Program - Symposium NN: DNA Nanotechnology

The structural plasticity and tunable interactions provided by selectively interacting DNA chains offer a broad range of possibilities to direct the organization of nanoscale objects into well defined systems, as well as to regulate the structural transformations on demand. We have studied the assembly of clusters and 3D architectures from nanoscale components of multiple types driven by DNA recognition. Our work explores how DNA-encoded interactions between inorganic nano-components can guide the formation of well-defined superlattices, how the morphology of self-organized structures can be regulated in-situ, and what molecular factors govern a phase behavior. The role of flexible chains, particle anisotropy, and external stimuli on a structure formation and its transformation will be discussed in details. Our recent progress on the assembly of particle arrays into designed symmetries, and realizations of switchable and tunable superlattices in 3D and 2D will be presented. Research is supported by the U.S. DOE Office of Science and Office of Basic Energy Sciences under contract No. DE-AC-02-98CH10886.

Many researchers are interested in developing methods for rationally assembling nanoparticle building blocks into periodic lattices. These high-order structures could, in principle, be used to create designer materials with unique properties, useful in material synthesis, optics, biomedicine, energy, and catalysis. For certain applications, it is necessary to control the orientation and placement of such assemblies on surfaces. Herein, we present a DNA-based strategy for achieving epitaxial growth of nanoparticle thin film superlattices. DNA is an ideal ligand for the programmable assembly of nanoparticles, as synthetically tunable variations in nucleotide structure allow for precise engineering of the nanoparticle hydrodynamic radius with nanometer scale precision in addition to the coordination environment. These factors, in turn, dictate the crystallographic structure, symmetry and lattice parameters of the assembly. By employing a DNA-functionalized surface, we show that thin film superlattices of DNA-functionalized nanoparticles can be grown in a layer-by-layer fashion, while maintaining registry with the underlying substrate. We describe DNA coordination environments that govern the crystallographic orientation of the superlattice with respect to the substrate and show fine control of the number of particle layers in the assembly (i.e., film thickness). We also present a theoretical understanding of the assembly process. Importantly, these nanoparticle superlattices can be patterned at arbitrary locations on a substrate using molecular printing techniques such as dip-pen nanolithography (DPN) and polymer pen lithography (PPL). The principles developed in this work represent a major advance in the bottom-up synthesis of nanomaterials and a major step towards the integration of nanoscale materials into functional device architectures.

The ability of noble metal nanostructures to translate local chemical information into a macroscopic optical signal has been used in numerous biosensing schemes: surface plasmon resonance (SPR) spectroscopy, colorimetric sensing or plasmon rulers. In order to design gold nanostructures with an optical response sensitive to one DNA strand, we assemble a particle dimer on a single dynamic DNA template exhibiting a specific recognition site. Electrophoretic purification allows us to observe the step-by-step assembly of the two-dimensional DNA scaffold on 8 nm diameter gold particles. The molecular template includes a stem-loop in order to switch its shape reversibly when binding to a target DNA strand. The two sides of the dimer are hybridized together before a second electrophoretic purification step which indicates that opening the stem-loop induces a clear increase of the dimer hydrodynamic volume. Inter-particle distances are estimated in cryo-electron microscopy in order to analyze the dimer topology without drying effects or particle-substrate interactions. In order to translate the dynamic shape switching of a single DNA scaffold in a measurable optical signal, we need to optimize the scattering cross-section and the plasmon coupling of the dimer by increasing the particle diameters. We recently demonstrated that polyethylene glycol stabilized gold particles with diameters of 27 or 36 nm that are conjugated to a single DNA strand as short as 10 nm can be purified by electrophoresis [1]. This result is obtained by effectively lengthening the DNA strand during the purification process with several 100 bases long molecules, hybridized to each other over 15 base pairs. Static dimers with substantial scattering cross-sections and plasmon coupling are then readily obtained after hybridization of complementary DNA strands. The optical properties of single groupings, inserted in microfluidic chambers, are studied by confocal scattering spectroscopy. Shortening the DNA linker induces a clear red shift of the plasmon resonance wavelength. A statistical analysis of scattering spectra is performed over dozens of dimers and correlated with cryo-electron microscopy images. This analysis indicates that the particle dimers are stretched by electrostatic interactions in buffer solutions with low ionic strengths [1]. Preliminary results on 36 nm gold particle dimers linked by a dynamic DNA strand demonstrate that opening and closing a 48 bases long stem-loop induces a reversible resonance wavelength shift of the order of 20 nm. These results open up numerous perspectives on the design of plasmon-based nanostructures with single molecule sensitivity. [1] M. P. Busson et al, Nano Lett. (2011), DOI: 10.1021/nl2032052

In structural DNA nanotechnology, DNA molecules are used to build novel nanoscale structures and devices. Taking advantage of the programmability of DNA based self-assembly, a diverse range of potential applications has emerged. We have used DNA nanostructures to spatially organize various photonic elements to achieve controlled energy transfer. We recently demonstrated DNA templated construction of a series of structurally well-defined light harvesting complexes, each with several different chromophores organized similar to natural light harvesting antenna. We also showed that quantum dots (QDs) with emissions spanning the entire UV-visible to near infrared spectrum can be precisely assembled on DNA nanostructures. Finally, through DNA templated assembly we showed that distance dependent plasmonic interactions between metal nanoparticles and fluorescent molecules can be systematically studied.

Self-assembly methods have shown promise for the fabrication of complex structures with extremely small feature sizes. DNA origami, in particular, provides a simple method for designing shapes in the sub-100-nm regime. The DNA origami technique can produce a wide variety of two-dimensional, as well as three-dimensional, structures by folding a long single-stranded DNA “scaffold” into a designed shape with the use of a large number of shorter “staple” DNA strands. A distinct advantage of DNA origami is that the staple strands can be adjusted to engineer site-specific attachment points throughout the structure by extending staple strands with additional nucleotides and hybridizing these “sticky ends” with a complementary sequence containing the desired functionality. Here we have used the ability to modify specific locations on the DNA to develop a method of fabricating electrically conductive nanowires from DNA origami templates. We have accomplished this by extending staple strands on our DNA origami in regions where we would like metallization. DNA modified gold nanoparticles are combined with the origami to allow base-paired attachment of the nanoparticles to the extended staple strands. Subsequent electroless plating increases the particle size until the gaps between neighboring particles are filled and a continuous nanowire is formed. In our process we have improved upon previously reported DNA origami metallization methods in at least three ways. 1) Our branched DNA origami structure allows for considerably longer wires than previously reported; 2) we have achieved a high gold nanoparticle seed density (median particle to particle gap size of 4.1 nm), which permits the fabrication of continuous metal structures of very small size; and 3) we have used electrical measurements to verify the conductivity of the DNA origami nanowires following the metallization process.

One-dimensional DNA nanofibers can be used as building blocks in bionanotechnology devices. So far, such structures have been produced by bottom-up self-assembly methods in discontinuous format. Continuous 100% DNA nanofibers were produced in this work using top-down electrospinning method. Nanofiber diameters were varied in the range from 50-500 nanometers by changing process parameters. Individual nanofibers were mechanically tested through failure using specially developed testing protocol. Significant improvement of nanofiber strength was observed with the decrease of nanofiber diameter while strain at failure remained constant within the experimental error. Stress-strain curves of individual nanofibers exhibited inverse S-shape and the toughness of DNA nanofibers far exceeded the toughness of the best structural fibers such as carbon or Kevlar and approached the toughness of spider silks. In addition to the double stranded (ds) DNA, nanofibers from single stranded (ss) DNA solutions were also prepared by a modified process. Mechanical testing of the ssDNA nanofibers exhibited qualitatively different scaling. In particular, strain at failure of the ssDNA nanofilaments increased with the decrease of their diameter. The highest strength values were on the par with structural polymer fibers strengths while toughness far exceeded structural fiber performance. The measured nanofiber strength also exceeded the published single DNA molecule strength by 4.5 times. Short range structural studies confirmed the conformational differences between the dsDNA and ssDNA nanofibers and the source DNA. Raman spectra revealed shifts of sugar-phosphate backbone and basepair vibrations peaks indicating possible transformations from B to A and Z duplexes in the dsDNA and ssDNA nanofibers. The observed unusual high mechanical performance of DNA nanofilaments, coupled with the recently demonstrated possibility to precision-assembly nanofilaments into controlled 1D, 2D, and 3D constructs, open up new exciting opportunities in DNA nanotechnology.

DNA-origami is a recently developed method to construct DNA nanostructures of arbitrary shape and property. The understanding of the mechanical behavior of nanostructures assembled by this technique is crucial for their application as rigid mechanical mediators or force sensing elements. We used magnetic tweezers that support direct force and torque measurements to determine the bending and torsional rigidities of four- and six-helical bundles of defined length. The bending rigidity was found to increase about 15-fold and 38-fold for 4-helix bundles and 6-helix bundles compared to double-strand DNA, respectively. In contrast, the torsional rigidity increased only 4-fold and 5.5-fold for 4-helix bundles and 6-helix bundles. We present a mechanical model explicitly including the crossovers between the individual helices in the origami structure that can describe the difference between bending and twisting mechanics of 3D DNA origami. We also show how the multi-helical structures can be rigidly attached to surfaces, which is an important prerequisite to effectively use their rigid properties in future nanomechanical applications.

Because it can be created inexpensively with atomic precision, DNA is an ideal candidate for a metrology standard. The force necessary to overstretch a double-stranded DNA molecule has been measured in a fashion traceable to the International System of Units, and provides an absolute calibration reference for atomic and molecular-scale force measurements. Details of the calibration and uncertainty analysis will be discussed, as will strategies for its use for calibration of a variety of small force measurment platforms.

A strand displacement-based system has been developed that substitutes inosine for guanosine in DNA sequences called “zippers”. Each zipper sequence employs traditional adenosine-thymine bonding as well as non-traditional inosine-cytidine bonding. The I-C bond consists of only 2 hydrogen bonds as opposed to the typical 3 hydrogen bonds found in G-C bonds. A zipper helix consists of one strand with A and C and a second strand with complementary I and T nucleotides. The second strand is displaced by the introduction of a strand with G and T nucleotides complementary to the first strand. These zippers can be introduced as an active element in larger DNA devices and be designed to be used in different situations. The first example is of zippers incorporated into single and double “spring” systems. The springs incorporate in such a manner that allow them be repeatedly extended and reset. Multiple springs can be incorporated into larger 2D and 3D DNA structures, allowing them to change between conformations on demand. Zippers can also be incorporated into a gating system for ion channels such as hemolysin and DNA tethered to a larger nanoparticle and passing through the hemolysin channel. Zippers at the end of such a strand could lock the DNA strand in place, effectively allowing the nanoparticle to block the channel on the other side. Finally DNA zippers have not been properly characterized by quantitative measurements yet. AFM or optical trap studies can be performed to study the binding energy of a zipper sequence.

We report a DNA zipper based actuator device termed ‘DNA- spring’ with tunable and repeated cycles of extension and contraction ability. DNA zipper is a double-stranded DNA system engineered to open upon its specific interaction with appropriately designed single strand DNA (ssDNA), opening of the zipper is driven by binding energy differences between the DNA strands. The zipper system is incorporated with defined modifications to function like a spring, capable of delivering ~9 pN force over a distance of ~13 nm, producing ~116 kJ/mol of work. Time-lapse fluorescence and fluorescent DNA gel electrophoresis analysis is utilized to evaluate and confirm the spring action. A second zipper incorporated into the spring provides the ability to couple/decouple to an object/substrate. Such devices would have wide application, including for conditionally triggered molecular delivery systems and as actuators in nano-devices.