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Lacroix A, Edwardson TGW, Hancock MA, Dore MD, Sleiman HF. Development of DNA Nanostructures for High-Affinity Binding to Human Serum Albumin. J Am Chem Soc 2017; 139:7355-7362. [DOI: 10.1021/jacs.7b02917] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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52
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Danis AS, Odette WL, Perry SC, Canesi S, Sleiman HF, Mauzeroll J. Cuvette-Based Electrogenerated Chemiluminescence Detection System for the Assessment of Polymerizable Ruthenium Luminophores. ChemElectroChem 2017. [DOI: 10.1002/celc.201600879] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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53
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Dai Z, Gao Q, Cheung MC, Leung HM, Lau TCK, Sleiman HF, Lai KWC, Lo PK. A highly versatile platform based on geometrically well-defined 3D DNA nanostructures for selective recognition and positioning of multiplex targets. NANOSCALE 2016; 8:18291-18295. [PMID: 27775745 DOI: 10.1039/c6nr05411k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We develop a versatile recognition system based on 3D triangular-shaped DNA nanotubes by integrating three different aptamer sequences along the three edges. This would allow multiple binding activities to be combined into a single system. The versatility of this nanotube platform can also provide a framework for spatial orientation and positioning of different aptamer-binding ligands in a 'pea-pod' architecture.
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54
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Bujold KE, Hsu JCC, Sleiman HF. Optimized DNA “Nanosuitcases” for Encapsulation and Conditional Release of siRNA. J Am Chem Soc 2016; 138:14030-14038. [PMID: 27700075 DOI: 10.1021/jacs.6b08369] [Citation(s) in RCA: 153] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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55
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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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56
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Lau KL, Sleiman HF. Minimalist Approach to Complexity: Templating the Assembly of DNA Tile Structures with Sequentially Grown Input Strands. ACS NANO 2016; 10:6542-6551. [PMID: 27303951 DOI: 10.1021/acsnano.6b00134] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Given its highly predictable self-assembly properties, DNA has proven to be an excellent template toward the design of functional materials. Prominent examples include the remarkable complexity provided by DNA origami and single-stranded tile (SST) assemblies, which require hundreds of unique component strands. However, in many cases, the majority of the DNA assembly is purely structural, and only a small "working area" needs to be aperiodic. On the other hand, extended lattices formed by DNA tile motifs require only a few strands; but they suffer from lack of size control and limited periodic patterning. To overcome these limitations, we adopt a templation strategy, where an input strand of DNA dictates the size and patterning of resultant DNA tile structures. To prepare these templating input strands, a sequential growth technique developed in our lab is used, whereby extended DNA strands of defined sequence and length may be generated simply by controlling their order of addition. With these, we demonstrate the periodic patterning of size-controlled double-crossover (DX) and triple-crossover (TX) tile structures, as well as intentionally designed aperiodicity of a DX tile structure. As such, we are able to prepare size-controlled DNA structures featuring aperiodicity only where necessary with exceptional economy and efficiency.
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57
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Fakhoury JJ, Edwardson TG, Conway JW, Trinh T, Khan F, Barłóg M, Bazzi HS, Sleiman HF. Correction: Antisense precision polymer micelles require less poly(ethylenimine) for efficient gene knockdown. NANOSCALE 2016; 8:10453. [PMID: 27126130 DOI: 10.1039/c6nr90089e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Correction for 'Antisense precision polymer micelles require less poly(ethylenimine) for efficient gene knockdown' by Johans J. Fakhoury, et al., Nanoscale, 2015, 7, 20625-20634.
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58
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Chidchob P, Edwardson TGW, Serpell CJ, Sleiman HF. Synergy of Two Assembly Languages in DNA Nanostructures: Self-Assembly of Sequence-Defined Polymers on DNA Cages. J Am Chem Soc 2016; 138:4416-25. [PMID: 26998893 DOI: 10.1021/jacs.5b12953] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA base-pairing is the central interaction in DNA assembly. However, this simple four-letter (A-T and G-C) language makes it difficult to create complex structures without using a large number of DNA strands of different sequences. Inspired by protein folding, we introduce hydrophobic interactions to expand the assembly language of DNA nanotechnology. To achieve this, DNA cages of different geometries are combined with sequence-defined polymers containing long alkyl and oligoethylene glycol repeat units. Anisotropic decoration of hydrophobic polymers on one face of the cage leads to hydrophobically driven formation of quantized aggregates of DNA cages, where polymer length determines the cage aggregation number. Hydrophobic chains decorated on both faces of the cage can undergo an intrascaffold "handshake" to generate DNA-micelle cages, which have increased structural stability and assembly cooperativity, and can encapsulate small molecules. The polymer sequence order can control the interaction between hydrophobic blocks, leading to unprecedented "doughnut-shaped" DNA cage-ring structures. We thus demonstrate that new structural and functional modes in DNA nanostructures can emerge from the synergy of two interactions, providing an attractive approach to develop protein-inspired assembly modules in DNA nanotechnology.
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59
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Avakyan N, Greschner AA, Aldaye F, Serpell CJ, Toader V, Petitjean A, Sleiman HF. Reprogramming the assembly of unmodified DNA with a small molecule. Nat Chem 2016; 8:368-76. [PMID: 27001733 DOI: 10.1038/nchem.2451] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 01/07/2016] [Indexed: 02/08/2023]
Abstract
The ability of DNA to store and encode information arises from base pairing of the four-letter nucleobase code to form a double helix. Expanding this DNA 'alphabet' by synthetic incorporation of new bases can introduce new functionalities and enable the formation of novel nucleic acid structures. However, reprogramming the self-assembly of existing nucleobases presents an alternative route to expand the structural space and functionality of nucleic acids. Here we report the discovery that a small molecule, cyanuric acid, with three thymine-like faces, reprogrammes the assembly of unmodified poly(adenine) (poly(A)) into stable, long and abundant fibres with a unique internal structure. Poly(A) DNA, RNA and peptide nucleic acid (PNA) all form these assemblies. Our studies are consistent with the association of adenine and cyanuric acid units into a hexameric rosette, which brings together poly(A) triplexes with a subsequent cooperative polymerization. Fundamentally, this study shows that small hydrogen-bonding molecules can be used to induce the assembly of nucleic acids in water, which leads to new structures from inexpensive and readily available materials.
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60
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Edwardson TGW, Lau KL, Bousmail D, Serpell CJ, Sleiman HF. Transfer of molecular recognition information from DNA nanostructures to gold nanoparticles. Nat Chem 2016; 8:162-70. [PMID: 26791900 DOI: 10.1038/nchem.2420] [Citation(s) in RCA: 172] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Accepted: 11/13/2015] [Indexed: 12/22/2022]
Abstract
DNA nanotechnology offers unparalleled precision and programmability for the bottom-up organization of materials. This approach relies on pre-assembling a DNA scaffold, typically containing hundreds of different strands, and using it to position functional components. A particularly attractive strategy is to employ DNA nanostructures not as permanent scaffolds, but as transient, reusable templates to transfer essential information to other materials. To our knowledge, this approach, akin to top-down lithography, has not been examined. Here we report a molecular printing strategy that chemically transfers a discrete pattern of DNA strands from a three-dimensional DNA structure to a gold nanoparticle. We show that the particles inherit the DNA sequence configuration encoded in the parent template with high fidelity. This provides control over the number of DNA strands and their relative placement, directionality and sequence asymmetry. Importantly, the nanoparticles produced exhibit the site-specific addressability of DNA nanostructures, and are promising components for energy, information and biomedical applications.
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61
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de Rochambeau D, Barłóg M, Edwardson TGW, Fakhoury JJ, Stein RS, Bazzi HS, Sleiman HF. “DNA–Teflon” sequence-controlled polymers. Polym Chem 2016. [DOI: 10.1039/c6py00532b] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Efficient automated synthesis of sequence-controlled “DNA–Teflon” polymers with potential drug delivery and bioimaging applications.
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62
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Fakhoury JJ, Edwardson TG, Conway JW, Trinh T, Khan F, Barłóg M, Bazzi HS, Sleiman HF. Antisense precision polymer micelles require less poly(ethylenimine) for efficient gene knockdown. NANOSCALE 2015; 7:20625-20634. [PMID: 26597764 DOI: 10.1039/c5nr05157f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Therapeutic nucleic acids are powerful molecules for shutting down protein expression. However, their cellular uptake is poor and requires transport vectors, such as cationic polymers. Of these, poly(ethylenimine) (PEI) has been shown to be an efficient vehicle for nucleic acid transport into cells. However, cytotoxicity has been a major hurdle in the development of PEI-DNA complexes as clinically viable therapeutics. We have synthesized antisense-polymer conjugates, where the polymeric block is completely monodisperse and sequence-controlled. Depending on the polymer sequence, these can self-assemble to produce micelles of very low polydispersity. The introduction of linear poly(ethylenimine) to these micelles leads to aggregation into size-defined PEI-mediated superstructures. Subsequently, both cellular uptake and gene silencing are greatly enhanced over extended periods compared to antisense alone, while at the same time cellular cytotoxicity remains very low. In contrast, gene silencing is not enhanced with antisense polymer conjugates that are not able to self-assemble into micelles. Thus, using antisense precision micelles, we are able to achieve significant transfection and knockdown with minimal cytotoxicity at much lower concentrations of linear PEI then previously reported. Consequently, a conceptual solution to the problem of antisense or siRNA delivery is to self-assemble these molecules into 'gene-like' micelles with high local charge and increased stability, thus reducing the amount of transfection agent needed for effective gene silencing.
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63
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Rahbani JF, Hariri AA, Cosa G, Sleiman HF. Dynamic DNA Nanotubes: Reversible Switching between Single and Double-Stranded Forms, and Effect of Base Deletions. ACS NANO 2015; 9:11898-11908. [PMID: 26556531 DOI: 10.1021/acsnano.5b04387] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
DNA nanotubes hold great potential as drug delivery vehicles and as programmable templates for the organization of materials and biomolecules. Existing methods for their construction produce assemblies that are entirely double-stranded and rigid, and thus have limited intrinsic dynamic character, or they rely on chemically modified and ligated DNA structures. Here, we report a simple and efficient synthesis of DNA nanotubes from 11 short unmodified strands, and the study of their dynamic behavior by atomic force microscopy and in situ single molecule fluorescence microscopy. This method allows the programmable introduction of DNA structural changes within the repeat units of the tubes. We generate and study fully double-stranded nanotubes, and convert them to nanotubes with one, two and three single-stranded sides, using strand displacement strategies. The nanotubes can be reversibly switched between these forms without compromising their stability and micron-scale lengths. We then site-specifically introduce DNA strands that shorten two sides of the nanotubes, while keeping the length of the third side. The nanotubes undergo bending with increased length mismatch between their sides, until the distortion is significant enough to shorten them, as measured by AFM and single-molecule fluorescence photobleaching experiments. The method presented here produces dynamic and robust nanotubes that can potentially behave as actuators, and allows their site-specific addressability while using a minimal number of component strands.
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64
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Castor KJ, Metera KL, Tefashe UM, Serpell CJ, Mauzeroll J, Sleiman HF. Cyclometalated Iridium(III) Imidazole Phenanthroline Complexes as Luminescent and Electrochemiluminescent G-Quadruplex DNA Binders. Inorg Chem 2015; 54:6958-67. [PMID: 26125314 DOI: 10.1021/acs.inorgchem.5b00921] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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65
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Hamblin GD, Rahbani JF, Sleiman HF. Sequential growth of long DNA strands with user-defined patterns for nanostructures and scaffolds. Nat Commun 2015; 6:7065. [DOI: 10.1038/ncomms8065] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 03/25/2015] [Indexed: 02/07/2023] Open
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66
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Hariri AA, Hamblin GD, Gidi Y, Sleiman HF, Cosa G. Stepwise growth of surface-grafted DNA nanotubes visualized at the single-molecule level. Nat Chem 2015; 7:295-300. [DOI: 10.1038/nchem.2184] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Accepted: 01/15/2015] [Indexed: 11/09/2022]
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67
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Serpell CJ, Edwardson TGW, Chidchob P, Carneiro KMM, Sleiman HF. Precision Polymers and 3D DNA Nanostructures: Emergent Assemblies from New Parameter Space. J Am Chem Soc 2014; 136:15767-74. [PMID: 25325677 DOI: 10.1021/ja509192n] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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68
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Greschner AA, Bujold KE, Sleiman HF. Controlled Growth of DNA Structures From Repeating Units Using the Vernier Mechanism. Biomacromolecules 2014; 15:3002-8. [PMID: 24964288 DOI: 10.1021/bm500613s] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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69
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Edwardson TGW, Carneiro KMM, Serpell CJ, Sleiman HF. Titelbild: An Efficient and Modular Route to Sequence-Defined Polymers Appended to DNA (Angew. Chem. 18/2014). Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201401123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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70
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Edwardson TGW, Carneiro KMM, Serpell CJ, Sleiman HF. An Efficient and Modular Route to Sequence-Defined Polymers Appended to DNA. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201310937] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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71
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Edwardson TGW, Carneiro KMM, Serpell CJ, Sleiman HF. An efficient and modular route to sequence-defined polymers appended to DNA. Angew Chem Int Ed Engl 2014; 53:4567-71. [PMID: 24677769 DOI: 10.1002/anie.201310937] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Indexed: 01/01/2023]
Abstract
Inspired by biological polymers, sequence-controlled synthetic polymers are highly promising materials that integrate the robustness of synthetic systems with the information-derived activity of biological counterparts. Polymer-biopolymer conjugates are often targeted to achieve this union; however, their synthesis remains challenging. We report a stepwise solid-phase approach for the generation of completely monodisperse and sequence-defined DNA-polymer conjugates using readily available reagents. These polymeric modifications to DNA display self-assembly and encapsulation behavior-as evidenced by HPLC, dynamic light scattering, and fluorescence studies-which is highly dependent on sequence order. The method is general and has the potential to make DNA-polymer conjugates and sequence-defined polymers widely available.
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72
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Lau KL, Hamblin GD, Sleiman HF. Gold nanoparticle 3D-DNA building blocks: high purity preparation and use for modular access to nanoparticle assemblies. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:660-666. [PMID: 24115591 DOI: 10.1002/smll.201301562] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 07/12/2013] [Indexed: 06/02/2023]
Abstract
Using highly functional 'building-blocks' of AuNPs mono-conjugated to three-dimensional DNA 'rung' structures, both discrete and extended linear assemblies are controllably prepared via addition of various templating backbone strands. This unique approach presents a facile alternative to other methods of AuNP organization through DNA, and has potential utility in the fields of nanophotonics and nanoelectronics.
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73
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Bujold KE, Fakhoury J, Edwardson TGW, Carneiro KMM, Briard JN, Godin AG, Amrein L, Hamblin GD, Panasci LC, Wiseman PW, Sleiman HF. Sequence-responsive unzipping DNA cubes with tunable cellular uptake profiles. Chem Sci 2014. [DOI: 10.1039/c4sc00646a] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Here, we demonstrate a new approach for the design and assembly of a dynamic DNA cube with an addressable cellular uptake profile.
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74
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Fakhoury JJ, McLaughlin CK, Edwardson TW, Conway JW, Sleiman HF. Development and Characterization of Gene Silencing DNA Cages. Biomacromolecules 2013; 15:276-82. [DOI: 10.1021/bm401532n] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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75
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Castor KJ, Liu Z, Fakhoury J, Hancock MA, Mittermaier A, Moitessier N, Sleiman HF. A platinum(II) phenylphenanthroimidazole with an extended side-chain exhibits slow dissociation from a c-Kit G-quadruplex motif. Chemistry 2013; 19:17836-45. [PMID: 24249701 DOI: 10.1002/chem.201301590] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Revised: 09/16/2013] [Indexed: 01/05/2023]
Abstract
A series of three platinum(II) phenanthroimidazoles each containing a protonable side-chain appended from the phenyl moiety through copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) were evaluated for their capacities to bind to human telomere, c-Myc, and c-Kit derived G-quadruplexes. The side-chain has been optimized to enable a multivalent binding mode to G-quadruplex motifs, which would potentially result in selective targeting. Molecular modeling, high-throughput fluorescence intercalator displacement (HT-FID) assays, and surface plasmon resonance (SPR) studies demonstrate that complex 2 exhibits significantly slower dissociation rates compared to platinum phenanthroimidazoles without side-chains and other reported G-quadruplex binders. Complex 2 showed little cytotoxicity in HeLa and A172 cancer cell lines, consistent with the fact that it does not follow a telomere-targeting pathway. Preliminary mRNA analysis shows that 2 specifically interacts with the ckit promoter region. Overall, this study validates 2 as a useful molecular probe for c-Kit related cancer pathways.
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