Base Pair Orientation

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(Redirected from Aligned Pair)

AU pairs are most stable when opposed rather than when aligned.

Two consecutive base pairs of the same type can be oriented in two general ways. When base pairs are "aligned," the same bases appear on the same side of the stack. Energy varies with base pair alignment. While consecutive GC and AU pairs are most stable when opposed, opposing GU pairs are positive in energy and in most cases will not form.