Modeling DNA beacons at the mesoscopic scale

We report model calculations on DNA single strands which describe the equilibrium dynamics and kinetics of hairpin formation and melting. Modeling is at the level of single bases. Strand rigidity is described in terms of simple polymer models; alternative calculations performed using the freely rotating chain and the discrete Kratky-Porod models are reported. Stem formation is modeled according to the Peyrard-Bishop-Dauxois Hamiltonian. The kinetics of opening and closing is described in terms of a diffusion-controlled motion in an effective free energy landscape. Melting profiles, dependence of melting temperature on loop length, and kinetic time scales are in semiquantitative agreement with experimental data obtained from fluorescent DNA beacons forming poly(T) loops. Variation in strand rigidity is not sufficient to account for the large activation enthalpy of closing and the strong loop length dependence observed in hairpins forming poly(A) loops. Implications for modeling single strands of DNA or RNA are discussed.Comment: 15 pages, 17 figures, submitted to Eur. J. Phys.

A low-noise CMOS front-end for TOF-PET

An analogue CMOS front-end for triggering and amplification of signals produced by a silicon photomultiplier (SiPM) coupled to a LYSO scintillator is proposed. The solution is intended for time-of-flight measurement in compact Positron Emission Tomography (TOF-PET) medical imaging equipments where excellent timing resolution is required (approximate to 100 ps). A CMOS 0.13 mu m technology was used to implement such front end, and the design includes preamplification, shaping, baseline holder and biasing circuitry, for a total silicon area of 500x90 mu m. Waveform sampling and time-over-threshold (ToT) techniques are under study and the front-end provides fast and shaped outputs for time and energy measurements. Post layout simulation results show that, for the trigger of a single photoelectron, the time jitter due to the pre-amplifier noise can be as low as 15 ps (FWHM), for a photodetector with a total capacitance of 70 pF. The very low input impedance of the pre-amplifier (approximate to 5 Omega) allows 1.8 ns of peaking time, at the cost of 10 mW of power consumption

A low-noise CMOS front-end for TOF-PET

An analogue CMOS front-end for triggering and amplification of signals produced by a silicon photomultiplier (SiPM) coupled to a LYSO scintillator is proposed. The solution is intended for time-of-flight measurement in compact Positron Emission Tomography (TOF-PET) medical imaging equipments where excellent timing resolution is required (approximate to 100 ps). A CMOS 0.13 mu m technology was used to implement such front end, and the design includes preamplification, shaping, baseline holder and biasing circuitry, for a total silicon area of 500x90 mu m. Waveform sampling and time-over-threshold (ToT) techniques are under study and the front-end provides fast and shaped outputs for time and energy measurements. Post layout simulation results show that, for the trigger of a single photoelectron, the time jitter due to the pre-amplifier noise can be as low as 15 ps (FWHM), for a photodetector with a total capacitance of 70 pF. The very low input impedance of the pre-amplifier (approximate to 5 Omega) allows 1.8 ns of peaking time, at the cost of 10 mW of power consumption

A low-noise CMOS front-end for TOF-PET

An analogue CMOS front-end for triggering and amplification of signals produced by a silicon photomultiplier (SiPM) coupled to a LYSO scintillator is proposed. The solution is intended for time-of-flight measurement in compact Positron Emission Tomography (TOF-PET) medical imaging equipments where excellent timing resolution is required (approximate to 100 ps). A CMOS 0.13 mu m technology was used to implement such front end, and the design includes preamplification, shaping, baseline holder and biasing circuitry, for a total silicon area of 500x90 mu m. Waveform sampling and time-over-threshold (ToT) techniques are under study and the front-end provides fast and shaped outputs for time and energy measurements. Post layout simulation results show that, for the trigger of a single photoelectron, the time jitter due to the pre-amplifier noise can be as low as 15 ps (FWHM), for a photodetector with a total capacitance of 70 pF. The very low input impedance of the pre-amplifier (approximate to 5 Omega) allows 1.8 ns of peaking time, at the cost of 10 mW of power consumption

A low-noise CMOS front-end for TOF-PET

An analogue CMOS front-end for triggering and amplification of signals produced by a silicon photomultiplier (SiPM) coupled to a LYSO scintillator is proposed. The solution is intended for time-of-flight measurement in compact Positron Emission Tomography (TOF-PET) medical imaging equipments where excellent timing resolution is required (approximate to 100 ps). A CMOS 0.13 mu m technology was used to implement such front end, and the design includes preamplification, shaping, baseline holder and biasing circuitry, for a total silicon area of 500x90 mu m. Waveform sampling and time-over-threshold (ToT) techniques are under study and the front-end provides fast and shaped outputs for time and energy measurements. Post layout simulation results show that, for the trigger of a single photoelectron, the time jitter due to the pre-amplifier noise can be as low as 15 ps (FWHM), for a photodetector with a total capacitance of 70 pF. The very low input impedance of the pre-amplifier (approximate to 5 Omega) allows 1.8 ns of peaking time, at the cost of 10 mW of power consumption

Insights into the architecture and stoichiometry of Escherichia coli PepA•DNA complexes involved in transcriptional control and site-specific DNA recombination by atomic force microscopy

Multifunctional Aminopeptidase A (PepA) from Escherichia coli is involved in the control of two distinct DNA transaction processes: transcriptional repression of the carAB operon, encoding carbamoyl phosphate synthase and site-specific resolution of ColE1-type plasmid multimers. Both processes require communication at a distance along a DNA molecule and PepA is the major structural component of the nucleoprotein complexes that underlie this communication. Atomic Force Microscopy was used to analyze the architecture of PepA·carAB and PepA·cer site complexes. Contour length measurements, bending angle analyses and volume determinations demonstrate that the carP1 operator is foreshortened by ∼235 bp through wrapping around one PepA hexamer. The highly deformed part of the operator extends from slightly upstream of the –35 hexamer of the carP1 promoter to just downstream of the IHF-binding site, and comprises the binding sites for the PurR and RutR transcriptional regulators. This extreme remodeling of the carP1 control region provides a straightforward explanation for the strict requirement of PepA in the establishment of pyrimidine and purine-specific repression of carAB transcription. We further provide a direct physical proof that PepA is able to synapse two cer sites in direct repeat in a large interwrapped nucleoprotein complex, likely comprising two PepA hexamers

Mechanism of DNA flexibility enhancement by HMGB proteins

The mechanism by which sequence non-specific DNA-binding proteins enhance DNA flexibility is studied by examining complexes of double-stranded DNA with the high mobility group type B proteins HMGB2 (Box A) and HMGB1 (Box A+B) using atomic force microscopy. DNA end-to-end distances and local DNA bend angle distributions are analyzed for protein complexes deposited on a mica surface. For HMGB2 (Box A) binding we find a mean induced DNA bend angle of 78°, with a standard error of 1.3° and a SD of 23°, while HMGB1 (Box A+B) binding gives a mean bend angle of 67°, with a standard error of 1.3° and a SD of 21°. These results are consistent with analysis of the observed global persistence length changes derived from end-to-end distance measurements, and with results of DNA-stretching experiments. The moderately broad distributions of bend angles induced by both proteins are inconsistent with either a static kink model, or a purely flexible hinge model for DNA distortion by protein binding. Therefore, the mechanism by which HMGB proteins enhance the flexibility of DNA must differ from that of the Escherichia coli HU protein, which in previous studies showed a flat angle distribution consistent with a flexible hinge model

Theory of biopolymer stretching at high forces

We provide a unified theory for the high force elasticity of biopolymers solely in terms of the persistence length, $\xi_p$, and the monomer spacing, $a$. When the force f>\fh \sim k_BT\xi_p/a^2 the biopolymers behave as Freely Jointed Chains (FJCs) while in the range \fl \sim k_BT/\xi_p < f < \fh the Worm-like Chain (WLC) is a better model. We show that $\xi_p$ can be estimated from the force extension curve (FEC) at the extension $x\approx 1/2$ (normalized by the contour length of the biopolymer). After validating the theory using simulations, we provide a quantitative analysis of the FECs for a diverse set of biopolymers (dsDNA, ssRNA, ssDNA, polysaccharides, and unstructured PEVK domain of titin) for $x \ge 1/2$. The success of a specific polymer model (FJC or WLC) to describe the FEC of a given biopolymer is naturally explained by the theory. Only by probing the response of biopolymers over a wide range of forces can the $f$-dependent elasticity be fully described.Comment: 20 pages, 4 figure

A Cylindrical GEM Inner Tracker for the BESIII experiment at IHEP

The Beijing Electron Spectrometer III (BESIII) is a multipurpose detector that collects data provided by the collision in the Beijing Electron Positron Collider II (BEPCII), hosted at the Institute of High Energy Physics of Beijing. Since the beginning of its operation, BESIII has collected the world largest sample of J/{\psi} and {\psi}(2s). Due to the increase of the luminosity up to its nominal value of 10^33 cm-2 s-1 and aging effect, the MDC decreases its efficiency in the first layers up to 35% with respect to the value in 2014. Since BESIII has to take data up to 2022 with the chance to continue up to 2027, the Italian collaboration proposed to replace the inner part of the MDC with three independent layers of Cylindrical triple-GEM (CGEM). The CGEM-IT project will deploy several new features and innovation with respect the other current GEM based detector: the {\mu}TPC and analog readout, with time and charge measurements will allow to reach the 130 {\mu}m spatial resolution in 1 T magnetic field requested by the BESIII collaboration. In this proceeding, an update of the status of the project will be presented, with a particular focus on the results with planar and cylindrical prototypes with test beams data. These results are beyond the state of the art for GEM technology in magnetic field

Role of the Subunits Interactions in the Conformational Transitions in Adult Human Hemoglobin: an Explicit Solvent Molecular Dynamics Study

Hemoglobin exhibits allosteric structural changes upon ligand binding due to the dynamic interactions between the ligand binding sites, the amino acids residues and some other solutes present under physiological conditions. In the present study, the dynamical and quaternary structural changes occurring in two unligated (deoxy-) T structures, and two fully ligated (oxy-) R, R2 structures of adult human hemoglobin were investigated with molecular dynamics. It is shown that, in the sub-microsecond time scale, there is no marked difference in the global dynamics of the amino acids residues in both the oxy- and the deoxy- forms of the individual structures. In addition, the R, R2 are relatively stable and do not present quaternary conformational changes within the time scale of our simulations while the T structure is dynamically more flexible and exhibited the T\rightarrow R quaternary conformational transition, which is propagated by the relative rotation of the residues at the {\alpha}1{\beta}2 and {\alpha}2{\beta}1 interface.Comment: Reprinted (adapted) with permission from J. Phys. Chem. B DOI:10.1021/jp3022908. Copyright (2012) American Chemical Societ