The Basics of Molecular Pathology

Abstract

2As we will learn, hydrogen bonding is also important in understanding the interaction of proteins with each other and with other types of macromolecules. However, since proteins have many side chains that can be ionically charged, whereas DNA and RNA have only two and one such ionically charged units, respectively, on the entire macromolecule, the ionic potential will be much greater for proteins than for nucleic acids. Similarly, proteins will be able to form hydrophobic and hydrophilic pockets in regions of their sequence, which DNA and RNA macromolecules cannot do. The bottom line is that two related phenomenon will dictate the strength of the hybridization between DNA/DNA and cDNA/RNA: Hydrogen bonds 2. Breathability of the macromoleculeWe discuss the concept of breathability in much more detail later in this book. For now, let's simply understand the term as a way to denote the fact that hybridized macromolecules will have a tendency to separate and reattach. When in this state, they are more susceptible to complete separation. This tendency of RNA/cDNA and DNA/DNA hybrids to separate and reattach (and separate and reattach again) we call "breathability." THE BASIC UNITS OF DNA AND RNALet's look at how an understanding of the structure of DNA and RNA can help us when doing in situ hybridization. First, let's discuss the phosphodiester bond. Although the phosphodiester bond is strong, high temperatures can cause a small percentage of these bonds to break in formalin-fixed, paraffin-embedded tissues. During the paraffin embedding process, prolonged exposure to temperatures at 65°C are used. If you extract the DNA from such samples and compare it to fresh, unfixed samples of the same tissues, it will be evident that the high temperatures have induced rare nicks among the doublestranded human DNA or, as shown by multiple groups, in the doubled-stranded HPV DNA. The term "nick" simply refers to breakage of the phosphodiester bond. Since the two DNA strands are perfectly matched strands in parallel and antiparallel orientation, they certainly would be able to stay hybridized if a small percentage of the phosphodiester bonds were broken, much the same way that a zipper