Section 22.2.3.2. Nucleic acids

The three components of nucleic acids, i.e. phosphate groups, sugars and bases, all participate in hydrogen bonding to greater or lesser extent. The phosphate oxygen atoms can potentially act as acceptors of two or more hydrogen bonds and are frequently the recipients of hydrogen bonds from protein side chains in protein–DNA complexes. The sugar residues of RNA have a 2′-OH which can act as both hydrogen-bond donor and acceptor, and the 4′-O of both ribose and deoxyribose can potentially accept two hydrogen bonds.

It is the bases of DNA and RNA that have the greatest hydrogen-bonding potential, however, with a variety of hydrogen-bond donor or acceptor sites. Although each of the bases could theoretically occur in several tautomeric forms, only the canonical forms shown in Fig. 22.2.3.2 are actually observed in nucleic acids. This leads to clearly defined hydrogen-bonding patterns which are critical to both base pairing and protein–nucleic acid recognition. The —NH₂ and >NH groups act only as hydrogen-bond donors, and C=O only as acceptors, whereas the >N— centres are normally acceptors but at low pH can be protonated and act as hydrogen-bond donors.

Figure 22.2.3.2| top | pdf | Hydrogen-bonding potential of nucleic acid bases guanine (G), adenine (A), cytosine (C) and thymine (T) in their normal canonical forms.