27 research outputs found
Progress toward "Click"-based Small-molecule DNA Hybrids Part II: Di- and Tri-functionalized Core
Square-Planar Pd(II), Pt(II), and Au(III) Terpyridine Complexes: Their Syntheses, Physical Properties, Supramolecular Constructs, and Biomedical Activities
Cooperative Melting in Caged Dimers with Only Two DNA Duplexes
Small molecule−DNA hybrids with only two parallel DNA duplexes (rSMDH2) displayed sharper melting profiles compared to unmodified DNA duplexes, consistent with predictions from neighboring-duplex theory. Using adjusted thermodynamic parameters obtained from a coarse-grain dynamic simulation, the experimental data fit well to an analytical model
Hydrophobic Organic Linkers in the Self-Assembly of Small Molecule-DNA Hybrid Dimers: A Computational–Experimental Study of the Role of Linkage Direction in Product Distributions and Stabilities
Detailed
computational and experimental studies reveal the crucial
role that hydrophobic interactions play in the self-assembly of small
molecule-DNA hybrids (SMDHs) into cyclic nanostructures. In aqueous
environments, the distribution of the cyclic structures (dimers or
higher-order structures) greatly depends on how well the hydrophobic
surfaces of the organic cores in these nanostructures are minimized.
Specifically, when the cores are attached to the 3′-ends of
the DNA component strands, they can insert into the minor groove of
the duplex that forms upon self-assembly, favoring the formation of
cyclic dimers. However, when the cores are attached to the 5′-ends
of the DNA component strands, such insertion is hindered, leading
to the formation of higher-order cyclic structures. These computational
insights are supported by experimental results that show clear differences
in product distributions and stabilities for a broad range of organic
core-linked DNA hybrids with different linkage directions and flexibilities
Enhancing the Melting Properties of Small Molecule-DNA Hybrids through Designed Hydrophobic Interactions: An Experimental-Computational Study
Detailed experimental and computational studies revealed
the important
role that hydrophobic interactions play in the aqueous assembly of
rigid small molecule-DNA hybrid (rSMDH) building blocks into nanoscale
cage and face-to-face (ff) dimeric structures. In aqueous environments,
the hydrophobic surfaces of the organic cores in these nanostructures
are minimized by interactions with the core in another rSMDHs, with
the bases in the attached DNA strands, and/or with the base pairs
in the final assembled structures. In the case that the hydrophobic
surfaces of the cores could not be properly isolated in the assembly
process, an ill-defined network results instead of dimers, even at
low concentration of DNA. In contrast, if ff dimers can be formed
with good minimization of the exposed hydrophobic surfaces of the
cores, they are highly stable structures with enhanced melting temperatures
and cooperative melting behavior
Hydrophobic Organic Linkers in the Self-Assembly of Small Molecule-DNA Hybrid Dimers: A Computational–Experimental Study of the Role of Linkage Direction in Product Distributions and Stabilities
Detailed
computational and experimental studies reveal the crucial
role that hydrophobic interactions play in the self-assembly of small
molecule-DNA hybrids (SMDHs) into cyclic nanostructures. In aqueous
environments, the distribution of the cyclic structures (dimers or
higher-order structures) greatly depends on how well the hydrophobic
surfaces of the organic cores in these nanostructures are minimized.
Specifically, when the cores are attached to the 3′-ends of
the DNA component strands, they can insert into the minor groove of
the duplex that forms upon self-assembly, favoring the formation of
cyclic dimers. However, when the cores are attached to the 5′-ends
of the DNA component strands, such insertion is hindered, leading
to the formation of higher-order cyclic structures. These computational
insights are supported by experimental results that show clear differences
in product distributions and stabilities for a broad range of organic
core-linked DNA hybrids with different linkage directions and flexibilities
Successful Stabilization of Graphene Oxide in Electrolyte Solutions: Enhancement of Biofunctionalization and Cellular Uptake
Aqueous dispersions of graphene oxide are inherently unstable in the presence of electrolytes, which screen the electrostatic surface charge on these nanosheets and induce irreversible aggregation. Two complementary strategies, utilizing either electrostatic or steric stabilization, have been developed to enhance the stability of graphene oxide in electrolyte solutions, allowing it to stay dispersed in cell culture media and serum. The electrostatic stabilization approach entails further oxidation of graphene oxide to low C/O ratio (∼1.1) and increases ionic tolerance of these nanosheets. The steric stabilization technique employs an amphiphilic block copolymer that serves as a noncovalently bound surfactant to minimize the aggregate-inducing nanosheet–nanosheet interactions. Both strategies can stabilize graphene oxide nanosheets with large dimensions (>300 nm) in biological media, allowing for an enhancement of >250% in the bioconjugation efficiency of streptavidin in comparison to untreated nanosheets. Notably, both strategies allow the stabilized nanosheets to be readily taken up by cells, demonstrating their excellent performance as potential drug-delivery vehicles
The Significance of Multivalent Bonding Motifs and Bond Order in DNA-Directed Nanoparticle Crystallization
Directed Assembly of Nucleic Acid-Based Polymeric Nanoparticles from Molecular Tetravalent Cores
Complementary
tetrahedral small molecule-DNA hybrid (SMDH) building
blocks have been combined to form nucleic acid-based polymeric nanoparticles
without the need for an underlying template or scaffold. The sizes
of these particles can be tailored in a facile fashion by adjusting
assembly conditions such as SMDH concentration, assembly time, and
NaCl concentration. Notably, these novel particles can be stabilized
and transformed into functionalized spherical nucleic acid (SNA) structures
through the incorporation of capping DNA strands conjugated with functional
groups. These results demonstrate a systematic, efficient strategy
for the construction and surface functionalization of well-defined,
size-tunable nucleic acid particles from readily accessible molecular
building blocks. Furthermore, because these nucleic acid-based polymeric
nanoparticles exhibited enhanced cellular internalization and resistance
to DNase I compared to free synthetic nucleic acids, they should have
a plethora of applications in diagnostics and therapeutics