Nanoscale molecular arrayer

The present invention is a dedicated apparatus for the formation of array that includes one or more deposition domains comprised of one or more deposition materials. The present invention may include an X, Y controller, an X, Y translation stage, a loading substrate, a deposition substrate, a Z controller, and a deposition probe. A computer controls all of the relative positions of each of the components. Furthermore, the present invention utilizes a humidity control system to create a capillary bridge between the probe and the substrate for transferring the deposition material between the loading substrate, the deposition probe, and the deposition substrate

Decontamination device and method thereof

One embodiment of a decontamination device for a surface, such as a probe, and method thereof in accordance with the present invention includes a first electrode, a second electrode, and a transformer. The first electrode comprises a housing with an opening and one end of the second electrode is positioned in the opening. The second electrode has an elongated-shape which tapers to a point at the one end adjacent to the opening. The transformer is mounted in the housing and has first and second pairs of leads. One of the second pair of leads is coupled to the first electrode and the other of the second pair of leads is coupled to the second electrode. A surface to be cleaned is placed adjacent to the point and the device is turned on for a preset period of time to generate free radicals, such as ozone plasma, which remove debris build-up on the surface

Formation of novel hairpin structures by telemeric C-strand oligonucleotides

Telomeres are specialized structures at the ends of chromosomes that are required for long term chromosome stability and replication of the chromosomal terminus. Telomeric DNA consists of simple repetitive sequences with one strand G-rich relative to the other, C-rich, strand. Evolutionary conservation of this feature of telomeric repeat sequences suggests that they have specific structural characteristics involved in telomere function. Absorbance thermal denaturation, chemical modification and non-denaturing gel electrophoretic analyses showed that telomeric C-strand oligonucIeotides form stable non-Watson-Crick hairpin structures containing C.C + base pairs.Formation of such hairpins may facilitate previously reported G-strand exclusive interactions

Programmable DNA Nanosystem for Molecular Interrogation

We describe a self-assembling DNA-based nanosystem for interrogating molecular interactions. The nanosystem contains a rigid supporting dumbbell-shaped frame, a cylindrical central core, and a mobile ring that is coaxial with the core. Motion of the ring is influenced by several control elements whose force-generating capability is based on the transition of single-stranded DNA to double-stranded DNA. These forces can be directed to act in opposition to adhesive forces between the ring and the frame thereby providing a mechanism for molecular detection and interrogation at the ring-frame interface. As proof of principle we use this system to evaluate base stacking adhesion and demonstrate detection of a soluble nucleic acid viral genome mimic

Complex DNA Nanostructures from Oligonucleotide Ensembles

The first synthetic DNA nanostructures were created by self-assembly of a small number of oligonucleotides. Introduction of the DNA origami method provided a new paradigm for designing and creating two- and three-dimensional DNA nanostructures by folding a large single-stranded DNA and ‘stapling’ it together with a library of oligonucleotides. Despite its power and wide-ranging implementation, the DNA origami technique suffers from some limitations. Foremost among these is the limited number of useful single-stranded scaffolds of biological origin. This report describes a new approach to creating large DNA nanostructures exclusively from synthetic oligonucleotides. The essence of this approach is to replace the single-stranded scaffold in DNA origami with a library of oligonucleotides termed “scaples” (scaffold staples). Scaples eliminate the need for scaffolds of biological origin and create new opportunities for producing larger and more diverse DNA nanostructures as well as simultaneous assembly of distinct structures in a “single-pot” reaction

G-Wires: Self-Assembly of a Telomeric Oligonucleotide, d(GGGGTTGGGG), into Large Superstructures

The telomeric DNA oligonucleotide 5’-G4T~G4-3’ (Tet 1.5) spontaneously assembles into large superstructures we have termed G-wires. G-wires can be resolved by gel electrophoresis as a ladder pattern. The self-association of Tet 1.5 is noncovalent and exhibits characteristics of G4-DNA, a parallel fourstranded structure stabilized by guanine tetrads. Formation of G-wires is dependent upon the presence of Na+ and/or K+, and once formed, G-wires are resistant to denaturation. The results described here extend our understanding of the structural potential of G-rich nucleic acids and may provide insight into the possible roles of G-rich sequences and the novel structures they can form in biological systems

Method for solid state genome analysis

The invention is a solid state process for analyzing genomes by visualizing sequence specific markers (e.g., proteins that bind a defined DNA sequence elements) by scanning probe microscopy. The method includes linear display of the nucleic acid on a solid surface, image acquisition by the scanning probe microscope, and digital data analysis. The acts of the method result in a bar code type display of each fragment of the DNA sample. These bar codes are then used to place the fragments in the order they appear on the original DNA sample

Evaluating binding affinities by force stratification and force panning

The present invention is a method for selectively removing objects from a surface utilizing a probe. The probe is scanned over the surface utilizing a greater and greater relative amount of force so that a certain number of the objects are removed from the surface. The force required to remove the objects from the surface can be calculated utilizing Hook\u27s law and the spring constant of the probe. After removal of the objects that have a relatively weaker binding affinity with the surface, the remaining objects can be harvested, characterized, and subjected to further study

Pieces of nilpotent cones for classical groups

We compare orbits in the nilpotent cone of type $B_n$, that of type $C_n$, and Kato's exotic nilpotent cone. We prove that the number of \F_q-points in each nilpotent orbit of type $B_n$ or $C_n$ equals that in a corresponding union of orbits, called a type-$B$ or type-$C$ piece, in the exotic nilpotent cone. This is a finer version of Lusztig's result that corresponding special pieces in types $B_n$ and $C_n$ have the same number of \F_q-points. The proof requires studying the case of characteristic 2, where more direct connections between the three nilpotent cones can be established. We also prove that the type-$B$ and type-$C$ pieces of the exotic nilpotent cone are smooth in any characteristic.Comment: 32 page

Tip Reconstruction for the Atomic Force Microscope

Colloidal gold particles are used as hard, spherical imaging targets to assist in the reconstruction of the three-dimensional atomic force probe geometry. The mathematical model for this reconstruction is developed, and a solution is proposed. The voracity of the probe reconstruction depends on image noise and numerical derivative approximations