Immunochemical detection of N6-methyladenine in DNA

Antibodies to DNA

Antibodies that recognize specific conformational variations of DNA structure provide sensitive reagents for testing the extent to which such conformational heterogeneity occurs in nature. A most dramatic recent example has been the development and application of antibodies to left-handed Z-DNA. They provided the first identification of Z-DNA in fixed nuclei and chromosomes, and of DNA sequences that form Z-DNA under the influence of supercoiling. Antibodies have also been induced by chemically modified DNA and by synthetic polydeoxyribonucleotides that differ from the average B-DNA structure. These antibodies recognize only the features that differ from native DNA. In most experiments, native DNA itself is not immunogenic. Antibodies that do react with native DNA occur in sera of patients with autoimmune disease, but even monoclonal anti-DNA autoantibodies usually react with other polynucleotides as well. Anti-DNA antibodies, especially those of monoclonal origin, provide a model for the study of protein-nucleic acid recognition.

Reduced cleavage by sodium hydroxide of methyladenine in DNA sequencing

When the Maxam and Gilbert DNA sequencing method which is modified by Bencini et al. (Biotechniques Jan/Feb pp4-5, 1984) is applied to DNA containing methylated adenine in a GATC sequence, the cleavage reaction by sodium hydroxide is found to be greatly reduced in comparison to that of non-methylated adenine. Thus, a faint band in A greater than C reaction suggests a methyl adenine and can be used for its detection. That the faint band corresponds to a methyladenine was confirmed by Sanger sequencing of the same fragment and further by Maxam and Gilbert sequencing of the complementary strand of DNA, which was replicated in an E. coli strain either having or lacking methylation enzymes.

Specificity of deoxycytidylate antibodies

Antibodies to deoxycytidylate (dpC) were elicited in rabbits using a thyroglobulin (Tg) conjugate of dpC. The specificity of the antibodies was determined by measuring the inhibition of the binding of [3H]dpC to the antibodies by various non-radioactive nucleotides or derivatives. The antibodies were found to distinguish dpC from pC and DNA from RNA, probably due to their specificity for the conformation of the deoxycytidylate.

Quantitative reversed-phase high performance liquid chromatographic determination of major and modified deoxyribonucleosides in DNA

We have developed a method to accurately determine (< 3% RSD) the complete major and modified base composition of a few micrograms of unlabeled DNA. The DNA samples were quantitatively hydrolyzed with DNase 1, Nuclease P1, and bacterial alkaline phosphatase. The resulting deoxyribonucleosides were directly separated in 70 min by reversed-phase high performance liquid chromatography with detection by ultraviolet absorption at 254 nm and 280 nm (RP-HPLC). The highly sensitive and selective dual wavelength quantitation greatly enhances the precision and accuracy of the chromatographic analysis. Contamination of DNA preparations with RNA does not interfere with the DNA analysis due to the high resolution of the chromatography. We have used this method for the quantitation of m5dCyd in 5 microgram of calf thymus and salmon sperm DNA in which the m5dCyd comprises only 1 to 2% of the total bases. This method should be a useful research tool in studies on various DNAs and DNA subfractions and should help to elucidate the functions of methylation of DNA.