Table 1.

Rate constants for annealing (k_a) and reverse annealing (k_r) at 0.2 mM Mg²⁺ in the presence or absence of 889 nM NC

Parameter*	cTAR DNA	Zipper DNA	Loop DNA†	TAR RNA	Zipper RNA	Loop RNA†
ka (105 s−1·M−1)
−NC	0	0	0	0	0	0
+NC	8‡	10	1	2	0.1	0.06
kr (10−4 s−1)
−NC	0	1§	0.1§	0	5	0
+NC	0	18	4	0	5	3

*k_a denotes the annealing rate constant, and k_r denotes the reverse annealing rate constant. The annealing reaction kinetic curve is measured in the presence (+NC) or absence (−NC) of NC and fitted by a single exponential function. The single exponential rate constant k is k = k_r + k_a · [NA] (NA = reacting nucleic acid). k_r is determined by washing out the annealed product with NC (+NC) or buffer only (−NC) solution and fitting the kinetic curve by a single exponential function with a rate constant k_r. k_a is determined from k and k_r as k_a = (k− k_r)/[NA].

^†The loop annealing reaction kinetics is potentially complicated by steric interference of the biotin/streptavidin attachment group (denoted by ″B″ in Fig. 1). To avoid this complication, loop annealing kinetic were measured with an inverted TAR DNA construct, with the B group attached to the T64. Although there does not appear to be appreciable steric interference for the TAR DNA-loop DNA annealing (5), there is measurable steric interference of the TAR DNA-loop RNA annealing.

^‡This value is from our previously published data (17).

^§This value is based on the slow decay component of N_P. The fast decay component is associated with reverse annealing of one-armed annealed TAR DNA/zipper or loop DNA adduct.