Table 2.

Donor-Acceptor Distance Calculation for the Initially Relaxed Crystal Structure and Four Representative Conformations from the MD Simulations

Sample	RDA	σDA	EFRET
0_pdb	48.1	10.3	0.31
121_pdb	52.3	11.8	0.43
31_pdb	56.6	7.2	0.54
26_pdb	53.3	10.5	0.45
00_pdb	61.2	8.9	0.65

The DNA from the MD structures was extended with the DNA³⁰ sequence. All parameters were computed using the FPS toolkit. 0_pdb indicates the initially relaxed structure, R_DA indicates the dye-to-dye distance in Å, σ_DA indicates the standard deviation, and E_FRET values are FRET efficiencies calculated from the weighted R_DA−s assuming a Förster radius of R₀ = 55.6 Å.