Table 1.

Equilibrium binding of different RNAs and their mutants with extended or mutated 3′-ends to the full-length ProQ and its N-terminal domain (NTD)

	K d [nM]
32P-RNA	ProQ	NTD
MicA	15 ± 5.1	21 ± 10
SibA	2.4 ± 0.85	4.7 ± 0.89
cspE-3′	13 ± 4.5	4.5 ± 1.5a
malM-3′	12 ± 5.3a	12 ± 4.8
lpp-5′	21 ± 5.9a	>1000
hupA-5′	9.3 ± 4.1b	>1000
lpp-5′-mut	3 ± 1.3	1.3 ± 0.83
lpp-5′-term	3.6 ± 1.3	5.1 ± 1
lpp-5′-hp	20 ± 2.8b	n. d.
hupA-5′-mut	14 ± 8b	16 ± 4.7
hupA-5′-term	10 ± 5	8.5 ± 0.96
hupA-5′-hp	18 ± 1.9b	n. d.
cspE-3′-ext+5	31 ± 14a	17 ± 7.5
cspE-3′-ext+22	17 ± 8.7	n. d.
malM-3′-ext+5	33 ± 4.2	n. d.
malM-3′-ext+17	8.4 ± 2.6b	n. d.

The K_d values were obtained by fitting the data to the quadratic equation. The average K_d values with standard deviations were calculated from three to five independent experiments, except for malM-3′ binding to ProQ (nine replicates) and the NTD (eleven replicates), and cspE-3′ binding to ProQ (six replicates) and the NTD (seven replicates). All individual experiments of malM-3′ binding to the NTD are shown on Supplementary Figure S1.

^aThe endpoint value of 100% was assumed in the data fitting.

^bIn the K_d value calculations the fractions of both RNA–protein complexes were summed together.

n. d.: the binding was essentially undetectable up to 1 μM concentration of the NTD.