9 research outputs found
Reprogramming the assembly of unmodified DNA with a small molecule
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 âalphabetâ 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 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
The Role of Organic Linkers in Directing DNA Self-Assembly and Significantly Stabilizing DNA Duplexes
We show a simple method to control both the stability
and the self-assembly
behavior of DNA structures. By connecting two adjacent duplexes with
small synthetic linkers, factors such as linker rigidity and DNA strand
orientation can increase the thermal denaturation temperature of 17
base-pair duplexes by up to 10 °C, and significantly increase
the cooperativity of melting of the two duplexes. The same DNA sequence
can thus be tuned to melt at vastly different temperatures by selecting
the linker structure and DNA-to-linker connectivity. In addition,
a small rigid <i>m</i>-triphenylene linker directly affects
the self-assembly product distribution. With this linker, changes
in the orientation of the linked strands (e.g., 5âČ3âČ
vs 3âČ3âČ) can lead to dramatic changes in the self-assembly
behavior, from the formation of cyclic dimer and tetramer to higher-order
oligomers. These variations can be readily predicted using a simple
strand-end alignment model
DNA nanostructures prevent the formation of and convert toxic amyloid proteospecies into cytocompatible and biodegradable spherical complexes
Abstract The deposition of insoluble proteinaceous aggregates in the form of amyloid fibrils within the extracellular space of tissues is associated with numerous diseases. The development of molecular approaches to arrest amyloid formation and prevent cellular degeneration remains very challenging due to the complexity of the process of protein aggregation, which encompasses an infinite array of conformations and quaternary structures. Polyanionic biopolymers, such as glycosaminoglycans and RNAs, have been shown to modulate the selfâassembly of amyloidogenic polypeptides and to reduce the toxicity induced by the formation of oligomeric and/or preâfibrillar proteospecies. This study evaluates the effects of doubleâstranded DNA (dsDNA) nanostructures (1D, 2D, and 3D) on amyloid selfâassembly, fibril disaggregation, and the cytotoxicity associated with amyloidogenesis. Using the islet amyloid polypeptide (IAPP) whose pancreatic accumulation is the hallmark of type 2 diabetes, it was observed that dsDNA nanostructures inhibit amyloid formation by inducing the formation of spherical complexes in which the peptide adopts a random coil conformation. Interestingly, the DNA nanostructures showed a persistent ability to disassemble enzymatically and thermodynamically stable amyloid fibrils into nanoscale DNA/IAPP entities that are fully compatible with ÎČâpancreatic cells and are biodegradable by proteolysis. Notably, dsDNA nanostructures avidly trapped highly toxic soluble oligomeric species in complete cell culture media and converted them into nonâtoxic binary complexes. Overall, these results expose the potent modulatory effects of dsDNA on amyloidogenic pathways, and these DNA nanoscaffolds could be used as a source of inspiration for the design of molecules to fight amyloidârelated disorders
Intercalators as Molecular Chaperones in DNA Self-Assembly
DNA intercalation has found many
diagnostic and therapeutic applications.
Here, we propose the use of simple DNA intercalators, such as ethidium
bromide, as tools to facilitate the error-free self-assembly of DNA
nanostructures. We show that ethidium bromide can influence DNA self-assembly,
decrease the formation of oligomeric side products, and cause libraries
of multiple equilibrating structures to converge into a single product.
Using a variety of 2D- and 3D-DNA systems, we demonstrate that intercalators
present a powerful alternative for the adjustment of strand-end alignment,
favor the formation of fully duplexed âclosedâ structures,
and create an environment where the smallest, most stable structure
is formed. A new 3D-DNA motif, the ninja star, was self-assembled
in quantitative yield with this method. Moreover, ethidium bromide
can be readily removed using isoamyl alcohol extractions combined
with intercalator-specific spin columns, thereby yielding the desired
ready-to-use DNA structure
Controlled Growth of DNA Structures From Repeating Units Using the Vernier Mechanism
In
this report, we demonstrate the assembly of length-programmed
DNA nanostructures using a single 16 base sequence and its complement
as building blocks. To achieve this, we applied the Vernier mechanism
to DNA assembly, which uses a mismatch in length between two monomers
to dictate the final length of the product. Specifically, this approach
relies on the interaction of two DNA strands containing a different
number (<i>n</i>, <i>m</i>) of complementary binding
sites: these two strands will keep binding to each other until they
come into register, thus generating a larger assembly whose length
(<i>n</i> Ă <i>m</i>) is encoded by the number
of binding sites in each strand. While the Vernier mechanism has been
applied to other areas of supramolecular chemistry, here we present
an application of its principles to DNA nanostructures. Using a single
16 base repeat and its complement, and varying the number of repeats
on a given DNA strand, we show the consistent construction of duplexes
up to 228 base pairs (bp) in length. Employing specific annealing
protocols, strand capping, and intercalator chaperones allows us to
further grow the duplex to 392 base pairs. We demonstrate that the
Vernier method is not only strand-efficient, but also produces a cleaner,
higher-yielding product than conventional designs
Modulation of Charge Transport Across Double-Stranded DNA by the Site-Specific Incorporation of Copper Bis-Phenanthroline Complexes
The site-specific incorporation of
transition-metal complexes within
DNA duplexes, followed by their immobilization on a gold surface,
was studied by electrochemistry to characterize their ability to mediate
charge. Cyclic voltammetry, square-wave voltammetry, and control experiments
were carried out on fully matched and mismatched DNA strands that
are mono- or bis-labeled with transition-metal complexes. These experiments
are all consistent with the ability of the metal centers to act as
a redox probe that is well coupled to the DNA Ï-stack, allowing
DNA-mediated charge transport