A parallel stranded 2′-5′ double helical model for poly A: crystal structure of adenylyl-2′,5′-adenosine trihydrate and comparison with the tetrahydrate structure

Abstract

2′–5′ are second in importance only to 3′–5′ nucleic acids. They have attracted special attention in recent years because of their potential use in the design and synthesis of antisense oligomers. We have now obtained the crystal structure of adenylyl 2′–5′ adenosine trihydrate (A2′p5′A) as sequel to our earlier studies on A2′p5′A tetrahydrate and other 2′–5′ dinucleotide structures. A2′p5′A trihydrate crystals belong to the orthorhombic space group P2 12 1 2 1 with unit cell dimensions a=9.284 A ̊ (3), b=15.360 A ̊ (3) and c=21.610 A ̊ (3), one nucleotide and three water molecules in the asymmetric unit. CuKα diffractometer data were collected upto sin θ/λ=0.59 A ̊ −1. The structure was solved by direct methods and refined by full matrix least squares to an R value of 0.125. The 5′ and the 2′ end adenine bases are in the syn and anti conformations with respect to their ribose moieties as in the tetrahydrate structure. The syn conformation is stabilized by the N3–O5′ intramolecular hydrogen bond. The 5′ and 2′ ribose moieties show C3′ and C2′ endo puckering, respectively. The conformation about the phosphodiester bonds for the 5′ and 2′ ends are g − ,g − and about the C4′–C3′ bonds is g − t. Presumably, charge neutralization in A2′p5′A is achieved through the protonation of the base. Differences in the hydrogen bond network between the two hydrated structures are discussed. A parallel stranded 2′–5′double helical model for poly A bearing strong resemblance to the 3′–5′ poly AH + model earlier proposed from fiber diffraction studies has been proposed.