Ever since nucleic acids were discovered, the efforts of all those involved in investigation of their chemical properties had been focused, primarily at methods for breaking these compounds down as well as separation and identification of the resulting fragments. Intensive studies into the reactivity of nucleic acids began only after their primary structures had been definitively established. This field of organic chemistry received even greater attention since methods for isolating individual molecules of various types of RNA and DNA had been elaborated. Naturally, the first objects of directed chemical modification were tRNAs which are the simplest of all known nucleic acids. The functional importance of tRNAs was established soon after their discovery, and that immediately gave impetus to further research in this area.

As regards nucleic acids, our knowledge has grown tremendously about the major aspects of the reactivity of their constituent heterocyclic bases, N-glycosidic bonds, carbohydrate moieties, as well as internucleotide and terminal phosphate groups.

The macromolecules of nucleic acids enter into many reactions usually involving their monomer units. The mechanism of reactions of heterocyclic bases, N-glycosidic bonds, carbohydrate moieties and terminal phosphate (phosphomonoester) groups is generally the same as in the case of monomers. The internucleotide phosphate groups, which introduce a new element into the nucleic acid structure, impart new properties to nucleic acids. Other factors that render the reactivity of polynucleotides somewhat different also include their polyfunctionality and polymer structure. First of all, the presence of a great number of identical and structurally similar reactive sites in a nucleic acid molecule calls for judicious selection of the right conditions for conducting reactions in the desired direction. A major influence on the reactivity of heterocyclic bases is exerted by the steric factors associated with the presence of secondary and tertiary structures in nucleic acids. When reactions are conducted in aqueous solutions under conditions when the nucleic acid retains its ordered structure, some of the groups may be accessible to reagents, while others may be blocked. Thus, when reactions usually involving monomer units of nucleic acids are considered in the context of the nucleic acids themselves, one must first of all take into account the stereochemical factors governing their course.

It is known, for example, that a heterocyclic base may be attacked by a reagent at a right angle to the plane of the base, or the attack may proceed in the same plane. Certain reagents will readily interact with the base of a monomer, but in the broader environment of the entire nucleic acid such a base may be blocked in a particular way and thus inaccessible to one of the reagents (normally of the first type or even both). Such evidence accumulated while studying the chemical properties of nucleic acids has been extremely useful in investigating their structure. As has already been mentioned, it formed the basis of some methods for determining the nucleotide sequence of both RNA and DNA. Equally important are findings as regards the reactivity of heterocyclic bases for establishing the secondary and tertiary structure of nucleic acids. This approach is also widely used as a means to determine the structure of mixed biopolymers, such as nucleoproteins (in trying to elucidate the nature of the contacts between functionally significant nucleic acid sites of particular elements of the secondary and tertiary structure of proteins).

Binding heavy metal atoms to certain constituent bases of nucleic acids is instrumental in determining their structure from the results of X-ray analysis and electron microscopy. Controlled incorporation of paramagnetic and fluorescent groups into nucleic acids facilitates their investigation by spectroscopic techniques.

Knowledge about the reactivity of polynucleotides and nucleic acids has turned out to be beneficial not only for elucidating their structure, but also in many other ways. A case in point is activation of terminal groups in nucleic acids with the aid of special reagents. Nucleic acids modified in this manner may then be ligated (immobilized) to water-insoluble polymers for subsequent use in the separation of individual compounds from complex mixtures, the preparation of sorbents for affinity chromatography, and so on. In recent years, nucleic acids with groups capable of entering into covalent reactions have found wide application in biospecific marking of biopolymers. Such groups are usually coupled to terminal parts of nucleic acids.

Success of chemical modification of nucleic acids depends primarily on the specificity of the reagents used.

This chapter deals with the reactivity of individual constituents of nucleic acids, then some applications of the chemical nucleic acid modification method are described. Emphasis is placed on the reactivity of polynucleotides in aqueous solutions. There are two reasons for this: firstly, nucleic acids are readily soluble in water by virtue of their polyelectrolytic behavior and almost insoluble in organic solvents; secondly, it is only in aqueous solutions that the chemical modification method can be regarded as a tool for studying the three-dimensional structure and functioning of native nucleic acids (in organic solvents the native structure of nucleic acids is disturbed).