Nitroxide-labeled pyrimidines for non-covalent spin-labeling of abasic sites in DNA and RNA duplexes

Post-print (lokagerð höfundar)Non-covalent and site-directed spin labeling gives easy access to spin-labeled nucleic acids for the study of their structure and dynamics by electron paramagnetic resonance (EPR) spectroscopy. In a search for improved spin labels for non-covalent binding to abasic sites in duplex DNA and RNA, ten pyrimidine-derived spin labels were prepared in good yields and their binding was evaluated by continuous wave (CW)-EPR spectroscopy. Most of the spin labels showed lower binding affinity than the previously reported label c towards abasic sites in DNA and RNA. The most promising labels were triazole-linked spin labels and a pyrrolocytosine label. In particular, the N1-ethylamino derivative of a triazole-linked uracil spin label binds fully to both DNA and RNA containing an abasic site. This is the first example of a spin label that binds fully through non-covalent interactions with an abasic site in RNA.We thank the Icelandic Research Fund (110035022) and the University of Iceland Research Fund for financial support. S. A. S. acknowledges a doctoral fellowship from the University of Iceland Research Fund. We thank Dr S. Jonsdottir for assistance in collecting analytical data for structural characterization of the compounds that were prepared and members of the Sigurdsson research group for critical reading of the manuscript.Peer reviewe

Crystal structure of a DNA containing the planar, phenoxazine-derived bi-functional spectroscopic probe Ç

Previously, we developed the deoxycytosine analog Ç (C-spin) as a bi-functional spectroscopic probe for the study of nucleic acid structure and dynamics using electron paramagnetic resonance (EPR) and fluorescence spectroscopy. To understand the effect of Ç on nucleic acid structure, we undertook a detailed crystallographic analysis. A 1.7 Å resolution crystal structure of Ç within a decamer duplex A-form DNA confirmed that Ç forms a non-perturbing base pair with deoxyguanosine, as designed. In the context of double-stranded DNA Ç adopted a planar conformation. In contrast, a crystal structure of the free spin-labeled base ç displayed a ∼20° bend at the oxazine linkage. Density function theory calculations revealed that the bent and planar conformations are close in energy and exhibit the same frequency for bending. These results indicate a small degree of flexibility around the oxazine linkage, which may be a consequence of the antiaromaticity of a 16-π electron ring system. Within DNA, the amplitude of the bending motion is restricted, presumably due to base-stacking interactions. This structural analysis shows that the Ç forms a planar, structurally non-perturbing base pair with G indicating it can be used with high confidence in EPR- or fluorescence-based structural and dynamics studies

A Two-Sequence, Four-Period, Crossover, Full-Replicate Study to Demonstrate Bioequivalence of Carbamazepine Extended-Release Tablets in Healthy Subjects under Fasting and Fed Conditions

Carbamazepine is a first-line antiepileptic drug (AED) used for the treatment of partial and tonic-clonic seizures. We conducted an open label, balanced, randomized, two-treatment, two-sequence, four-period, single oral dose, full-replicate crossover study to assess and compare the  bioequivalence of  test  product  Carbamazepine extended release tablets USP 400 mg with reference  product Tegretol®-XR 400 mg (Carbamazepine extended release tablets), respectively in  healthy subjects under fasting and fed conditions. Blood samples were collected pre-dose and at regular intervals post-dose up to 240.00 hours. The plasma concentration was analyzed by a validated LC-MS/MS method and the reference-scaled and the unscaled procedure was used to determine bioequivalence for the pharmacokinetics parameters, Cmax, AUC0–t, AUC0-inf, Tmax, T½, Kel and AUC extrapolated was calculated. The results showed that the geometric mean ratios of Cmax, AUC0–t and AUC0-inf were 113.04%, 108.33% and 108.15% respectively, in the fasting conditions and 113.99%, 110.13% and 111.41%, respectively, in the fed conditions and the 90% confidence intervals were all within the range of 80.00% to 125.00%. It can be concluded from the result that the test product Carbamazepine extended release tablets based on osmotic release system (OROS) are bioequivalent to the reference product Tegretol®-XR tablets. Keywords:  Bioequivalence, Carbamazepine, Sodium Channel Modulators and Epileps

Calculations of codoping effects between combinations of donors (P/As/Sb) and acceptors (B/Ga/In) in Si

Site-directed spin labeling and pulsed electron–electron double resonance (PELDOR or DEER) have previously been applied successfully to study the structure and dynamics of nucleic acids. Spin labeling nucleic acids at specific sites requires the covalent attachment of spin labels, which involves rather complicated and laborious chemical synthesis. Here, we use a noncovalent label strategy that bypasses the covalent labeling chemistry and show that the binding specificity and efficiency are large enough to enable PELDOR or DEER measurements in DNA duplexes and a DNA duplex bound to the Lac repressor protein. In addition, the rigidity of the label not only allows resolution of the structure and dynamics of oligonucleotides but also the determination of label orientation and protein-induced conformational changes. The results prove that this labeling strategy in combination with PELDOR has a great potential for studying both structure and dynamics of oligonucleotides and their complexes with various ligands.Publisher PDFPeer reviewe