A theoretical framework is proposed for the analysis of adhesion between cells or of cells to surfaces when the adhesion is mediated by reversible bonds between specific molecules such as antigen and antibody, lectin and carbohydrate, or enzyme and substrate. From a knowledge of the reaction rates for reactants in solution and of their diffusion constants both in solution and on membranes, it is possible to estimate reaction rates for membrane-bound reactants. Two models are developed for predicting the rate of bond formation between cells and are compared with experiments. The force required to separate two cells is shown to be greater than the expected electrical forces between cells, and of the same order of magnitude as the forces required to pull gangliosides and perhaps some integral membrane proteins out of the cell membrane.

https://science.sciencemag.org/content/sci/200/4342/618.full.pdf

Models for the specific adhesion of cells to cells

An understanding of DNA methylation and its potential role in gene control during development, aging and cancer has been hampered by a lack of sensitive methods which can resolve exact methylation patterns from only small quantities of DNA. We have now developed a genomic sequencing technique which is capable of detecting every methylated cytosine on both strands of any target sequence, using DNA isolated from fewer than 100 cells. In this method, sodium bisulphite is used to convert cytosine residues to uracil residues in single-stranded DNA, under conditions whereby 5-methylcytosine remains non-reactive. The converted DNA is amplified with specific primers and sequenced. All the cytosine residues remaining in the sequence represent previously methylated cytosines in the genome. The work described has defined procedures that maximise the efficiency of denaturation, bisulphite conversion and amplification, to permit methylation mapping of single genes from small amounts of genomic DNA, readily available from germ cells and early developmental stages.

/pdf/high-sensitivity-mapping-of-methylated-cytosines-2111z737na.pdf

High sensitivity mapping of methylated cytosines.

Oxidative Nucleobase Modifications Leading to Strand Scission

During these last years, a powerful methodology has been developed to study the secondary and tertiary structure of RNA molecules either free or engaged in complex with proteins. This method allows to test the reactivity of every nucleotide towards chemical or enzymatic probes. The detection of the modified nucleotides and RNase cleavages can be conducted by two different paths which are oriented both by the length of the studied RNA and by the nature of the probes used. The first one uses end-labeled RNA molecule and allows to detect only scissions in the RNA chain. The second approach is based on primer extension by reverse transcriptase and detects stops of transcription at modified or cleaved nucleotides. The synthesized cDNA fragments are then sized by electrophoresis on polyacrylamide:urea gels. In this paper, the various structure probes used so far are described, and their utilization is discussed.

Probing the structure of RNAs in solution

Organic Synthesis on Soluble Polymer Supports: Liquid-Phase Methodologies.

Publisher Summary This chapter discusses that nucleic acids are labile in solutions of extreme pHs and at high temperatures; the chemical modification must preferably be performed at a pH region around neutrality and at a temperature near 37°C or below. Chemical reactions that satisfy these requirements have been developed and used in nucleic acid studies. Bisulfite deaminates cytosine to give uracil. The reaction conditions are satisfactorily mild, and no deamination of adenine or guanine moieties takes place under the conditions employed. Although bisulfite does react with uracil and thymine under similar conditions, the bisulfite adducts formed are easily reverted to the parent pyrimidines. Therefore, cytosine residues in nucleic acids can be selectively transformed into uracil residues by the use of bisulfite. The most important feature of bisulfite reactions is their strict selectivity for the single-stranded regions of nucleic acids. Thus, bisulfite is a reagent that meets in excellent fashion the requirements to serve as a probe of nucleic acid functions and structures. In spite of the fact that the bisulfite reactions of nucleic acid components were discovered only several years ago, extensive studies of the reaction at the polynucleotide level have already been made and a number of applications reported. These involve (1) application for synthetic purposes, (2) studies on physical and biochemical properties of bisulfite-treated polynucleotides, (3) cross-linking of nucleic acid with protein, (4) chemical modifications of transfer RNA with the purpose of elucidating functional sites and conformations, and (5) induction of mutation in microorganisms.

Bisulfite modification of nucleic acids and their constituents.

The selective degradation of pyrimidines in nucleic acids by permanganate oxidation.

The mutagenic action of sodium bisulfite.

The permanganate oxidation of thymine.

/pdf/reaction-of-sodium-hypochlorite-with-nucleic-acids-and-their-4l5y36jt74.pdf

Hikoya Hayatsu

Papers

Bisulfite modification of nucleic acids and their constituents.

The selective degradation of pyrimidines in nucleic acids by permanganate oxidation.

The mutagenic action of sodium bisulfite.

The permanganate oxidation of thymine.

Reaction of Sodium Hypochlorite with Nucleic Acids and Their Constituents