Nearest-neighbor parameters for 7-deaza-adenosine·uridine base pairs in RNA duplexes

Abstract

One of the major limitations in RNA structure prediction is the lack of information about the effect of nonstandard nucleotides on stability. The nonstandard nucleotide 7-deaza-adenosine (7DA) is a naturally occurring analog of adenosine that has been studied for medicinal purposes and is commonly referred to as tubercidin. In 7DA, the nitrogen in the 7 position of adenosine is replaced by a carbon. Differences in RNA duplex stability due to the removal of this nitrogen can be attributed to a possible change in hydration and a difference in base stacking interactions resulting from changes in the electrostatics of the ring. In order to determine how 7DA affects the stability of RNA, optical melting experiments were conducted on RNA duplexes that contain either internal or terminal 7DA·U pairs with all possible nearest-neighbor combinations. On average, duplexes containing 7DA·U pairs are 0.43 and 0.07 kcal/mol less stable than what is predicted for the same duplex containing internal and terminal A-U pairs, respectively. Thermodynamic parameters for all nearest-neighbor combinations of 7DA·U pairs were derived from the data. These parameters can be used to more accurately predict the secondary structure and stability of RNA duplexes containing 7DA·U pairs.

Keywords: 7-deaza-adenosine; nearest-neighbor parameters; nonstandard nucleotide; optical melting.

FIGURE 1.

Likely conformation of a Watson–Crick A-U base pair (A), I·U pair (B), A·Ψ pair (C), and 7DA·U pair (D).

FIGURE 2.

Computed Mulliken charges (A,B) and electrostatic potential maps (C,D) for adenosine and 7DA, respectively.

FIGURE 3.

The ability of the C7 (blue) on 7DA (red) to impact stacking interactions is likely decided by the positioning (5′ or 3′) of the 7DA relative to the adjacent base (green). Stacks are shown as follows: (A) 5′-U7-3′; (B) 5′-G7-3′; (C) 5′-7U-3′; and (D) 5′-7G-3′. These stacks were generated using InsightII (Accelrys) for standard A-form geometries and PyMOL (The PyMOL Molecular Graphics System, Version 1.7.4, Schrödinger) for visualization.