani S, Bombelli FB, Berti D, Hauss T, Dante S, Baglioni P. Structural investigation of bilayers formed by 1-palmitoyl-2-oleoylphosphatidylnucleosides. Biophys J 2006; 90:1260-9. [PMID: 16326904 PMCID: PMC1367277 DOI: 10.1529/biophysj.105.067645] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2005] [Accepted: 10/31/2005] [Indexed: 11/18/2022] Open
Abstract
Bilayers of palmitoyl-oleoylphosphatidylnucleoside derivatives (1-palmitoyl-2-oleoyl-phosphatidyl-adenosine and 1-palmitoyl-2-oleoyl-phosphatidyl-uridine) were synthesized and investigated in the low-water content regime by a combination of neutron diffraction and Fourier transform infrared linear dichroism (LD-FTIR). Attention was focused on the modulation of structural properties operated by the presence of nucleic acid bases (either adenosine or uridine, a purine and a pyrimidine that are complementary in RNA). Base substitution causes major differences in phase behavior of the phospholipids, i.e., water sorption from a controlled humidity atmosphere and smectic periodicity. The profile of scattering length density can be inferred from five diffraction orders for 1-palmitoyl-2-oleoyl-phosphatidyl-uridine lamellar phase. 1-Palmitoyl-2-oleoyl-phosphatidyl-adenosine is characterized by lower and less ready hydration, giving rise to a powder-like sample. A linear dichroism FTIR investigation on the same lamellar phases was undertaken with the purpose of gathering details at the submolecular level on different portions of the molecule. 1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayers were also investigated with the same technique for the sake of comparison. Besides a confirmation of the diffraction data interpretation, FTIR has provided evidence that the same chemical groups at the bilayer interface (namely the sugar-phosphate) have a different orientation depending on whether the base is a purine or a pyrimidine. A very simple geometrical optimization agrees with this observation. This indicates that a different pattern of base interaction is operating in the two cases and that base substitution acts as a modulator of the phase properties.
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Affiliation(s)
- Silvia Milani
- Department of Chemistry and CSGI (Consorzio Interuniversitario per lo sviluppo dei Sistemi a Grande Interfase), University of Florence, Florence, Italy
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Charier S, Meglio A, Alcor D, Cogné-Laage E, Allemand JF, Jullien L, Lemarchand A. Reactant Concentrations from Fluorescence Correlation Spectroscopy with Tailored Fluorescent Probes. An Example of Local Calibration-Free pH Measurement. J Am Chem Soc 2005; 127:15491-505. [PMID: 16262413 DOI: 10.1021/ja053909w] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The present account is concerned with the measurement of local reactant concentrations by observing specific fluorescent probes in fluorescence correlation spectroscopy (FCS). The Theoretical Analysis section revisits the photophysical, thermodynamic, and kinetic information that is contained in the corresponding FCS correlation curves. In particular, we examine the conditions under which FCS is revealed as a superior tool to measure concentrations of reactive species. Careful molecular engineering of the specific fluorescent probes that simultaneously integrates photophysical, thermodynamic, and kinetic constraints will be required to benefit most from FCS. We illustrate the FCS titration approach with a series of fluorescent probes that we tailored to measure pH at around 4-6 by FCS after two-photon excitation. We show that an optimal design allows one to access pH without any preliminary calibrations such as the determination of the protonation constant or the photophysical properties of the fluorescent probe.
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Affiliation(s)
- Sandrine Charier
- Département de Chimie (CNRS UMR 8640), Ecole Normale Supérieure, 24 rue Lhomond, 75231 Paris Cedex 05, France
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Alcor D, Allemand JF, Cogné-Laage E, Croquette V, Ferrage F, Jullien L, Kononov A, Lemarchand A. Stochastic Resonance to Control Diffusive Motion in Chemistry. J Phys Chem B 2004; 109:1318-28. [PMID: 16851097 DOI: 10.1021/jp0468307] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This paper reports on a novel procedure to tune the effective diffusion coefficient of a field-sensitive reactant in the presence of a periodic external field. We investigate the motion of two negatively charged azo dyes interacting with alpha-cyclodextrin (alpha-CD) upon action of a periodic square wave electrical field. We show that the dyes exhibit an effective diffusion coefficient D(eff) that depends on the rate constants for dye complexation within alpha-CD, the period and the amplitude of the field. UV-vis absorption, gradient field (1)H NMR, and fluorescence correlation spectroscopy (FCS) after two photon excitation are used to evidence that D(eff) may be increased far beyond its intrinsic value when specific relations interpreted as a stochastic resonance are fulfilled. The present results may find useful applications in chemical kinetics as well as for molecular sorting.
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Affiliation(s)
- Damien Alcor
- Ecole Normale Supérieure, Département de Chimie, C.N.R.S. U.M.R. 8640, 24, rue Lhomond, 75231 Paris Cedex 05, France
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47
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Scheidt HA, Flasche W, Cismas C, Rost M, Herrmann A, Liebscher J, Huster D. Design and Application of Lipophilic Nucleosides as Building Blocks to Obtain Highly Functional Biological Surfaces. J Phys Chem B 2004. [DOI: 10.1021/jp046606h] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Holger A. Scheidt
- Junior Research Group “Solid-state NMR Studies of the Structure of Membrane-associated Proteins”, Biotechnological-Biomedical Center, University of Leipzig, Liebigstr. 27, D-04103 Leipzig, Germany, Institute of Chemistry, Humboldt-University Berlin, Brook-Taylor-Str. 2, D-12489 Berlin, Germany, Institute of Biology/Biophysics, Humboldt-University Berlin, Invalidenstr. 42, D-10115 Berlin, Germany, and Institute of Medical Physics and Biophysics, University of Leipzig, Liebigstr. 27, D-04103 Leipzig, Germany
| | - Wolfgang Flasche
- Junior Research Group “Solid-state NMR Studies of the Structure of Membrane-associated Proteins”, Biotechnological-Biomedical Center, University of Leipzig, Liebigstr. 27, D-04103 Leipzig, Germany, Institute of Chemistry, Humboldt-University Berlin, Brook-Taylor-Str. 2, D-12489 Berlin, Germany, Institute of Biology/Biophysics, Humboldt-University Berlin, Invalidenstr. 42, D-10115 Berlin, Germany, and Institute of Medical Physics and Biophysics, University of Leipzig, Liebigstr. 27, D-04103 Leipzig, Germany
| | - Crina Cismas
- Junior Research Group “Solid-state NMR Studies of the Structure of Membrane-associated Proteins”, Biotechnological-Biomedical Center, University of Leipzig, Liebigstr. 27, D-04103 Leipzig, Germany, Institute of Chemistry, Humboldt-University Berlin, Brook-Taylor-Str. 2, D-12489 Berlin, Germany, Institute of Biology/Biophysics, Humboldt-University Berlin, Invalidenstr. 42, D-10115 Berlin, Germany, and Institute of Medical Physics and Biophysics, University of Leipzig, Liebigstr. 27, D-04103 Leipzig, Germany
| | - Maximilian Rost
- Junior Research Group “Solid-state NMR Studies of the Structure of Membrane-associated Proteins”, Biotechnological-Biomedical Center, University of Leipzig, Liebigstr. 27, D-04103 Leipzig, Germany, Institute of Chemistry, Humboldt-University Berlin, Brook-Taylor-Str. 2, D-12489 Berlin, Germany, Institute of Biology/Biophysics, Humboldt-University Berlin, Invalidenstr. 42, D-10115 Berlin, Germany, and Institute of Medical Physics and Biophysics, University of Leipzig, Liebigstr. 27, D-04103 Leipzig, Germany
| | - Andreas Herrmann
- Junior Research Group “Solid-state NMR Studies of the Structure of Membrane-associated Proteins”, Biotechnological-Biomedical Center, University of Leipzig, Liebigstr. 27, D-04103 Leipzig, Germany, Institute of Chemistry, Humboldt-University Berlin, Brook-Taylor-Str. 2, D-12489 Berlin, Germany, Institute of Biology/Biophysics, Humboldt-University Berlin, Invalidenstr. 42, D-10115 Berlin, Germany, and Institute of Medical Physics and Biophysics, University of Leipzig, Liebigstr. 27, D-04103 Leipzig, Germany
| | - Jürgen Liebscher
- Junior Research Group “Solid-state NMR Studies of the Structure of Membrane-associated Proteins”, Biotechnological-Biomedical Center, University of Leipzig, Liebigstr. 27, D-04103 Leipzig, Germany, Institute of Chemistry, Humboldt-University Berlin, Brook-Taylor-Str. 2, D-12489 Berlin, Germany, Institute of Biology/Biophysics, Humboldt-University Berlin, Invalidenstr. 42, D-10115 Berlin, Germany, and Institute of Medical Physics and Biophysics, University of Leipzig, Liebigstr. 27, D-04103 Leipzig, Germany
| | - Daniel Huster
- Junior Research Group “Solid-state NMR Studies of the Structure of Membrane-associated Proteins”, Biotechnological-Biomedical Center, University of Leipzig, Liebigstr. 27, D-04103 Leipzig, Germany, Institute of Chemistry, Humboldt-University Berlin, Brook-Taylor-Str. 2, D-12489 Berlin, Germany, Institute of Biology/Biophysics, Humboldt-University Berlin, Invalidenstr. 42, D-10115 Berlin, Germany, and Institute of Medical Physics and Biophysics, University of Leipzig, Liebigstr. 27, D-04103 Leipzig, Germany
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