TABLE 2.

List of oligonucleotides used and their Gibbs free energy (kcal mol⁻¹)

Oligo name	DNA oligo sequence (5′-3′)	Complementary RNA sequence (5′-3′)	$\text{[math]}$ (kcal mol⁻¹)^a	Length
+10	TCAAGTCGTCATCTAAACAT	UACAAAUCUACUGCUGAACU	−21.5	20
+11	CTCAAGTCGTCATCTAAACA	ACAAAUCUACUGCUGAACUC	−22.4	20
+12	GCTCAAGTCGTCATCTAAAC	CAAAUCUACUGCUGAACUCG	−22	20
+13	CGCTCAAGTCGTCATCTAAA	AAAUCUACUGCUGAACUCGC	−23.8	20
+14	TCGCTCAAGTCGTCATCTAA	AAUCUACUGCUGAACUCGCU	−23.7	20
+15	GTCGCTCAAGTCGTCATCTA	AUCUACUGCUGAACUCGCUG	−24.2	20
+16	CGTCGCTCAAGTCGTCATCT	UCUACUGCUGAACUCGCUGC	−26.1	20
Name	RNA sequence (5′-3′)		$\text{[math]}$ (kcal mol⁻¹)^b	Length
dnaX	ACCGGCAGCCGCUACCCGCGCGCGGCCGGU		−18.2	30

^a $\text{[math]}$ for the RNA–DNA duplexes has been manually calculated based on measured values in 1 M NaCl (Sugimoto et al. 1995).
^b $\text{[math]}$ for the self-complementary RNA hairpin, dnaX, has been predicted using Mfold in 1 M NaCl (Zuker 2003).

The influence of downstream structured elements within mRNA on the dynamics of intersubunit rotation in ribosomes