Correction: DNA Sequence Determinants Controlling Affinity, Stability and Shape of DNA Complexes Bound by the Nucleoid Protein Fis.

[This corrects the article DOI: 10.1371/journal.pone.0150189.].

There is an error in Tables 2, 3 and 4. The numbering in the first row of the second column does not line up with the corresponding DNA base sequence below. For example, in the sequence aaatttGTTTGAATTTTGAGCaaattt, the fourth capital “T” should be directly below the number 0. The publisher apologizes for the errors.

Table 2

Effects of flanking DNA substitutions on Fis-DNA binding affinity and complex stability

			Fold-
	-10 -9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10	Kd (nM)	difference2	t1/2 (min)
F1(±8T)	aaatttGTTTGAATTTTGAGCaaattt	0.2 ± 0.07	1	41 ± 4
F1±8A	aaattaGTTTGAATTTTGAGCtaattt	2.1 ± 0.2	10	5 ± 0.5
F1±8C	aaattcGTTTGAATTTTGAGCgaattt	0.7 ± 0.2	3	14 ± 1
F1±8G	aaattgGTTTGAATTTTGAGCcaattt	30 ± 6	150	< 0.25
F1±9A	aaatatGTTTGAATTTTGAGCatattt	0.5 ± 0.2	3	22 ± 2
F1±9C	aaatctGTTTGAATTTTGAGCagattt	0.3 ± 0.1	2	30 ± 2
F1±9G	aaatgtGTTTGAATTTTGAGCacattt	0.6 ± 0.2	3	25 ± 2
F1±10A	aaaattGTTTGAATTTTGAGCaatttt	0.5 ± 0.1	3	36 ± 5
F1±10C	aaacttGTTTGAATTTTGAGCaagttt	0.3 ± 0.1	2	44 ± 1
F1±10G	aaagttGTTTGAATTTTGAGCaacttt	0.5 ± 0.1	3	38 ± 5
F14	gggtttGTTTGAATTTTGAGCaaaccc	0.5 ± 0.1	3	ND3
F15	ccctttGTTTGAATTTTGAGCaaaggg	0.4 ± 0.2	2	ND
F16	gcggttGTTTGAATTTTGAGCaaccgc	0.5 ± 0.2	3	ND
F33	aaaggtGTTTGAATTTTGAGCaccttt	0.6 ± 0.1	6	ND
F34	aagcttGTTTGAATTTTGAGCaacgtt	0.2 ± 0.1	1	8 ± 1
INV	tttaaaGTTTGAATTTTGAGCtttaaa	33 ± 3	165	< 0.25
INV±8G	tttaagGTTTGAATTTTGAGCcttaaa	250 ± 20	1250	ND
INV±8C	tttaacGTTTGAATTTTGAGCgttaaa	6.0 ± 2	30	ND
INV±8T	tttaatGTTTGAATTTTGAGCattaaa	2.3 ± 0.7	12	4 ± 0.7
INV-CAT	tttcatGTTTGAATTTTGAGCatgaaa	2.9 ± 1.0	15	ND
INV-GAT	tttgatGTTTGAATTTTGAGCatcaaa	2.0 ± 0.6	10	ND
INV±9-10T	tttattGTTTGAATTTTGAGCaataaa	0.4 ± 0.1	2	ND

1Upper case letters represent the 15 bp core Fis binding site sequence and those in lower case represent flanking DNA. Underlined and bold nucleotides highlight those that differ from F1.

2Fold-difference relative to the apparent equilibrium dissociation constant (Kd) for WT Fis with F1 DNA.

3Not determined.

Table 3

Interplay between Fis residues contacting the flanking sequences and binding site variants

	-10 -9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10	Fis protein	Kd (nM)	Fold-difference1
F1	aaatttGTTTGAATTTTGAGCaaattt	WT	0.2 ± 0.05	1
		R71A	0.5 ± 0.2	2.5
		T75A	0.3 ± 0.8	1.5
		N73A	29 ± 0.2	140
F27	aaatttGTTTGAACTTTGAGCaaattt	WT	0.2 ± 0.1	1
		R71A	2.8 ± 0.5	14
		T75A	3.5 ± 0.9	18
F28	aaatttGTTTGAGCGTTGAGCaaattt	WT	28 ± 4	140
		R71A	470 ± 100	2300
		T75A	> 1000	> 5000
F32	aaatttGGAGGAATTTTCTCCaaattt	WT	28 ± 5	140
		R71A	73 ± 11	370
		T75A	76 ± 10	380
F1±8G	aaattgGTTTGAATTTTGAGCcaattt	WT	30 ± 0.8	150
		R71A	450 ± 20	2270
		T75A	48 ± 5	240

1Fold-difference relative to the apparent equilibrium dissociation constant (Kd) for WT Fis with F1 DNA.

Table 4

Effects of flanking and core substitutions on Fis-induced DNA bending

		Gel mobility assay		In-gel FRET assay
		(Bend angle°)		(FRET efficiency)
		Free	Complex	Free	Complex	Distance (Å)	Angle (°)
	-10 -9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10					(complex)1	(complex)2
F1	aaatttGTTTGAATTTTGAGCaaattt	51 ± 3	119 ± 3	0.09 ± 0.01	0.27 ± 0.01	82.6	68
F1±8A	aaattaGTTTGAATTTTGAGCtaattt	48 ± 3	109 ± 3	-	-	-	-
F1±8C	aaattcGTTTGAATTTTGAGCgaattt	47 ± 3	126 ± 2	0.13 ± 0.01	0.26 ± 0.01	83.3	66
F1±8G	aaattgGTTTGAATTTTGAGCcaattt	41 ± 1	99 ± 1	0.09 ± 0.01	0.23 ± 0.01	85.6	61
F1±9A	aaatatGTTTGAATTTTGAGCatattt	46 ± 3	104 ± 2	-	-	-	-
F1±9C	aaatctGTTTGAATTTTGAGCagattt	45 ± 1	99 ± 1	-	-	-	-
F1±9G	aaatgtGTTTGAATTTTGAGCacattt	42 ± 2	89 ± 2	0.08 ± 0.03	0.18 ± 0.04	90.1	50
INV	tttaaaGTTTGAATTTTGAGCtttaaa	≤ 36	62 ± 1	0.06 ± 0.04	0.14 ± 0.01	94.7	36
F34	aagcttGTTTGAATTTTGAGCaacgtt	~ 0	62 ± 3	0.12 ± 0.02	0.26 ± 0.02	83.3	66
F18	aaatttGTTGGAATTTTCAGCaaattt	51 ± 2	116 ± 1	-	-	-	-
F31	aaatttGTAGGAATTTTCTGCaaattt	51 ± 2	108 ± 2	-	-	-	-
F32	aaatttGGAGGAATTTTCTCCaaattt	52 ± 1	106 ± 2	-	-	-	-

1Inter-fluorophore distance calculated from FRET efficiency as detailed in the Methods.

2Angle calculated assuming a single central bend in the Fis-bound DNA as detailed in the Methods.