Nucleobase recognition at alkaline pH and apparent pKa of single DNA bases immobilised within a biological nanopore

The four DNA bases are recognized in immobilized DNA strands at high alkaline pH by nanopore current recordings. Ionic currents through the biological nanopores are also employed to measure the apparent pK(a) values of single nucleobases within the immobilised DNA strands.     

Examiner repeatability of patellar cartilage T2 values

Aim

The purpose of this study was to evaluate the intra- and interexaminer resegmentation precision of patellar cartilage T₂ mapping measurements in healthy subjects.

Materials and Methods

T₂-weighted images of patellar cartilage for 10 subjects were acquired. Two individuals manually segmented patellar cartilage at each slice location twice, once on each of two separate days. Bulk average and zonal T₂ values for the superficial, middle, and deep layers of cartilage were calculated. The root mean square (RMS) and coefficient of variation (COV) were calculated using the repeated measurements of each slice of each subject by each examiner.

Results

The intraexaminer bulk T₂ differences were 0.2±1.0 ms, with an RMS error of 0.7 ms and a COV of 1.9%. The differences of interexaminer bulk T₂ values was 1.0±1.4 ms, with an RMS error of 1.2 ms and a COV of 3.3%. The superficial zone of cartilage had the highest zonal variability of T₂ values. The average interexaminer T₂ values for the superficial, middle and deep zones were 42.2±5.6, 38.1±5.3 and 31.9±4.6 ms, respectively.

Conclusion

The interexaminer variability of calculated T₂ values highlights the difficulty of interpreting significant differences of T₂ values which are similar in magnitude. The repeatability measurements of patellar cartilage T₂ values were less than reported intersession T₂ repeatability.     

Voltammetric Label‐free Detection of DNA Hypermethylation Using Polypyrrole‐modified Microelectrode Array

An alternative strategy for the label‐free electrochemical detection of DNA hypermethylation using a microelectrode array as an oligodinucleotide (ODN) detector is presented. It relies on the oligonucleotide dependent electrostatic affinity interaction firstly with unmethylated ODN and then follow‐up with methylated DNA. The methylated cytosine status is quantified by monitoring the relative change in the exchange current at the ODN‐detector before and after the bisulfite treated DNA samples. This novel aproach displays unique advantages such as small working volumes of the analytes, low damage to DNA samples, easy integration of oligonucleides on the detector and signal evaluation.     

Structure and linear spectroscopic properties of near IR polymethine dyes

We performed a detailed experimental investigation and quantum-chemical analysis of a new series of near IR polymethine dyes with 5-butyl-7,8-dihydrobenzo[cd]furo[2,3-f]indolium terminal groups. We also synthesized and studied two neutral dyes, squaraine and tetraone, with the same terminal groups and performed a comparison of the spectroscopic properties of this set of “near IR” dyes (polymethine, squaraine, and tetraone) with an analogous set of “visible” dyes with simpler benzo[e]indolium terminal groups. From these measurements, we find that the dyes with dihydrobenzo[cd]furo[2,3-f]indolium terminal groups are characterized by a remarkably large shift ≈300 nm (≈200 nm for tetraone) of their absorption bands towards the red region. We discuss the difference in electronic structure for these molecules and show that the “near IR” dyes are characterized by an additional weak fluorescence band from the higher lying excited states connected with the terminal groups. Absorption spectra for the longest polymethines are solvent-dependent and are characterized by a broadening of the main band in polar solvents, which is explained by ground state symmetry breaking and reduced charge delocalization within the polymethine chromophore. The results of these experiments combined with the agreement of quantum chemical calculations moves us closer to a predictive capability for structure-property relations in cyanine-like molecules.     

The Instability of Nonmonotonic Wave Solutions of Parabolic Equations

We consider the class of equations u_t=f(u_xx, u_x, u) under the restriction that for all a,b,c. We first consider this equation over the unbounded domain ? ∞ < x < + ∞, and we show that very nearly every bounded nonmonotonic solution of the form u(t, x)=?(x?ct) is unstable to all nonnegative and all nonpositive perturbations. We then extend these results to nonmonotonic plane wave solutions u(t, x, y)=?(x?ct) of u_t = F(u_xx, u_xy, u_x, u_y, u). Finally, we consider the class of equations u_t=f(u_xx, u_x, u) over the bounded domain 0 < x < 1 with the boundary conditions u(t, x)=A at x=0 and u(t, x)=B at x=1, and we find the stability of all steady solutions u(t, x)=?(x).     

Structure and H(2)-Loss Energies of OsHX(H(2))(CO)L(2) Complexes (L = P(t-Bu)(2)Me, P(i-Pr)(3); X = Cl, I, H): Attempted Correlation of (1)J(H-D), T(1min), and DeltaG()

1J(H-D), T(1min) and k(1) for H(2) dissociation from OsHX(H(2))(CO)L(2) have been measured for X = Cl, I, H (L = P(t-Bu)(2)Me or P(i-Pr)(3)), as well as for OsCl(2)(H(2))(CO)(P(i-Pr)(3))(2). For comparison, new data (including previously unobserved coupling constants) have been reported for W(HD)(CO)(3)(P(i-Pr)(3))(2). A comprehensive consideration of T(1min) data for over 20 dihydrogen complexes containing only 1-2 phosphines cis to H(2), together with a consideration of the shortest "conceivable" H-H distance for H(2) bound to a d(4) or d(6) metal, is used to argue that the "fast spinning" model is not appropriate for determining r(H-H) in such complexes. Regarding OsHX(H(2))(CO)L(2), the stronger electron-donor (lighter) halide, when cis to H(2), facilitates loss of H(2). The complete absence of pi-donor ability when X = H renders H(2) loss most difficult. However, a pi-donor trans to H(2) also makes H(2) loss unobservable. Within the series of isoelectronic, structurally analogous Os complexes, a longer H-H bond shows a larger DeltaG() for H(2) loss. However, this correlation does not continue to W(H(2))(CO)(3)(P(i-Pr)(3))(2), which has r(H-H) comparable to that of OsH(halide)(H(2))(CO)(P(i-Pr)(3))(2), but a significantly higher DeltaG(). This may originate from lack of a pi-donor ligand to compensate as H(2) leaves W.     

Structural, electronic, and vibrational characterization of Fe-HNO porphyrinates by density functional theory

A recent report of the structural and vibrational properties of heme-bound HNO in myoglobin, MbHNO, revealed a long Fe-N(HNO) bond with the hydrogen atom bonded to the coordinated N atom. The Fe-N(H)-O moiety was reported to exhibit an unusually high Fe-N(HNO) stretching frequency relative to those of the corresponding [FeNO]6 and [FeNO]7 porphyrinates, despite the Fe-N(HNO) bond being longer than either of its Fe-N(NO) counterparts. Herein, we present results from density functional theory calculations of an active site model of MbHNO that support the previous assignment and clarify this seemingly contradictory result. The results are consistent with the experimental evidence for a ground-state Fe-N(H)-O structure having a long Fe-N(HNO) bond and a uniquely high nu(Fe)(-)(N(HNO)) frequency. This high frequency is the result of the correspondingly low reduced mass of the normal mode, which is largely attributable to significant motion of the N-bound hydrogen atom. Additionally, the calculations show the Fe-N(H)O bonding in this complex to be remarkably insensitive to whether the HNO and ImH ligand planes are parallel or perpendicular. This is attributed to insensitivities of the Fe-L(axial) characters of molecular orbitals to the relative HNO and ImH orientation in both the parallel and perpendicular conformers.