Hoogsteen Base Pairing (Molecular Biology)

Hoogsteen Base Pairing (Molecular Biology)

Nucleic acid bases can form a variety of base pairs. In all canonical duplex structures including B-DNA, A-DNA, and Z-DNA, the so-called Watson-Crick base pairs are found. The Watson-Crick base-pairings of guanine with cytosine and adenine with thymine are shown in Figure 1. The G to C and A to T complementarities are provided by specific hydrogen bond donors and acceptors between the bases. In a G:C base pair three hydrogen bonds are found between G-O6 and C-N4, G-N1 and C-N3, and G-N2 and C-O2 positions, and in an A:T base pair two hydrogen bonds are found between A-N6 and T-O4, and A-N1 and T-N3 positions. The two C1′ atoms within a G:C base pair and an A:T base pair are equidistant (~10.5 A). Thus the G:C and A:T base pairs in the Watson-Crick conformation are nearly iso-structural, from the point of the view of the sugar-phosphate backbone.

Figure 1. Schematic illustration of the A:T and G:C Watson-Crick and Hoogsteen base pairs. Hydrogen bonds are shown as dashed lines, and the distance between two C1′ atoms (shown as open squares) is drawn with a thin line. The numbering system of the purine and pyrimidine rings is shown.

In earlier crystallographic analyses of nucleic acid base pairs,it was found that an A:T base pair can also adopt a different conformation. Instead of using the N1 position of adenine to base pair with N3 of thymine, the N7 position of adenine was used. This type of A:T base pair was named Hoogsteen base pair (1). A striking difference between those two types of base pairs is that the C1′-C1′ distance in the Hoogsteen base pair of 8.65 A is significantly shorter than that of the Watson-Crick base pair of 10.5 A. Therefore the Hoogsteen base pair is not compatible structurally with the Watson-Crick base pair in B-DNA. The incorporation of a Hoogsteen base pair in B-DNA destabilizes the duplex structure. A similar G:C Hoogsteen base pair is not stable unless the C is protonated at the N3 position.

However,certain chemical modifications may enhance the stability of the Hoogsteen base pair. It was shown that the modified nucleoside 3-isodeoxyadenosine (iA) forms a stable base pair with thymine (T) using the Hoogsteen conformation, and the iA:T base pair is fully compatible with the normal Watson-Crick base pair as evident from the stable duplex of d(CG[iA]TCG) 2 shown by NMR analysis (2). Another modification which stabilizes the Hoogsteen base pair involves the use of 8-amino-adenine in which the amino group at the C8 position can form an additional hydrogen bond with the O2 of thymine (3). Those modified bases may find applications when the Hoogsteen base pairing is needed in nucleic acid structures.