Immunochemical detection of minor bases in nucleic acids

RNA modifications in aging-associated cardiovascular diseases

Cardiovascular disease (CVD) is a leading cause of morbidity and mortality worldwide that bears an enormous healthcare burden and aging is a major contributing factor to CVDs. Functional gene expression network during aging is regulated by mRNAs transcriptionally and by non-coding RNAs epi-transcriptionally. RNA modifications alter the stability and function of both mRNAs and non-coding RNAs and are involved in differentiation, development, and diseases. Here we review major chemical RNA modifications on mRNAs and non-coding RNAs, including N6-adenosine methylation, N1-adenosine methylation, 5-methylcytidine, pseudouridylation, 2′ -O-ribose-methylation, and N7-methylguanosine, in the aging process with an emphasis on cardiovascular aging. We also summarize the currently available methods to detect RNA modifications and the bioinformatic tools to study RNA modifications. More importantly, we discussed the specific implication of the RNA modifications on mRNAs and non-coding RNAs in the pathogenesis of aging-associated CVDs, including atherosclerosis, hypertension, coronary heart diseases, congestive heart failure, atrial fibrillation, peripheral artery disease, venous insufficiency, and stroke.

DNA Replication: From Radioisotopes to Click Chemistry

The replication of nuclear and mitochondrial DNA are basic processes assuring the doubling of the genetic information of eukaryotic cells. In research of the basic principles of DNA replication, and also in the studies focused on the cell cycle, an important role is played by artificially-prepared nucleoside and nucleotide analogues that serve as markers of newly synthesized DNA. These analogues are incorporated into the DNA during DNA replication, and are subsequently visualized. Several methods are used for their detection, including the highly popular click chemistry. This review aims to provide the readers with basic information about the various possibilities of the detection of replication activity using nucleoside and nucleotide analogues, and to show the strengths and weaknesses of those different detection systems, including click chemistry for microscopic studies.

Hypermethylated Chromosome Regions in Nine Fish Species with Heteromorphic Sex Chromosomes

Sites and amounts of 5-methylcytosine (5-MeC)-rich chromosome regions were detected in the karyotypes of 9 Brazilian species of Characiformes fishes by indirect immunofluorescence using a monoclonal anti-5-MeC antibody. These species, belonging to the genera Leporinus, Triportheus and Hoplias, are characterized by highly differentiated and heteromorphic ZW and XY sex chromosomes. In all species, the hypermethylated regions are confined to constitutive heterochromatin. The number and chromosome locations of hypermethylated heterochromatic regions in the karyotypes are constant and species-specific. Generally, heterochromatic regions that are darkly stained by the C-banding technique are distinctly hypermethylated, but several of the brightly fluorescing hypermethylated regions merely exhibit moderate or faint C-banding. The ZW and XY sex chromosomes of all 9 analyzed species also show species-specific heterochromatin hypermethylation patterns. The analysis of 5-MeC-rich chromosome regions contributes valuable data for comparative cytogenetics of closely related species and highlights the dynamic process of differentiation operating in the repetitive DNA fraction of sex chromosomes.

Development of a new bimodal imaging methodology: a combination of fluorescence microscopy and high-resolution secondary ion mass spectrometry

In this paper, we present a new experimental methodology to combine mass spectrometry (NanoSIMS) with fluorescence microscopy to provide subcellular information on the location of small molecules in cultured cells. We demonstrate this by comparing the distribution of 5-bromo-2-deoxyuridine in the same cells given by both NanoSIMS analysis and by fluorescence immunohistochemistry. Fiducial markers in the substrates ensured that the images formed by SIMS mapping of bromine ions could be co-registered exactly with images from fluorescence microscopy. The NanoSIMS was shown to faithfully reproduce the information from fluorescence microscopy, but at a much higher spatial resolution. We then show preliminary SIMS images on the distribution of ATN-224, a therapeutic copper chelator for which there is no fluorescent marker, co-registered with conventional Lysotracker and Hoechst stains on the same cells.

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.

Double labeling and in vitro versus in vivo incorporation of bromodeoxyuridine in patients with acute nonlymphocytic leukemia

A monoclonal antibody against bromodeoxyuridine (BrdUrd) was produced, and a rapid slide technique (RPMB technique) was developed for the estimation of S-phase cells in a population using this antibody. Bone marrow cells from patients with acute nonlymphocytic leukemia (ANLL) were studied by both the RPMB technique and tritiated thymidine (3HdThd) labeling index studies. The percentage of S-phase cells obtained by each method was compared in 50 samples, and the correlation coefficient was r = 0.89. A "double label" method is also described in which cells were simultaneously incubated with either BrdUrd and 3HdThd or BrdUrd and tritiated cytosine arabinoside (3HAra-C). The samples were first processed by the RPMB technique and then by autoradiography. Results showed only black grains overlying the nuclei of fluorescent cells in each group. An automated microphotometer was used to quantitate grains and fluorescence from each cell. This demonstrated an almost direct relationship between grains and fluorescence from BrdUrd + 3HdThd slides, whereas different patterns of relationship were noted from BrdU + 3HAra-C slides of leukemic patients. Their implications are discussed in the text. Finally, intravenous infusions of BrdUrd was given to five leukemic patients. S-phase cells were recognized distinctly within 5 min of starting the infusion. The percentage of S-phase cells was almost identical from in vivo and in vitro samples. Various possibilities of studying the biological behavior of acute leukemias and analyzing cell cycle characteristics are discussed.

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.

Fine structure mapping of an avian tumor virus RNA by immunoelectron microscopy

The RNA of a deleted strain (lacking Src gene) of an avian sarcoma virus (ASV) was examined by a newly developed immunoelectron microscopic procedure which uses anti-nucleotide antibodies as probes. After denaturation of the RNA and reaction with a high affinity, highly specific anti-7-methylguanosine-5'-phosphate (anti-pm 7G), 81% of 106 molecules examined were found to have antibody at one terminus, in agreement with the presence of a pm 7G cap in ASV-RNA. Hapten inhibition by pm 7G could be demonstrated. Experiments with anti-A and with anti-poly A gave results consistent with the known structure of ASV-RNA, in particular the presence of a 3' poly A tail. These studies illustrate the feasibility of using anti-nucleotide antibodies in a combined immunochemical and electron microscopic study of the fine structure of nucleic acids.

Immunochemical detection of N6-methyladenine in DNA

Antibodies to N6-methyladenosine were produced in rabbit by means of immunization with N6-methyladenosine coupled to bovine serum albumin via periodate oxidation. Cross-reacting antibodies were removed by bovine serum albumin-Sepharose and appropriate nucleoside-human serum albumin absorbents. Nucleoside-specific antibodies were isolated by affinity chromatography of N6-methyladenosine-human serum albumin-Sepharose. The specificity of the purified antibodies has been demonstrated by complement fixation inhibition analyses using nucleoside analogues as inhibition than dAMP. Anti-N6-methyladenosine was used to detect N6-methyladenine in denatured DNAs from various sources by complement fixation. Practically no complement fixation has been found with DNAs containing no N6-methyladenine, such as calf thymus, salmon sperm, Micrococcus radiodurans, Streptomyces chrysomallus and Streptomyces hygroscopicus, whereas a weak reactivity occurred in the case of Bacillus subtilis DNA and Sarcina maxima DNA. For DNA from Proteus mirabilis, Escherichia coli K-12, E. coli B, E. coli WF+, lambda, T2 phages quantitative differences in the immunochemical reactivity were observed, which only partially correlate with the N6-methyladenine content of the DNAs. Other factors, influencing the accessibility of N6-methyladenine to the antibody-combining site have to be taken into consideration.

Characterization of antibodies specific for N6-methyladenosine and for 7-methylguanosine

Antibodies specific for N6-methyladenosine (m6A) and for 7-methylguanosine (m7G) were prepared by immunization of rabbits with nucleoside conjugates of bovine serum albumin (i.e, m6A--BSA and m7G-BSA). Specificity of each antibody was assessed by inhibition of the homologous precipitin reaction with various nucleosides. These analyses revealed that the antibodies elicited in response to m6A--BSA were specific for the N6-methyl moiety of adenosine with minimal or no cross-reactivity with BSA, adenosine, and guanosine. Although a major fraction of antibodies elicited in response to m7G--BSA were specific for m7G, considerable cross-reactivity was observed with BSA. These latter antibodies were removed by affinity chromatography utilizing BSA-Sepharose adsorbent. In similar fashion, antibodies specific for m6A and m7G were isolated by immunospecific adsorption to antigen-coupled Sepharose (e.g. m6A--BSA-Sepharose), eluted, and coupled to Sepharose. The ability of these antibody-coupled adsorbents to retain specific methylated [methyl-3H]nucleosides derived from [methyl-3H]tRNA digests was assessed. Both the anti-m7G and anti-m6A antibody adsorbents quantitatively and exclusively retained 7-[3H]methylguanosine and N6-[3H]methyladenosine, respectively. The application of these adsorbents to fractionate oligonucleotides and nucleic acids is discussed.

Denaturing effect of x-irradiation on deoxyribonucleic acid aqueous solutions: An immunochemical study

The denaturation of calf thymus DNA aqueous solutions following x-ray radiation (x-DNA) has been investigated with the help of a rabbit antidenatured DNA antiserum. These antibodies were shown to recognize exclusively single-stranded DNA determinants on DNA molecule in double immunodiffusion analysis. By means of this method it was possible to demonstrate that increasing numbers of single-stranded DNA determinants were formed in DNA solutions exposed to increasing doses of radiation. The rabbit serum appeared to be a highly sensitive reagent (0.5 mug/ml of single-stranded DNA) capable of detecting DNA denaturation when low ionizing doses were used and when only minor changes in DNA physico-chemical parameters were measurable. Antigenic comparison between x-DNA and heat-denatured DNA demonstrated that antigenic determinants are shared by the two molecules. The possible application of immunochemical methods to the study of nucleic acid denaturation by different physical and chemical agents is discussed.