Search

We studied the directed self-assembly of two types of complementary single-stranded DNA (ssDNA) strands [i.e., poly(dA) and poly(dT)] into more complex, organized, and percolating networks in dilute solutions and at surfaces. Understanding ssDNA self-assembly into 2D networks on surfaces is important for the use of such networks in the fabrication of well-defined nanotechnological devices, as, for instance, required in nanoelectronics or for biosensing. To control the formation of 2D networks on surfaces, it is important to know whether DNA assemblies are formed already in dilute solutions or only during the drying/immobilization process at the surface, where the concentration automatically increases. Fluorescence cross-correlation spectroscopy clearly shows the presence of larger DNA complexes in mixed poly(dA) and poly(dT) solutions already at very low DNA concentrations (<1 nM), that is, well below the overlap concentration. Here, we describe for the first time such supramolecular complexes in solution and how their structure depends on the ssDNA length and concentration and ionic strength. Hence, future attempts to control such networks should also focus on network precursors in solution and not only on their immobilization on surfaces.

Combining surface-initiated, TdT (terminal deoxynucleotidyl transferase) catalyzed enzymatic polymerization (SI-TcEP) with precisely engineered DNA origami nanostructures (DONs) presents an innovative pathway for the generation of stable, polynucleotide brush-functionalized DNA nanostructures. We demonstrate that SI-TcEP can site-specifically pattern DONs with brushes containing both natural and non-natural nucleotides. The brush functionalization can be precisely controlled in terms of the location of initiation sites on the origami core and the brush height and composition. Coarse-grained simulations predict the conformation of the brush-functionalized DONs that agree well with the experimentally observed morphologies. We find that polynucleotide brush-functionalization increases the nuclease resistance of DONs significantly, and that this stability can be spatially programmed through the site-specific growth of polynucleotide brushes. The ability to site-specifically decorate DONs with brushes of natural and non-natural nucleotides provides access to a large range of functionalized DON architectures that would allow for further supramolecular assembly, and for potential applications in smart nanoscale delivery systems., (© 2021 Wiley-VCH GmbH.)

Understanding of how to integrate DNA molecules with graphene materials is important for the development of biosensors and biomolecular logic circuits. For some of these applications, controlling DNA structural conformation on the graphene substrate is critically important and can be achieved through the use of self-assembled monolayers. Here, we performed all-atom molecular dynamics simulations to understand how various 1-octadecylamine (ODA) coatings of the graphene surface affect the conformation of double-stranded DNA (dsDNA) on the surface. The simulation results demonstrated that dsDNA structures become more stable as ODA concentration increases due to the formation of DNA-ODA hydrogen bonds and reduction of DNA-surface interactions, which aid in retaining internal DNA interactions. Specifically, the interaction of ODA molecules with DNA prevents nucleobases from forming π-π stacking interactions with the surface. Some dsDNA conformations, such as sharp kinks or unwinding, can occur more frequently in DNA with A-T sequences due to weaker pairing interactions than with G-C sequences. Furthermore, our results conclude that both DNA sequence and ODA concentration play an essential role in experimentally observed conformational changes of DNA on the graphene surface.

The recognition that nucleic acids can be used as polymeric materials led to the blossoming of the field of DNA nanotechnology, with a broad range of applications in biotechnology, biosensors, diagnostics, and drug delivery. These applications require efficient methods to synthesize and chemically modify high molecular weight DNA. Here, we discuss terminal deoxynucleotidyl transferase (TdT)-catalyzed enzymatic polymerization (TcEP) as an alternative to conventional enzymatic and solid-phase DNA synthesis. We describe biochemical requirements for TcEP and provide step-by-step protocols to carry out TcEP in solution and from surfaces., (© 2019 Elsevier Inc. All rights reserved.)

We demonstrate the reversible micellar aggregation of a DNA-azobenzene conjugate in aqueous conditions, in which the photoisomerization of the initially apolar trans-azobenzene moiety to the polar cis isomer causes disassembly of the aggregates. The molecular basis for this phenomena is a change in the hydrophobic/hydrophilic balance of the conjugate as the more polar cis azobenzene isomer is formed upon exposure to 365 nm irradiation. The conjugates were prepared by copper-free Click chemistry between an azide-modified, 53-base ssDNA and a cyclooctyne derivative of azobenzene. The photocontrolled aggregation of the conjugate was studied by dynamic light scattering and atomic force microscopy. The reversible micellar aggregation for a DNA-azobenzene conjugate has not been previously reported and holds promise for photocontrolled drug delivery applications., (Copyright © 2015 Elsevier B.V. All rights reserved.)

This review focuses on surface-grafted DNA, and its use as a molecular building block that exploits its unique properties as a directional (poly)anion that exhibits molecular recognition. The selected examples highlight innovative applications of DNA at surfaces and interfaces ranging from molecular diagnostics and sequencing to biosensing.

Nucleic acid nanostructures are useful as templates for bionanofabrication of composite molecular nanostructures in materials science, molecular electronics, and biosensing. Here, we demonstrate that terminal deoxynucleotidyl transferase, which repetitively adds mononucleotides to the 3' end of a short DNA initiator, can be used to rapidly fabricate DNA nanostructures up to 121 nm high with lateral dimensions from 0.1 to 4 mum in 2 h. These programmable scaffolds can potentially be employed to build more complex nanostructures consisting of natural or unnatural nucleotides with selective docking sites along the single-stranded DNA.

We present terminal deoxynucleotidyl transferase-catalyzed enzymatic polymerization (TcEP) for the template-free synthesis of high-molecular-weight, single-stranded DNA (ssDNA) and demonstrate that it proceeds by a living chain-growth polycondensation mechanism. We show that the molecular weight of the reaction products is nearly monodisperse, and can be manipulated by the feed ratio of nucleotide (monomer) to oligonucleotide (initiator), as typically observed for living polymerization reactions. Understanding the synthesis mechanism and the reaction kinetics enables the rational, template-free synthesis of ssDNA that can be used for a range of biomedical and nanotechnology applications. [ABSTRACT FROM AUTHOR]