Nucleic acid chemical reactivity

Several chemical compounds may cause inflammation or constriction of the blood vessel wall (vasoconstriction). Ergot alkaloids at high doses cause constriction and thickening of the vessel wall. Allylamine may also induce constriction of coronary arteries, thickening of their smooth muscle walls, and a disease state that corresponds to coronary heart disease. The culprit is a toxic reactive metabolite of allylamine, acrolein, that binds covalently to nucleophilic groups of proteins and nucleic acids in the cardiac myocytes. 

When thinking about chemical reactivity, chemists usually focus their attention on bonds, the covalent interactions between atoms within individual molecules. Also important, hotvever, particularly in large biomolecules like proteins and nucleic acids, are a variety of interactions between molecules that strongly affect molecular properties. Collectively called either intermolecular forces, van der Waals forces, or noncovalent interactions, they are of several different types dipole-dipole forces, dispersion forces, and hydrogen bonds. 

Quinone methides have been shown to be important intermediates in chemical synthesis,1 2 in lignin biosynthesis,3 and in the activity of antitumor and antibiotic agents.4 They react with many biologically relevant nucleophiles including alcohols,1 thiols,5-7 nucleic acids,8-10 proteins,6 11 and phosphodiesters.12 The reaction of nucleophiles with ortho- and /iara-quinone methides is pH dependent and can occur via either acid-catalyzed or uncatalyzed pathways.13-17 The electron transfer chemistry that is typical of the related quinones does not appear to play a role in the nucleophilic reactivity of QMs.18... 

Pullman, A., and B. Pullman. 1980. Electrostatic Effect of Macromolecular Structure on the Biochemical Reactivity of the Nucleic Acids. Significance for Chemical Carcinogenesis. Int. I. Quant. Chem., Quant. Biol. Symp. 7, 245. 

The reaction of metabolically generated polycyclic aromatic diol epoxides with DNA Ua vivo is believed to be an important and critical event in chemical carcinogenesis Cl,2). In recent years, much attention has been devoted to studies of diol epoxide-nucleic acid interactions in aqueous model systems. The most widely studied reactive intermediate is benzo(a)pyrene-7,8-diol-9,10-epoxide (BaPDE), which is the ultimate biologically active metabolite of the well known and ubiquitous environmental pollutant benzo(a)pyrene. There are four different stereoisomers of BaPDE (Figure 1) which are characterized by differences in biological activities, and reactivities with DNA (2-4). In this review, emphasis is placed on studies of reaction mechanisms of BPDE and related compounds with DNA, and the structures of the adducts formed. 

Chemical attachment of a detectable component to an oligonucleotide forms the basis for constructing a sensitive hybridization reagent. Unfortunately, the methods developed to crosslink or label other biological molecules such as proteins do not always apply to nucleic acids. The major reactive sites on proteins involve primary amines, sulfhydryls, carboxylates, or phenolates— groups that are relatively easy to derivatize. RNA and DNA contain none of these functionalities. 

Many of the chemical derivatization methods employed in these strategies involve the use of an activation step that produces a reactive intermediary. The activated species then can be used to couple a molecule containing a nucleophile, such as a primary amine or a thiol group. The following sections describe the chemical modification methods suitable for derivatizing individual nucleic acids as well as oligonucleotide polymers. 

Methods currently available for chemiluminescent detection of nucleic acids are not based on derivatization techniques that directly recognize one of the nucleic acid bases or nucleotides. For chemical derivatization-based chemiluminescent detection, the specific reactivity of alkyl glyoxals and arylglyoxals with adenine or guanine nucleotides has been investigated. 

Buta-1,3-diene (10.101, Fig. 10.24) is a gaseous chemical used heavily in the rubber and plastics industry, the presence of which in the atmosphere is also a concern. Butadiene is suspected of increasing the risks of hematopoietic cancers, and it is classified as a probable human carcinogen. Butadiene must undergo metabolic activation to become toxic the metabolites butadiene monoepoxide (10.102, a chiral compound) and diepoxybutane (10.103, which exists in two enantiomeric and one meso-form) react with nucleic acids and glutathione [160 - 163], as does a further metabolite, 3,4-epoxybutane-l,2-diol (10.105). Interestingly, butadiene monoepoxide is at least tenfold more reactive than diepoxybutane toward nucleic acids or H20. Conjugation between the C=C bond and the oxirane may account for this enhanced reactivity. 

In 2004, Rayner and coworkers reported a dynamic system for stabilizing nucleic acid duplexes by covalently appending small molecules [34]. These experiments started with a system in which 2-amino-2 -deoxyuridine (U-NH ) was site-specifically incorporated into nucleic acid strands via chemical synthesis. In the first example, U-NH was incorporated at the 3 end of the self-complementary U(-NH2)GCGCA DNA. This reactive amine-functionalized uridine was then allowed to undergo imine formation with a series of aldehydes (Ra-Rc), and aldehyde appendages that stabilize the DNA preferentially formed in the dynamic system. Upon equilibration and analysis, it was found that the double-stranded DNA modified with nalidixic aldehyde Rc at both U-NH positions was amplified 34% at the expense of Ra and Rb (Fig. 3.16). The Rc-appended DNA stabilizing modification corresponded to a 33% increase in (melting temperature). Furthermore, imine reduction of the stabilized DNA complex with NaCNBH, resulted in a 57% increase in T. ... 

The terminology nucleotide or nucleoside immediately directs our thoughts towards nucleic acids. Remarkably, nucleosides and nucleotides play other roles in biochemical reactions that are no less important than their function as part of nucleic acids. We also encounter more stmctural diversity. It is rare that the chemical and biochemical reactivities of these derivatives relate specihcally to the base plus sugar part of the structure, and usually reside elsewhere in the molecule. Almost certainly, it is this base plus sugar part of the structure that provides a recognition... 

Figure 5.8. Some members of the furanocoumarins family of NPs showing the key feature (red) shared by each structure that allows each to react chemically with some nucleic acid and proteins. Possessing hiological activity due to an inherent chemical reactivity is very rare among NPs for reasons explained in the text.

Seeman, N.C., Kallenbach, N.R. (1988) Nucleic acid junctions A successful experiment in macromolecular design. In Molecular Structure Chemical Reactivity and Biological Activity (Stezowski, J.J., Huang, J.L., Shao, M.C., eds.) Oxford University Press, Oxford, pp 189-194. 

The study of the reactivity of the nucleic acid bases utilizes indices based on the knowledge of the molecular electronic structure. There are two possible approaches to the prediction of the chemical properties of a molecule, the isolated and reacting-molecule models (or static and dynamic ones, respectively). Frequently, at least in the older publications, the chemical reactivity indices for heteroaromatic compounds were calculated in the -electron approximation, but in principle there is no difficulty to define similar quantities in the all-valence or allelectron methods. The subject is a very broad one, and we shall here mention only a new approach to chemical reactivity based on non-empirical calculations, namely the so-called molecular isopotential maps. 

The purines and pyrimidines are relatively stable compounds with considerable aromatic character. Nevertheless, they react with many different reagents and, under some relatively mild conditions, can be completely degraded to smaller molecules. The chemistry of these reactions is complex and is made more so by the fact that a reaction at one site on the ring may enhance the reactivity at other sites. The reactions of nucleic acids are largely the same as those of the individual nucleosides or nucleotides, the rates of reaction are often influenced by the position in the polynucleotide chain and by whether the nucleic acid is single or double stranded. The reactions of nucleosides and nucleotides are best understood in terms of the electronic properties of the various positions in the bases.26 33 Most of the chemical reactions are nucleophilic addition or displacement reactions of types that are discussed in Chapters 12 and 13. 

Formaldehyde is a toxic substance that reacts spontaneously with amino groups of proteins and nucleic acids, hydroxymethylating them and forming methylene-bridge crosslinks between them. Free formaldehyde therefore wreaks havoc in living cells and could not serve as a useful hydroxymethylating agent. In the form of A5,A10-methylenetetrahydrofolate, however, its chemical reactivity is attenuated but retained in a potentially available form where needed for specific enzymatic action. Formate, how-... 

---