Use of nucleic Acid analogs for the study of nucleic Acid interactions

Abstract

Unnatural nucleosides have been explored to expand the properties and the applications of oligonucleotides. This paper briefly summarizes nucleic acid analogs in which the base is modified or replaced by an unnatural stacking group for the study of nucleic acid interactions. We also describe the nucleoside analogs of a base pair-mimic structure that we have examined. Although the base pair-mimic nucleosides possess a simplified stacking moiety of a phenyl or naphthyl group, they can be used as a structural analog of Watson-Crick base pairs. Remarkably, they can adopt two different conformations responding to their interaction energies, and one of them is the stacking conformation of the nonpolar aromatic group causing the site-selective flipping of the opposite base in a DNA double helix. The base pair-mimic nucleosides can be used to study the mechanism responsible for the base stacking and the flipping of bases out of a nucleic acid duplex.

Figure 1

(a) Watson-Crick A/T and C/G base pairs. C1′ represents the 1′ carbon atom of deoxyribose in DNA. (b) Interbase hydrogen bonding and stacking interactions formed in a DNA duplex. A compensatory relationship is suggested between the interaction energies of the hydrogen bonding and the base stacking.

Figure 2

(a) Structures of unnatural nucleosides as a base analog with an aromatic hydrocarbon group in place of the purine and pyrimidine bases. (b) Structures of the base pair analogs that provide the interstrand crosslinking sites. The covalent bonds linking the nucleic acid bases are highlighted in blue.

Figure 3

Structures of the base pair-mimic nucleosides of deoxyadenosine and deoxycytidine derivatives tethering the nonpolar aromatic group (colored in red) through an ureido linker (blue).

Figure 4

(a) and (b) Possible conformations of the deoxyadenosine and deoxycytidine derivatives, the nonpolar group stacking conformation (a) and the base pair conformation (b). indicates the phenyl or naphthyl group. The arrow indicates the site of hydrogen bonding with a complementary base. (c) Comparison of the major interaction forces for the stacking of the A/T and C/G base pairs and the stacking of the A^phe and C^phe. The nonpolar aromatic group in the base pair-mimic nucleosides is indicated in red, and the complementary base is indicated in green.

Figure 5

(a) Stacking conformations of the dangling A^phe and C^phe (colored in red) at the 5′-end of a DNA duplex. (b) Side view of the DNA double helix, representing the interaction mechanism of the dangling end stacking (upper) and the Watson-Crick base pairing (lower). Cooperative interaction in the base pair-mimic nucleoside is suggested between stacking of the base moiety and stacking of the nonpolar group.

Figure 6

(a) The stacking conformation of A^phe opposite an abasic site F in the center of a DNA duplex. (b) Hybridization of the DNA strand bearing A^phe with a complementary target strand, followed by the formation of the flipped-out conformation. (c) The base flipping conformation induced by A^phe in an RNA/DNA duplex. The hybridized RNA strand is cleaved site-selectively at the 5′-side of the phosphodiester bond of the flipped-out ribonucleotide.

Figure 7

The equilibria between the conformations of the nonpolar group stacking and the base pairing of the deoxycytidine (a) and deoxyadenosine derivatives (b), where R indicates the nonpolar aromatic group of the phenyl or naphthyl group.