Kurt V. Gothelf

Self-assembly of a nanoscale DNA box with a controllable lid

The unique structural motifs and self-recognition properties of DNA can be exploited to generate self-assembling DNA nanostructures of specific shapes using a ‘bottom-up’ approach. Several assembly strategies have been developed for building complex three-dimensional (3D) DNA nanostructures. Recently, the DNA ‘origami’ method was used to build two-dimensional addressable DNA structures of arbitrary shape that can be used as platforms to arrange nanomaterials with high precision and specificity. A long-term goal of this field has been to construct fully addressable 3D DNA nanostructures. Here we extend the DNA origami method into three dimensions by creating an addressable DNA box 42 × 36 × 36 nm3 in size that can be opened in the presence of externally supplied DNA ‘keys’. We thoroughly characterize the structure of this DNA box using cryogenic transmission electron microscopy, small-angle X-ray scattering and atomic force microscopy, and use fluorescence resonance energy transfer to optically monitor the opening of the lid. Controlled access to the interior compartment of this DNA nanocontainer could yield several interesting applications, for example as a logic sensor for multiple-sequence signals or for the controlled release of nanocargos.

Single-molecule chemical reactions on DNA origami

DNA nanotechnology and particularly DNA origami, in which long, single-stranded DNA molecules are folded into predetermined shapes, can be used to form complex self-assembled nanostructures. Although DNA itself has limited chemical, optical or electronic functionality, DNA nanostructures can serve as templates for building materials with new functional properties. Relatively large nanocomponents such as nanoparticles and biomolecules can also be integrated into DNA nanostructures and imaged. Here, we show that chemical reactions with single molecules can be performed and imaged at a local position on a DNA origami scaffold by atomic force microscopy. The high yields and chemoselectivities of successive cleavage and bond-forming reactions observed in these experiments demonstrate the feasibility of post-assembly chemical modification of DNA nanostructures and their potential use as locally addressable solid supports.

DNA origami: a quantum leap for self-assembly of complex structures

The spatially controlled positioning of functional materials by self-assembly is one of the fundamental visions of nanotechnology. Major steps towards this goal have been achieved using DNA as a programmable building block. This tutorial review will focus on one of the most promising methods: DNA origami. The basic design principles, organization of a variety of functional materials and recent implementation of DNA robotics are discussed together with future challenges and opportunities.

DNA-programmed assembly of nanostructures

DNA is a unique material for nanotechnology since it is possible to use base sequences to encode instructions for assembly in a predetermined fashion at the nanometre scale. Synthetic oligonucleotides are readily obtained by automated synthesis and numerous techniques have been developed for conjugating DNA with other materials. The exact spatial positioning of materials is crucial for the future development of complex nanodevices and the emerging field of DNA-nanotechnology is now exploring DNA-programmed processes for the assembly of organic compounds, biomolecules, and inorganic materials.

Toward reliable gold nanoparticle patterning on self-assembled DNA nanoscaffold

Assembly of gold nanoparticles (AuNP) into designer architectures with reliablity is important for nanophotonics and nanoelectronics applications. Toward this goal we present a new strategy to prepare AuNPs monofunctionalized with lipoic acid modified DNA oligos. This strategy offers increased bonding strength between DNA oligos and AuNP surface. These conjugates are further selectively mixed with other DNA strands and assembled into fixed sized DNA nanostructures carring a discrete number of AuNPs at desired positions. Atomic force microscopy imaging reveals a dramatically improved yield of the AuNPs on DNA tile structure compared to the ensembles using monothiolate AuNP-DNA conjugates.

DNA Origami Design of Dolphin-Shaped Structures with Flexible Tails

The DNA origami method allows the folding of long, single-stranded DNA sequences into arbitrary two-dimensional structures by a set of designed oligonucleotides. The method has revealed an unexpected strength and efficiency for programmed self-assembly of molecular nanostructures and makes it possible to produce fully addressable nanostructures with wide-reaching application potential within the emerging area of nanoscience. Here we present a user-friendly software package for designing DNA origami structures ( http://www.cdna.dk/origami ) and demonstrate its use by the design of a dolphin-like DNA origami structure that was imaged by high-resolution AFM in liquid. The software package provides automatic generation of DNA origami structures, manual editing, interactive overviews, atomic models, tracks the design history, and has a fully extendable toolbox. From the AFM images, it was demonstrated that different designs of the dolphin tail region provided various levels of flexibility in a predictable fashion. Finally, we show that the addition of specific attachment sites promotes dimerization between two independently self-assembled dolphin structures, and that these interactions stabilize the flexible tail.

Catalytic Enantioselective Addition of Nitro Compounds to Imines—A Simple Approach for the Synthesis of Optically Active β-Nitro-α-Amino Esters†

The catalytic and asymmetric nitro-Mannich reaction of nitro compounds to α-imino esters catalyzed by chiral bisoxazoline-copper complexes [Eq. (1); Pg = protecting group] gave β-nitro-α-amino esters with excellent diastereo- and enantioselectivities. The reactions can be performed under ambient conditions.

A DNA tweezer-actuated enzyme nanoreactor

The functions of regulatory enzymes are essential to modulating cellular pathways. Here we report a tweezer-like DNA nanodevice to actuate the activity of an enzyme/cofactor pair. A dehydrogenase and NAD(+) cofactor are attached to different arms of the DNA tweezer structure and actuation of enzymatic function is achieved by switching the tweezers between open and closed states. The enzyme/cofactor pair is spatially separated in the open state with inhibited enzyme function, whereas in the closed state, enzyme is activated by the close proximity of the two molecules. The conformational state of the DNA tweezer is controlled by the addition of specific oligonucleotides that serve as the thermodynamic driver (fuel) to trigger the change. Using this approach, several cycles of externally controlled enzyme inhibition and activation are successfully demonstrated. This principle of responsive enzyme nanodevices may be used to regulate other types of enzymes and to introduce feedback or feed-forward control loops.

Single-step rapid assembly of DNA origami nanostructures for addressable nanoscale bioreactors.

Self-assembled DNA origami nanostructures have shown great promise for bottom-up construction of complex objects with nanoscale addressability. Here we show that DNA origami-based 1D nanoribbons and nanotubes are one-pot assembled with controllable sizes and nanoscale addressability with high speed (within only 10-20 min), exhibiting extraordinarily high cooperativity that is often observed in assembly of natural molecular machines in cells (e.g. ribosome). By exploiting the high specificity of DNA-based self-assembly, we can precisely anchor proteins on these DNA origami nanostructures with sub-10 nm resolution and at the single-molecule level. We attach a pair of enzymes (horseradish peroxidase and glucose oxidase) at the inner side of DNA nanotubes and observe high coupling efficiency of enzyme cascade within this confined nanospace. Hence, DNA nanostructures with such unprecedented properties shed new light on the design of nanoscale bioreactors and nanomedicine and provide an artificial system for studying enzyme activities and cascade in highly organized and crowded cell-mimicking environments.

RNA Aptamer-Based Electrochemical Biosensor for Selective and Label-Free Analysis of Dopamine

The inherent redox activity of dopamine enables its direct electrochemical in vivo analysis ( Venton , B. J.; Wightman, M. R. Anal. Chem. 2003, 75, 414A). However, dopamine analysis is complicated by the interference from other electrochemically active endogenous compounds present in the brain, including dopamine precursors and metabolites and other neurotransmitters (NT). Here we report an electrochemical RNA aptamer-based biosensor for analysis of dopamine in the presence of other NT. The biosensor exploits a specific binding of dopamine by the RNA aptamer, immobilized at a cysteamine-modified Au electrode, and further electrochemical oxidation of dopamine. Specific recognition of dopamine by the aptamer allowed a selective amperometric detection of dopamine within the physiologically relevant 100 nM to 5 μM range in the presence of competitive concentrations of catechol, epinephrine, norepinephrine, 3,4-dihydroxy-phenylalanine (L-DOPA), 3,4-dihydroxyphenylacetic acid (DOPAC), methyldopamine, and tyramine, which gave negligible signals under conditions of experiments (electroanalysis at 0.185 V vs Ag/AgCl). The interference from ascorbic and uric acids was eliminated by application of a Nafion-coated membrane. The aptasensor response time was <1 s, and the sensitivity of analysis was 62 nA μM(-1) cm(-2). The proposed design of the aptasensor, based on electrostatic interactions between the positively charged cysteamine-modified electrode and the negatively charged aptamer, may be used as a general strategy not to restrict the conformational freedom and binding properties of surface-bound aptamers and, thus, be applicable for the development of other aptasensors.