Design, Synthesis, and Analysis of Minor Groove Binder Pyrrolepolyamide-𝟐^′-Deoxyguanosine Hybrids

Table 1

Δ𝑇_𝑚 values (°C) for the DNA duplexs with ligand (Hybrid 1, Hybrid 2, Hybrid 3, or Dst) at several [ligand]/[duplex] ratios in buffer consisting of 10 mM sodium phosphate, 10 mM NaCl, and 0.1 mM Na₂EDTA at pH 7.0.

[ligand]/[duplex]		1∶1	2∶1	3∶1
	DNA 1	2.1	2.3	—
Hybrid 1	DNA 2	− 0.1	0.2	—
	DNA 3	−0.4	0.3	—
	DNA 1	2.7	3.8	3.9
Hybrid 2	DNA 2	−0.3	−0.2	− 0.1
	DNA 3	0.2	0.3	0.3
	DNA 1	5.6	5.7	5.8
Hybrid 3	DNA 2	0.1	0.2	0.5
	DNA 3	− 0.3	−0.5	−0.2
	DNA 1	22.9	22.9	23.5
Dst	DNA 2	3.0	6.5	6.9
	DNA 3	15.2	16.3	16.3

^∗Δ𝑇_m value = (𝑇_m value in the presence of ligand)-(𝑇_m value in the absence of ligand).
**DNA duplexs: DNA 1= d-(5^-CGCAAATTGGC-3^)-d-(3^-GCGTTTAACCG-5^) 𝑇_m= 32.2°C.
DNA 2= d-(5^-CGCAGACTGGC-3^)-d-(3^-GCGTCTGACCG-5^) 𝑇_m= 39.5°C.
DNA 3= d-(5^-GCACGACTACG-3^)-d-(3^-CGTGCTGATGC-5^) 𝑇_m= 33.9°C.
DNA 1 contains the high affinity binding site (5^-AAATT-3^) of Dst.