Fluorescence Assay for Polymerase Arrival Rates

To engineer complex synthetic biological systems will require modular design, assembly, and characterization strategies. The RNA polymerase arrival rate (PAR) is defined to be the rate that RNA polymerases arrive at a specified location on the DNA. Designing and characterizing biological modules in terms of RNA polymerase arrival rates provides for many advantages in the construction and modeling of biological systems. PARMESAN is an in vitro method for measuring polymerase arrival rates using pyrrolo-dC, a fluorescent DNA base that can substitute for cytosine. Pyrrolo-dC shows a detectable fluorescence difference when in single-stranded versus double-stranded DNA. During transcription, RNA polymerase separates the two strands of DNA, leading to a change in the fluorescence of pyrrolo-dC. By incorporating pyrrolo-dC at specific locations in the DNA, fluorescence changes can be taken as a direct measurement of the polymerase arrival rate.

An Application of Augmented Reality (AR) in the Teaching of an Arc Welding Robot

Augmented Reality (AR) is an emerging technology that utilizes computer vision methods to overlay virtual objects onto the real world scene so as to make them appear to co-exist with the real objects. Its main objective is to enhance the user’s interaction with the real world by providing the right information needed to perform a certain task. Applications of this technology in manufacturing include maintenance, assembly and telerobotics. In this paper, we explore the potential of teaching a robot to perform an arc welding task in an AR environment. We present the motivation, features of a system using the popular ARToolkit package, and a discussion on the issues and implications of our research.

Assembly Design and Evaluation in an Augmented Reality Environment

The technologies and methodologies of assembly design and evaluation in the early design stage are highly significant to product development. This paper looks at a promising technology to mix real components (e.g. physical prototypes, assembly tools, machines, etc.) with virtual components to create an Augmented Reality (AR) interface for assembly process evaluation. The goal of this paper is to clarify the methodologies and enabling technologies of how to establish an AR assembly simulation and evaluation environment. The architecture of an AR assembly system is proposed and the important functional modules including AR environment set-up, design for assembly (DFA) analysis and AR assembly sequence planning in an AR environment are discussed in detail.

Core-Shell Assisted Bimetallic Assembly of Pt and Ru Nanoparticles by DNA Hybridization

We have discovered that the current protocols to assemble Au nanoparticles based on DNA hybridization do not work well with the small metal nanoparticles (e.g. 5 nm Au, 3.6 nm Pt and 3.2 nm Ru particles). Further investigations revealed the presence of strong interaction between the oligonucleotide backbone and the surface of the small metal nanoparticles. The oligonucleotides in this case are recumbent on the particle surface and are therefore not optimally oriented for hybridization. The nonspecific adsorption of oligonucleotides on small metal nanoparticles must be overcome before DNA hybridization can be accepted as a general assembly method. Two methods have been suggested as possible solutions to this problem. One is based on the use of stabilizer molecules which compete with the oligonucleotides for adsorption on the metal nanoparticle surface. Unfortunately, the reported success of this approach in small Au nanoparticles (using K₂BSPP) and Au films (using 6-mercapto-1-hexanol) could not be extended to the assembly of Pt and Ru nanoparticles by DNA hybridization. The second approach is to simply use larger metal particles. Indeed most reports on the DNA hybridization induced assembly of Au nanoparticles have made use of relatively large particles (>10 nm), hinting at a weaker non-specific interaction between the oligonucleotides and large Au nanoparticles. However, most current methods of nanoparticle synthesis are optimized to produce metal nanoparticles only within a narrow size range. We find that core-shell nanoparticles formed by the seeded growth method may be used to artificially enlarge the size of the metal particles to reduce the nonspecific binding of oligonucleotides. We demonstrate herein a core-shell assisted growth method to assemble Pt and Ru nanoparticles by DNA hybridization. This method involves firstly synthesizing approximately 16 nm core-shell Ag-Pt and 21 nm core-shell Au-Ru nanoparticles from 9.6 nm Ag seeds and 17.2 nm Au seeds respectively by the seed-mediated growth method. The core-shell nanoparticles were then functionalized by complementary thiolated oligonucleotides followed by aging in 0.2 M PBS buffer for 6 hours. The DNA hybridization induced bimetallic assembly of Pt and Ru nanoparticles could then be carried out in 0.3 M PBS buffer for 10 hours.