Nucleotide exchange and excision technology (NExT) DNA shuffling: a robust method for DNA fragmentation and directed evolution

DNA shuffling is widely used for optimizing complex properties contained within DNA and proteins. Demonstrated here is the amplification of a gene library by PCR using uridine triphosphate (dUTP) as a fragmentation defining exchange nucleotide with thymidine, together with the three other nucleotides. The incorporated uracil bases were excised using uracil-DNA-glycosylase and the DNA backbone subsequently cleaved with piperidine. These end-point reactions required no adjustments. Polyacrylamide urea gels demonstrated adjustable fragmentation size over a wide range. The oligonucleotide pool was reassembled by internal primer extension to full length with a proofreading polymerase to improve yield over Taq. We present a computer program that accurately predicts the fragmentation pattern and yields all possible fragment sequences with their respective likelihood of occurrence, taking the guesswork out of the fragmentation. The technique has been demonstrated by shuffling chloramphenicol acetyltransferase gene libraries. A 33% dUTP PCR resulted in shuffled clones with an average parental fragment size of 86 bases even without employment of a fragment size separation, and revealed a low mutation rate (0.1%). NExT DNA fragmentation is rational, easily executed and reproducible, making it superior to other techniques. Additionally, NExT could feasibly be applied to several other nucleotide analogs

Structure and Stability of Si(114)-(2x1)

We describe a recently discovered stable planar surface of silicon, Si(114). This high-index surface, oriented 19.5 degrees away from (001) toward (111), undergoes a 2x1 reconstruction. We propose a complete model for the reconstructed surface based on scanning tunneling microscopy images and first-principles total-energy calculations. The structure and stability of Si(114)-(2x1) arises from a balance between surface dangling bond reduction and surface stress relief, and provides a key to understanding the morphology of a family of surfaces oriented between (001) and (114).Comment: REVTeX, 4 pages + 3 figures. A preprint with high-resolution figures is available at http://cst-www.nrl.navy.mil/papers/si114.ps . To be published in Phys. Rev. Let

Para to Ortho transition of metallic dimers on Si(001)

Extensive electronic structure calculations are performed to obtain the stable geometries of metals like Al, Ga and In on the Si(001) surface at 0.5 ML and 1 ML coverages. Our results coupled with previous theoretical findings explain the recent experimental data in a comprehensive fashion. At low coverages, as shown by previous works, `Para' dimers give the lowest energy structure. With increasing coverage beyond 0.5 ML, `Ortho' dimers become part of low energy configurations leading toward a `Para' to `Ortho' transition at 1 ML coverage. For In mixed staggered dimers (`Ortho' and `Para') give the lowest energy configuration. For Ga, mixed dimers are non-staggered, while for Al `Para' to `Ortho' transition of dimers is complete. Thus at intermediate coverages between 0.5 and 1 ML, the `Ortho' and `Para' dimers may coexist on the surface. Consequently, this may be an explanation of the fact that the experimental observations can be successfully interpreted using either orientation. A supported zigzag structure at 0.5 ML, which resembles ${\rm (CH)_x}$, does not undergo a dimerization transition, and hence stays semi-metallic. Also, unlike ${\rm (CH)_x}$ the soliton formation is ruled out for this structure.Comment: 8 pages, 6 figure

Telecom networking with a diamond quantum memory

Practical quantum networks require interfacing quantum memories with existing channels and systems that operate in the telecom band. Here we demonstrate low-noise, bidirectional quantum frequency conversion that enables a solid-state quantum memory to directly interface with telecom-band systems. In particular, we demonstrate conversion of visible-band single photons emitted from a silicon-vacancy (SiV) center in diamond to the telecom O-band, maintaining low noise ($g^2(0)<0.1$) and high indistinguishability ($V=89\pm8\%$). We further demonstrate the utility of this system for quantum networking by converting telecom-band time-bin pulses, sent across a lossy and noisy 50 km deployed fiber link, to the visible band and mapping their quantum states onto a diamond quantum memory with fidelity $\mathcal{F}=87\pm 2.5 \%$. These results demonstrate the viability of SiV quantum memories integrated with telecom-band systems for scalable quantum networking applications.Comment: 9 pages, 5 figures + Supplemental Material

Integrating Signals from the T-Cell Receptor and the Interleukin-2 Receptor

T cells orchestrate the adaptive immune response, making them targets for immunotherapy. Although immunosuppressive therapies prevent disease progression, they also leave patients susceptible to opportunistic infections. To identify novel drug targets, we established a logical model describing T-cell receptor (TCR) signaling. However, to have a model that is able to predict new therapeutic approaches, the current drug targets must be included. Therefore, as a next step we generated the interleukin-2 receptor (IL-2R) signaling network and developed a tool to merge logical models. For IL-2R signaling, we show that STAT activation is independent of both Src- and PI3-kinases, while ERK activation depends upon both kinases and additionally requires novel PKCs. In addition, our merged model correctly predicted TCR-induced STAT activation. The combined network also allows information transfer from one receptor to add detail to another, thereby predicting that LAT mediates JNK activation in IL-2R signaling. In summary, the merged model not only enables us to unravel potential cross-talk, but it also suggests new experimental designs and provides a critical step towards designing strategies to reprogram T cells

Synthesis and characterization of naphthalimide-functionalized polynorbornenes

ABSTRACT: Highly fluorescent and photostable (2-alkyl)-1H-benzo[de]isoquinoline-1,3(2H)-diones with a polymerizable norbornene scaffold have been synthesized and polymerized using ring-opening metathesis polymerization. The monomers presented herein could be polymerized in a living fashion, using different comonomers and different monomer ratios. All obtained materials showed good film-forming properties and bright fluorescence caused by the incorporated push–pull chromophores. Additionally, one of the monomers containing a methylpiperazine functionality showed protonation-dependent photoinduced electron transfer which opens up interesting applications for logic gates and sensing. GRAPHICAL ABSTRACT: [Image: see text