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Condon JE, Jayaraman A. Effect of oligonucleic acid (ONA) backbone features on assembly of ONA-star polymer conjugates: a coarse-grained molecular simulation study. SOFT MATTER 2017; 13:6770-6783. [PMID: 28825068 DOI: 10.1039/c7sm01534h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Understanding the impact of incorporating new physical and chemical features in oligomeric DNA mimics, termed generally as "oligonucleic acids" (ONAs), on their structure and thermodynamics will be beneficial in designing novel materials for a variety of applications. In this work, we conduct coarse-grained molecular simulations of ONA-star polymer conjugates with varying ONA backbone flexibility, ONA backbone charge, and number of arms in the star polymer at a constant ONA strand volume fraction to elucidate the effect of these design parameters on the thermodynamics and assembly of multi-arm ONA-star polymer conjugates. We quantify the thermo-reversible behavior of the ONA-star polymer conjugates by quantifying the hybridization of the ONA strands in the system as a function of temperature (i.e. melting curve). Additionally, we characterize the assembly of the ONA-star polymer conjugates by tracking cluster formation and percolation as a function of temperature, as well as cluster size distribution at temperatures near the assembly transition region. The key results are as follows. The melting temperature (Tm) of the ONA strands decreases upon going from a neutral to a charged ONA backbone and upon increasing flexibility of the ONA backbone. Similar behavior is seen for the assembly transition temperature (Ta) with varying ONA backbone charge and flexibility. While the number of arms in the ONA-star polymer conjugate has a negligible effect on the ONA Tm in these systems, as the number of ONA-star polymer arms increase, the assembly temperature Ta increases and local ordering in the assembled state improves. By understanding how factors like ONA backbone charge, backbone flexibility, and ONA-star polymer conjugate architecture impact the behavior of ONA-star polymer conjugate systems, we can better inform how the selection of ONA chemistry will influence resulting ONA-star polymer assembly.
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Affiliation(s)
- Joshua E Condon
- Department of Chemical and Biomolecular Engineering, Colburn Laboratory, University of Delaware, 150 Academy Street, Newark, DE 19716, USA.
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Qu L, Wu Y, Sun P, Zhang K, Liu Z. Cyclopropenone-masked dibenzocyclooctyne end-functionalized polymers from reversible addition-fragmentation chain transfer polymerization. POLYMER 2017. [DOI: 10.1016/j.polymer.2017.02.071] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Zhang C, Hao L, Calabrese CM, Zhou Y, Choi CHJ, Xing H, Mirkin CA. Biodegradable DNA-Brush Block Copolymer Spherical Nucleic Acids Enable Transfection Agent-Free Intracellular Gene Regulation. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 11:5360-8. [PMID: 26297167 PMCID: PMC4710492 DOI: 10.1002/smll.201501573] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 07/09/2015] [Indexed: 05/25/2023]
Abstract
By grafting multiple DNA strands onto one terminus of a polyester chain, a DNA-brush block copolymer that can assemble into micelle structure is constructed. These micelle spherical nucleic acids have a density of nucleic acids that is substantively higher than linear DNA block copolymer structures, which makes them effective cellular transfection and intracellular gene regulation agents.
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Affiliation(s)
- Chuan Zhang
- Department of Chemistry, International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3113, USA
| | - Liangliang Hao
- Department of Chemistry, International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3113, USA
| | - Colin M. Calabrese
- Department of Chemistry, International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3113, USA
| | - Yu Zhou
- Department of Materials Science and Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3113, USA
| | - Chung Hang J. Choi
- Department of Chemistry, International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3113, USA
| | - Hang Xing
- Department of Chemistry, International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3113, USA
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Vyborna Y, Vybornyi M, Häner R. From Ribbons to Networks: Hierarchical Organization of DNA-Grafted Supramolecular Polymers. J Am Chem Soc 2015; 137:14051-4. [DOI: 10.1021/jacs.5b09889] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Yuliia Vyborna
- Department of Chemistry and
Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Mykhailo Vybornyi
- Department of Chemistry and
Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Robert Häner
- Department of Chemistry and
Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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Vyborna Y, Vybornyi M, Rudnev AV, Häner R. DNA-Grafted Supramolecular Polymers: Helical Ribbon Structures Formed by Self-Assembly of Pyrene-DNA Chimeric Oligomers. Angew Chem Int Ed Engl 2015; 54:7934-8. [DOI: 10.1002/anie.201502066] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 03/31/2015] [Indexed: 12/31/2022]
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Vyborna Y, Vybornyi M, Rudnev AV, Häner R. DNA-Grafted Supramolecular Polymers: Helical Ribbon Structures Formed by Self-Assembly of Pyrene-DNA Chimeric Oligomers. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502066] [Citation(s) in RCA: 7] [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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Sun P, Yan G, Tang Q, Chen Y, Zhang K. Well-defined cyclopropenone-masked dibenzocyclooctyne functionalized polymers from atom transfer radical polymerization. POLYMER 2015. [DOI: 10.1016/j.polymer.2014.10.041] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Kedracki D, Filippov SK, Gour N, Schlaad H, Nardin C. Formation of DNA-Copolymer Fibrils Through an Amyloid-Like Nucleation Polymerization Mechanism. Macromol Rapid Commun 2015; 36:768-73. [DOI: 10.1002/marc.201400728] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 01/19/2015] [Indexed: 12/12/2022]
Affiliation(s)
- Dawid Kedracki
- Department of Inorganic and Analytical Chemistry; University of Geneva; Quai Ernest Ansermet 30, 1211, Geneva 4 Switzerland
| | - Sergey K. Filippov
- Institute of Macromolecular Chemistry; AS CR, Heyrovsky Sq. 2 Prague Prague 6 162 06 Czech Republic
| | - Nidhi Gour
- Department of Inorganic and Analytical Chemistry; University of Geneva; Quai Ernest Ansermet 30, 1211, Geneva 4 Switzerland
| | - Helmut Schlaad
- Institute of Chemistry; University of Potsdam; Karl-Liebknecht-Straße 24-25 14476 Potsdam Germany
- Max Planck Institute of Colloids and Interfaces; Department of Colloid Chemistry; Research Campus Golm; 14424 Potsdam Germany
| | - Corinne Nardin
- Department of Inorganic and Analytical Chemistry; University of Geneva; Quai Ernest Ansermet 30, 1211, Geneva 4 Switzerland
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Kedracki D, Chekini M, Maroni P, Schlaad H, Nardin C. Synthesis and self-assembly of a DNA molecular brush. Biomacromolecules 2014; 15:3375-82. [PMID: 25105945 DOI: 10.1021/bm5008713] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We report herein on the polymer-crystallization-assisted thiol-ene photosynthesis of an amphiphilic comb/graft DNA copolymer, or molecular brush, composed of a hydrophobic poly(2-oxazoline) backbone and hydrophilic short single-stranded nucleic acid grafts. Coupling efficiencies are above 60% and thus higher as compared with the straight solid-phase-supported synthesis of amphiphilic DNA block copolymers. The DNA molecular brushes self-assemble into sub-micron-sized spherical structures in water as evidenced by light scattering as well as atomic force and electron microscopy imaging. The nucleotide sequences remain functional, as assessed by UV and fluorescence spectroscopy subsequent to isoindol synthesis at the surface of the structures. The determination of a vesicular morphology is supported by encapsulation and subsequent spectroscopy monitoring of the release of a water-soluble dye and spectroscopic quantification of the hybridization efficiency (30% in average) of the functional nucleic acid strands engaged in structure formation: about one-half of the nucleotide sequences are available for hybridization, whereas the other half are hindered within the self-assembled structure. Because speciation between complementary and non complementary sequences in the medium could be ascertained by confocal laser scanning microscopy, the stable self-assembled molecular brushes demonstrate the potential for sensing applications.
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Affiliation(s)
- Dawid Kedracki
- Department of Inorganic and Analytical Chemistry and ‡Department of Physical Chemistry, University of Geneva , Quai Ernest Ansermet 30, 1211 Geneva 4, Switzerland
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Yang X, Wang S, Yan Y, Wu Y, Zhang K, Chen Y. Well-defined dibenzocyclooctyne end functionalized polymers from atom transfer radical polymerization. POLYMER 2014. [DOI: 10.1016/j.polymer.2014.01.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Humenik M, Scheibel T. Nanomaterial building blocks based on spider silk-oligonucleotide conjugates. ACS NANO 2014; 8:1342-1349. [PMID: 24405063 DOI: 10.1021/nn404916f] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Self-assembling protein nanofibrils are promising structures for the "bottom-up" fabrication of bionanomaterials. Here, the recombinant protein eADF4(C16), a variant of Araneus diadematus dragline silk ADF4, which self-assembles into nanofibrils, and short oligonucleotides were modified for site-specific azide-alkyne coupling. Corresponding oligonuleotide-eADF4(C16) "click" conjugates were hybridized in linear or branched fashion according to the designed complementarities of the DNA moieties. Self-assembly properties of higher ordered structures of the spider silk-DNA conjugates were dominated by the silk component. Assembled β-sheet rich conjugate fibrils were similar in appearance to fibrils of unmodified eADF4(C16) but enabled the specific attachment of neutravidin-modified gold nanoparticles on their surface directed by complementary biotin-oligonucleotides, providing the basis for functionalization of such conjugates.
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Affiliation(s)
- Martin Humenik
- Lehrstuhl Biomaterialien, Fakultät für Ingenieurwissenschaften, Universität Bayreuth , Universitätsstraße 30, 95440 Bayreuth, Germany
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