Table 1.

3′6-carboxyfluorescein (6-Fam)-labeled RNA oligonucleotides used in this study

Oligonucleotide	Sequence	Kd for NusA–SKK (µM)
nutR boxA-spacer	5′-cgcucuuacacauucca-3′	126 ± 4
nutL boxA-spacer	5′-cgcucuuaaaaauuaa-3′	71 ± 4
rrn cac-boxA-spacer	5′-CACugcucuuuaacaauuua-3′	14 ± 0.2
nutR boxA	5′-cgcucuua-3′	n.d.
nutR spacer	5′-cacauucca-3′	137 ± 17
nutL spacer	5′-aaaauuaa-3′	24 ± 2.2
nutR boxA5-spacer	5′-cucucuuacacauucca-3′	124 ± 7
nutR boxA16-spacer	5′-cgcuauuacacauucca-3′	106 ± 4
nutR boxA69-spacer	5′-auagcggccacauucca-3′	n.d.
nutL boxA-spacer (mut)	5′-cgcucuuaaaaaggaa-3′	n.d.
rrn boxA	5′-ugcucuuua-3′	194 ± 38
rrn-upstream-boxA’ (I)	5′-CACugcuc-3′	26 ± 0.8
rrn-upstream (II)	5′-AGCGGCAC-3′	30 ± 1.9
rrn spacer (III)	5′-acaauuua-3′	71 ± 3.3
nutR boxB	5′-agcccugaaaaagggc-3′	n.d.

boxA nucleotides are shown in bold. Mutated nucleotides are underlined. Flanking regions of rrn-boxA are in capital letters. The spacer is shown in italic.