FIGURE 2.

Base orientation at the first energy minimum of the Watson–Crick, wobble, pyrimidine•pyrimidine mismatch, modified pyrimidine, and inosine pairs. (A) C•G, U•A, and U•G and the modified U•A, and U•G. The modified uridines for the U•A and U•G pairs include 2-thiouridine [s²U; (d),(e)]; 5-methylaminomethyluridine [mnm⁵U; (f),(g)]; 5-methoxycarbonylmethyl-2-thiouridine [mcm⁵s²U; (j),(k)]; 5-oxyacetic acid uridine [cmo⁵U; (l),(m)]; and 5-methylaminomethyl-2-thiouridine [mnm⁵s²U; (h),(i)]. (B) Pyrimidine•pyrimidine base-pairing of the ribonucleoside-5′phosphates. The geometries of the unmodified U•U and U•C pairs at the global energy minimum result in short ribose C1′–C1′ distances not compatible with A-form RNA helices [(a),(b), respectively]. The modified U•U and U•C pairs including 2-thiouridine [s²U; (e),(f)], and 5-oxyacetic acid uridine [cmo⁵U; (g),(h)] also result in short C1′–C1′ distances. However, base-pairing of the pyrimidine to pyrimidine ribonucleoside-5′-monophosphates exhibited a second energy minimum at which a hydrogen bonding distance conformed to the diameter of an A-form RNA duplex [figures (c),(d),(i),(j)]. Stability of this interaction was achieved through a bridging by one or two H₂O molecules. (C) Base-pair orientation of the pseudouridine (Ψ) and inosine (I) base pairs with A, G, C, and U at global energy minimum. Two hydrogen bonds are formed between Ψ and A [(a)], Ψ and G [(b)], and Ψ and C [(c)]. Inosine (I) binds A, C, and U with two hydrogen bonds each [(d)–(f)]. Stick models have oxygen in red, nitrogen in blue, and sulfur in yellow.