Platination of full length tRNA(Ala) and truncated versions of the acceptor stem and anticodon loop

Nuclear DNA is a well characterized target for many low molecular metal-based drugs, with cisplatin and related antineoplastic compounds as typical examples. Much less is known concerning to what extent targeting of RNA may influence the activity spectrum of these types of drugs. In a preliminary communication by us (Papsai et al., Dalton Trans., 2006, 3515) we were able to show that the folded, three-dimensionally well defined structure of tRNA(Ala) readily interacts with cisplatin. In the present study we have further analyzed the binding preferences within the preferentially targeted stem region (sMh(Ala)) by modulation of the sequence around the G-U wobble base-pair and the net charge of the 3' and 5' ends. Our data show that the adduct profile is strongly influenced by the presence of the 5' end phosphate group. Further, the adduct formation reaction can be prevented by replacement of the G-U wobble base-pair with the fully complementary G-C pair. To further investigate the influence from local sequence on the platination process, a model of the anticodon region (acMh(Ala)) was also investigated. In the absence of consecutive guanine-residues in the stem- and anticodon regions, preferential platination was found to take place at the terminal AG-site in the stem region. However, after introduction of a GG-pair in the anticodon loop, platination was observed also here. At 37 degrees C, pH 6.3 and C(Pt) = 0.10 mM the rate of platination was determined to be ca. 1 x 10(-4) s(-1), with the most rapid reaction observed for interaction with the anticodon model carrying two adjacent guanines in the single-stranded loop. Together, these data show that platination of RNA is highly sequence- and structure-dependent.     

Do Sulfonamides Interact with Aromatic Rings?

Aromatic rings form energetically favorable interactions with many polar groups in chemical and biological systems. Recent molecular studies have shown that sulfonamides can chelate metal ions and form hydrogen bonds, however, it is presently not established whether the polar sulfonamide functionality also interacts with aromatic rings. Here, synthetic, spectroscopic, structural, and quantum chemical analyses on 2,6-diarylbenzenesulfonamides are reported, in which two flanking aromatic rings are positioned close to the central sulfonamide moiety. Fine-tuning the aromatic character by substituents on the flanking rings leads to linear trends in acidity and proton affinity of sulfonamides. This physical-organic chemistry study demonstrates that aromatic rings have a capacity to stabilize sulfonamides via through-space NH–π interactions. These results have implications in rational drug design targeting electron-rich aromatic rings in proteins.     

A comparison of nano‐electrospray gas‐phase electrophoretic mobility macromolecular analysis and matrix‐assisted laser desorption/ionization linear time‐of‐flight mass spectrometry for the characterization of the recombinant coagulation glycoprotein von Willebrand factor

Von Willebrand factor (VWF), an adhesive glycoprotein with an approximate molecular weight (MW) of the monomer of 260 kDa, circulates in human blood plasma as a series of multimers ranging in size up to 20.000 kDa; thus the determination of the accurate MW of the monomer is of great importance and due to its high MW quite challenging. In this study accurate MW determination of intact recombinant VWF monomer (rVWF) was performed with GEMMA (gas‐phase electrophoretic mobility macromolecular analysis) and MALDI TOF MS (matrix‐assisted laser desorption/ionization linear time‐of‐flight mass spectrometry). Three rVWF preparations with differing buffer systems and glycoprotein concentrations were analyzed. First investigations directed towards heterogeneity determination by means of capillary gel electrophoresis (CGE)‐on‐the‐chip with a laser‐induced fluorescence detector revealed two compounds (MW of 277 kDa (migration time 44.3 s) and 341 kDa (migration time 49.5 s)) present in each sample to varying extents, namely mature and pro‐rVWF. MALDI MS analysis in the linear positive ion mode allowed the detection of mature rVWF with an exact MW of 256.1 kDa (±0.8%) and pro‐rVWF with a MW of 349.8 kDa (±0.8%). Two samples containing pro‐rVWF in very minor concentration resulted in GEMMA detection of the mature rVWF with a MW of 227.4 kDa (±2.5%), derived from the measured globular size of 10.9 nm. For one sample containing both rVWF species in almost equal concentrations no differentiation of the two species was possible with GEMMA. Due to its lower resolution only a peak representing a mixture of both species at 11.8 nm could be observed, yielding a MW of 298.8 kDa (±1.6%). Copyright © 2010 John Wiley & Sons, Ltd.     

Kinetic preference for interaction of cisplatin with the G-C-rich wobble basepair region in both tRNAAla and MhAla

The anticancer active complex cisplatin interacts preferentially with the common, G-C rich, wobble base pair region of both tRNA(Ala) and Mh(Ala) in a reaction that at pH 6.3 is rate limited by the acid hydrolysis of the metal complex.     

Wigner-Ville distribution for pulse propagation in random media: pulsed plane wave

The time-frequency Wigner-Ville distribution for a pulsed plane-wave signal propagating in a continuous random medium is found, based on the previously derived modal series expression for the two-frequency coherence function. The theory can address propagation in any homogeneous isotropic random medium, but closed-form expressions are specifically derived for a general power-law medium. Two alternative formulations are presented: a modal-wavefront approach wherein each mode is asymptotically transformed to the time domain and a collective approach wherein the mode series is summed collectively and then transformed to the time domain using pole contributions. The physical interpretation of these two different representations in the time-frequency domain as either a superposition of localized wavefronts or collective excitations is established, and their applications to the calculation of local moments are considered.     

Modal theory for the two-frequency mutual coherence function in random media: general theory and plane wave solution: I

In this paper, the modal expansion theory is presented as a new analytical approach together with the resulting new physical parameters. In particular, the features of an arbitrary power-law structure function are investigated. The exact expression for the Gaussian spectrum is rederived. An approximate analytical expression for the two-frequency coherence function evaluated at equal positions for the Kolmogorov spectrum is presented and comparison with the numerical solution in the literature exhibits a remarkable agreement. As a result of the modal decomposition, general properties for a transversally homogeneous and isotropic medium are demonstrated, such as the exponential decay of the amplitude of the solution and the linear phase behaviour at large propagation distances.