Thermodynamic and Structural Analysis of DNA Damage Architectures Related to Replication

Table 3

Thermodynamic parameters obtained from differential scanning calorimetry for replication relevant DNA architectures containing individual 3′ and 5′ overhangs, a terminal phosphate, and presence of both an overhang and phosphate. The presence of a 3′ or 5′ phosphate (PO₄), hydroxyl (OH) and a 6 mer overhang is indicated as an “X” or “Y” in the core dsDNA sequences.

ID	Base Sequence		𝑇𝑚 (°C)	Δ𝐻DSC; (kcal/mol)	Δ𝐻vH; (kcal/mol)	Δ𝑆; (cal/mol*K)	Δ𝐺25 (kcal/mol)	Δ𝑇𝑚 (°C)	ΔΔ𝐻DSC; (kcal/mol)	ΔΔ𝑆; (cal/mol*K)	ΔΔ𝐺25; (kcal/mol)
1	5^′-CGCAACCTGAAAX
	3^′-GCGTTGGACTTTY
1G	X = OH	Y = OH	60.91 ± 0.10	−77.28 ± 0.82	−62.39 ± 0.29	−231.4 ± 2.5	−8.34 ± 0.07	—	—	—	—
1H	X = OH	Y = PO4	60.62 ± 0.05	−74.67 ± 0.21	−62.34 ± 0.11	−223.7 ± 0.7	−8.01 ± 0.02	−0.29^a	+2.61^a	+7.7^a	+0.33^a
1I	X = AAAAAA	Y = OH	59.01 ± 0.05	−70.93 ± 0.12	−63.90 ± 0.08	−213.6 ± 0.4	−7.29 ± 0.01	−1.90^b	+6.35^b	+17.8^b	+1.05^b
1J	X = AAAAAA	Y = PO4	57.79 ± 0.02	−80.85 ± 0.39	−60.66 ± 0.12	−244.3 ± 1.2	−8.05 ± 0.04	−2.83^b	−6.18^b	−20.6^b	−0.04^b
								−1.22^a	−9.92^a	−30.7^a	−0.76^a
1K	X = GACTGT	Y = OH	58.72 ± 0.07	−73.83 ± 0.40	−61.58 ± 0.07	−222.5 ± 1.2	−7.53 ± 0.05	−2.19^b	+3.45^b	+8.9^b	+0.81^b
1L	X = GACTGT	Y = PO4	58.16 ± 0.03	−74.32 ± 0.73	−62.22 ± 0.36	−224.3 ± 2.2	−7.47 ± 0.07	−2.46^b	+0.35^b	−0.6^b	+0.54^b
								−0.56^a	−0.49^a	−1.8^a	+0.06^a
2	5^′-GCGTTGGACTTTX
	3^′-CGCAACCTGAAAY
2G	X = OH	Y = OH	61.88 ± 0.08	−88.31 ± 0.44	−61.38 ± 0.34	−263.6 ± 1.4	−9.76 ± 0.03	—	—	—	—
2H	X = PO4	Y = OH	61.37 ± 0.05	−86.31 ± 0.65	−59.81 ± 0.36	−258.0 ± 1.9	−9.42 ± 0.08	−0.51^a	+2.00^a	+5.6^a	+0.34^a
2I	X = OH	Y = AAAAAA	61.04 ± 0.02	−88.48 ± 0.36	−68.32 ± 0.11	−264.8 ± 1.1	−9.58 ± 0.04	−0.84^b	−0.17^b	−1.2^b	+0.18^b
2J	X = PO4	Y = AAAAAA	60.15 ± 0.13	−81.38 ± 0.15	−68.64 ± 0.16	−244.2 ± 0.4	−8.62 ± 0.04	−1.22^b	+4.93^b	+13.8^b	+0.80^b
								−0.89^a	+7.10^a	+20.6^a	+0.96^a
2K	X = OH	Y = GACTGT	60.37 ± 0.01	−90.36 ± 0.50	−64.46 ± 0.33	−270.9 ± 1.5	−9.62 ± 0.06	−1.51^b	−2.05^b	−7.3^b	+0.14^b
2L	X = PO4	Y = GACTGT	59.88 ± 0.07	−84.91 ± 0.30	−65.66 ± 0.20	−255.0 ± 0.9	−8.93 ± 0.04	−1.49^b	+1.40^b	+3.0^b	+0.49^b
								−0.49^a	+5.45^a	+15.9^a	+0.69^a

aIndicates the effects introduced by an individual phosphate. ΔΔ𝐻_DSC, ΔΔ𝑆, and ΔΔ𝐺₂₅ were determined by subtracting substrate G from H, I from J, and K from L. ^bIndicates the effects introduced by an individual overhang. ΔΔ𝐻_DSC, ΔΔ𝑆, and ΔΔ𝐺₂₅ were determined by subtracting substrate G from I, G from K, H from J, and H from L.