Cooperative RNA Polymerase Molecules Behavior on a Stochastic Sequence-Dependent Model for Transcription Elongation

The transcription process is crucial to life and the enzyme RNA polymerase (RNAP) is the major component of the transcription machinery. The development of single-molecule techniques, such as magnetic and optical tweezers, atomic-force microscopy and single-molecule fluorescence, increased our understanding of the transcription process and complements traditional biochemical studies. Based on these studies, theoretical models have been proposed to explain and predict the kinetics of the RNAP during the polymerization, highlighting the results achieved by models based on the thermodynamic stability of the transcription elongation complex. However, experiments showed that if more than one RNAP initiates from the same promoter, the transcription behavior slightly changes and new phenomenona are observed. We proposed and implemented a theoretical model that considers collisions between RNAPs and predicts their cooperative behavior during multi-round transcription generalizing the Bai et al. stochastic sequence-dependent model. In our approach, collisions between elongating enzymes modify their transcription rate values. We performed the simulations in Mathematica® and compared the results of the single and the multiple-molecule transcription with experimental results and other theoretical models. Our multi-round approach can recover several expected behaviors, showing that the transcription process for the studied sequences can be accelerated up to 48% when collisions are allowed: the dwell times on pause sites are reduced as well as the distance that the RNAPs backtracked from backtracking sites. © 2013 Costa et al.

Upconversion luminescence in Er3+ doped Ga10Ge 25S65 glass and glass-ceramic excited in the near-infrared

The infrared-to-visible frequency upconversion was investigated in Er 3+-doped Ga10Ge25S65 glass and in the transparent glass-ceramic obtained by heat-treatment of the glass above its glass-transition temperature. Continuous-wave and pulsed lasers operating at 980 nm and 1480 nm were used as excitation sources. The green (2H 11/2 → 4I15/2; 4S3/2 → 4I15/2) and red (4F9/2 → 4I15/2) photoluminescence (PL) signals due to the Er3+ ions were characterized. The PL decay times were influenced by energy transfer among Er3+ ions, by cross-relaxation processes and by energy transfer from the Er3+ ions to the host material. The PL from the Er3+ ions hosted in the crystalline phase was distinguished only when the glass-ceramic was excited by the 1480 nm pulsed laser. The excitation pathways responsible for the green and red PL bands are discussed to explain the differences between the spectra observed under continuous-wave and pulsed excitation. © 2013 American Institute of Physics.

Luminescence Enhancement of Carboxyl-Coated CdTe Quantum Dots by Silver Nanoparticles

Metallic nanoparticles (NPs) have been used to improve the sensibility of biosensors and bioassays either by enhancing radiative emission or inducing quenching process on fluorescent probes. The aim of this research was to study the interaction of silver and silver-pectin NPs with water-dispersed carboxyl-coated cadmium telluride (CdTe) quantum dots (QDs). Metallic NPs were observed to change the emission of these fluorophores through local field effects. In a solution-base platform, an increase of 82 % was observed for the CdTe emission due to the interaction of QDs and silver-pectin NPs. QDs interaction with silver NPs without pectin was also investigated and a smaller emission enhancement of 20 % was detected. We observed that the NPs' nature and QDs' surface charge and concentration are important parameters for NPs-QDs interaction. Moreover, the presence of the pectin polymer shows to be a key component to the observed fluorescence enhancement. © 2013 Springer Science+Business Media New York.