Table 3.

Formal electrostatic potentials (EP in kT/e) of the G·U pairs embedded in RNA helices and the interphosphate distances, compared with their canonical counterparts

RNA helices		EP at the major groove			Cross-strand phosphate distance
		GU	GC	AU	GU	GC	AU
Single G·U	1HLX	−2.2	−3.3	−3.2	19.1	15.2	15.2
	1IKD	−3.5	−3.0	−2.9	14.1	15.2	15.2
	434D*	−2.9	−2.6	−2.8	15.1	15.2	15.2
Motif I	1EKA	−1.9	−3.0	−3.0	19.8	15.2	15.2
	1QET	−2.8	−3.1	−3.0	17.2	15.2	15.2
	315D	−2.5	−3.1	−3.0	18.4	15.2	15.2
Motif II	1C0O	−2.7	−2.9	−2.8	14.1	15.2	15.2
	1GUC	−3.2	−3.0	−3.0	14.9	15.2	15.2
	1QES	−2.9	−2.9	−3.0	16.2	15.2	15.2
Motif III	1AJF	−3.4	−3.2	−3.1	15.1	15.2	15.2
	433D	−2.9	−3.4	−3.3	17.8	15.2	15.2
	472D	−3.3	−3.0	−3.0	15.4	15.2	15.2

Calculation of ‘formal’ potentials is accomplished by ‘turning off ’ charges for the bases and sugars, so that only contributions from the phosphates are considered.