Selective derivatization of cytosine and methylcytosine moieties with 2-bromoacetophenone for submicrogram DNA methylation analysis by reversed phase HPLC with spectrofluorimetric detection.

In eukaryotes, actual DNA methylation patterns provide biologically important information, for which both, genome-wide and locus-specific methylation at cytosine residues have been extensively studied. The original contribution of this work relies on the selective derivatization of cytosine moieties with 2-bromoacetophenone for the determination of global DNA methylation by reversed phase high performance liquid chromatography with spectrofluorimetric detection. The important features of the proposed procedure are as follows: (1) no need for the elimination of RNA, (2) detection limits for cytidine, 2'-deoxycytidine, 5-methylcytidine, and 5-methyl-2'-deoxycytidine in the range of 14.4-22.7 fmol, (3) feasibility for the detection of 0.06% of methylation in a low amount of DNA (80 ng), (4) potential viability for the evaluation of RNA methylation, and (5) relative simplicity in terms of analytical instrumentation and personnel training. The results obtained in the analysis of salmon testes DNA and nucleic acids from plant, human blood, and earthworms demonstrate the utility of the proposed procedure in biological studies and, in particular, for evaluation of the potential effect of environmental factors on actual DNA methylation in different types of living organisms.

High-performance liquid chromatography determination of 5-methyl-2'-deoxycytidine, 2'-deoxycytidine, and other deoxynucleosides and nucleosides in DNA digests.

This work has undertaken liquid chromatographic separation of nucleosides and deoxynucleosides. Two different columns with three mobile phases (A, deionized water; B, 50 mM phosphate buffer (pH 4.0); C, methanol) and slightly different gradient programs were used. The elution order was as follows: cytidine (C), 2'-deoxycytidine (dC), uridine (U), 5-methyl-2'-cytidine (5mC), 5-methyl-2'-deoxycytidine (5mdC), guanosine (G), deoxyguanosine (dG), 2'-deoxythymidine (dT), adenosine (A), and 2'-deoxyadenine (dA). Using a Luna C18 Phenomenex column (150 x 4.6 mm, 5 microm), the separation was performed at 40 degrees C with a total flow rate of 1 ml/min and a run time of 10 min. The second column was an Agilent C18 (50 x 3 mm, 1.8 microm), for which the run time was 4.5 min with a flow rate of 0.6 ml/min (25 degrees C). In application to the DNA digests from human THP-1 cells, the quantification of C, dC, U, 5mC, 5mdC, G, dG, and A was performed. The percentages of global methylation were evaluated based on the 5mdC and dC concentrations (c(5mdC) / [c(5mdC)+c(dC)], where c is concentration in microg/ml) and compared with those calculated from the respective peak areas (A(5mdC) / [A(5mdC)+A(dC)], where A is peak area at 254 nm). For peak area measurements, excellent agreement was obtained with the results reported previously in the same cell line. In the quantitative approach, the results of DNA methylation were higher but consistent with the previous data obtained using mass spectrometric detection. Comparing the analytical features of the two procedures, the use of a smaller column could be recommended because it provides efficient separation (capacity factors in the range of 1.29-10.66), a short run time, and feasibility of nucleoside and deoxynucleoside quantification in real-world samples and because it also minimizes the use of reagents.

Polysaccharide-based chiral phase under polar organic mode of elution in the determination of the enantiomeric purity of emtricitabine an anti-HIV analogue nucleoside.

This work reports the separation of FTC enantiomers using an amylose tris[(S)-1-phenylethylcarbamate] coated onto APS-Nucleosil (7 microm particle size, 500 A pore size, 20% w/w, 15 x 0.46 cm ID) chiral column under polar organic elution mode. Good enantioselectivity (alpha=1.9) with excellent enantioresolution (R(S)=3.3) was achieved by the use of methanol with 0.02% of triethylamine acetate as mobile phase. The method allows the accurate determination of as low as 0.2% of each enantiomer as an impurity. The validated method proved to be reliable and sensitive for the quantification of both enantiomers as impurity in different batches of emtricitabine and beta-D-(+)-FTC.

Monoclonal antibody affinities of structurally related modified nucleosides.

A scale of relative affinities of a series of 2'-deoxycytidine and cytidine (CD) derivatives was established based on the data of cross-reactivities of these compounds as well as the displacements obtained from a competitive ELISA. No correlation could be established between the nucleosides modifying structures and the affinities. This can be explained by the possibilities of the modifying structures of intra- and intermolecular nonimmunospecific interactions owing to their degree of functionalization.