. 2022 Aug 17;121(20):3987–4000. doi: 10.1016/j.bpj.2022.08.015

Table 1.

The 20-mer DNA sequences used for simulation in complex with Exd-Ubx homeodomain transcription factor

#Sl	System	Sequence (5ʹ→3′)
1	HH	GC C₁C₂G₃A₄ T₅G₆A₇T₈T₉T₁₀A₁₁T₁₂ G₁₃G₁₄C₁₅C₁₆ GC
2	LH	GC C₁C₂C₃C₄ T₅G₆A₇T₈T₉T₁₀A₁₁T₁₂ G₁₃G₁₄C₁₅C₁₆ GC
3	LH1	GC A₁A₂A₃A₄ T₅G₆A₇T₈T₉T₁₀A₁₁T₁₂ G₁₃G₁₄C₁₅C₁₆ GC
4	HL	GC C₁C₂G₃A₄ T₅G₆A₇T₈T₉T₁₀A₁₁T₁₂ A₁₃A₁₄A₁₅A₁₆ GC
5	LL	GC C₁C₂C₃C₄ T₅G₆A₇T₈T₉T₁₀A₁₁T₁₂ A₁₃A₁₄A₁₅A₁₆ GC
6	LL1	GC A₁A₂A₃A₄ T₅G₆A₇T₈T₉T₁₀A₁₁T₁₂ A₁₃A₁₄A₁₅A₁₆ GC

All sequences comprised of the core motif preferentially bound by the homeodomain, flanked by varying 4-mer sequences on the 5′ and 3′ ends. All sequences were capped with a basepaired GC dinucleotide to prevent end fraying during the simulation. H, high-affinity flank; L, low-affinity flank; e.g., LH, low (L) affinity 5′ flank and high (H) affinity 3′ flank. GC cap; 3′ flank; 5′ flank; core motif; GC cap.