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

Discovery of Associated Absorption Lines in an X-Ray Warm Absorber: Hubble Space Telescope Faint Object Spectrograph Observations of MR 2251–178

The presence of a "warm absorber" was first suggested to explain spectral variability in an X-ray spectrum of the radio-quiet quasi-stellar object (QSO) MR 2251-178. A unified picture, in which X-ray warm absorbers and "intrinsic" UV absorbers are the same, offers the opportunity to probe the nuclear environment of active galactic nuclei. To test this scenario and understand the physical properties of the absorber, we obtained a UV spectrum of MR 2251-178 with the Faint Object Spectrograph on board the Hubble Space Telescope (HST). The HST spectrum clearly shows absorption due to Lyα, N V, and C IV, blueshifted by 300 km s^-1 from the emission redshift of the QSO. The rarity of both X-ray and UV absorbers in radio-quiet QSOs suggests these absorbers are physically related, if not identical. Assuming the unified scenario, we place constraints on the physical parameters of the absorber and conclude the mass outflow rate is essentially the same as the accretion rate in MR 2251-178

Automated requirements analysis for a molecular watchdog timer

Dynamic systems in DNA nanotechnology are often programmed using a chemical reaction network (CRN) model as an intermediate level of abstraction. In this paper, we design and analyze a CRN model of a watchdog timer, a device commonly used to monitor the health of a safety critical system. Our process uses incremental design practices with goal-oriented requirements engineering, software verification tools, and custom software to help automate the software engineering process. The watchdog timer is comprised of three components: an absence detector, a threshold filter, and a signal amplifier. These components are separately designed and verified, and only then composed to create the molecular watchdog timer. During the requirements-design iterations, simulation, model checking, and analysis are used to verify the system. Using this methodology several incomplete requirements and design flaws were found, and the final verified model helped determine specific parameters for biological experiments

Black Ring Deconstruction

We present a sample microstate for a black ring in four and five dimensional language. The microstate consists of a black string microstate with an additional D6-brane. We show that with an appropriate choice of parameters the piece involving the black string microstate falls down a long AdS throat, whose M-theory lift is AdS_3 X S^2. We wrap a spinning dipole M2-brane on the S^2 in the probe approximation. In IIA, this corresponds to a dielectric D2-brane carrying only D0-charge. We conjecture this is the first approximation to a cloud of D0-branes blowing up due to their non-abelian degrees of freedom and the Myers effect.Comment: 10 pages, 2 figure