. Author manuscript; available in PMC: 2014 Oct 4.

Published in final edited form as: J Org Chem. 2013 Sep 25;78(19):10.1021/jo4015936. doi: 10.1021/jo4015936

Table 1.

ΔT_m values of duplexes between ONs modified with pyrene-functionalized thymine/uracil monomers and complementary DNA, measured relative to unmodified duplexes.^a

ON	Duplex	ΔT_m/°C
ON	Duplex	B =	O^b	N^b	W^b	X^b	Y^b	Z^b	Q^c	S^c	V^c	P^c
B1	5′-GBG ATA TGC		+2.5	-2.0	+7.0	+10.0	+10.5	+0.5	+5.0	-6.0	-0.5	+5.0
D2	3′-CAC TAT ACG		+2.5	-2.0	+7.0	+10.0	+10.5	+0.5	+5.0	-6.0	-0.5	+5.0

B2	5′-GTG ABA TGC		+6.0	+0.5	+14.0	+19.0	+15.5	+6.0	+14.0	+3.0	+6.0	+12.5
D2	3′-CAC TAT ACG		+6.0	+0.5	+14.0	+19.0	+15.5	+6.0	+14.0	+3.0	+6.0	+12.5

B3	5′-GTG ATA BGC		+3.0	-1.0	+10.5	+14.0	+11.5	-	-	-	-	+8.0^d
D2	3′-CAC TAT ACG		+3.0	-1.0	+10.5	+14.0	+11.5	-	-	-	-	+8.0^d

D1	5′-GTG ATA TGC		+3.5	-0.5	+6.5	+10.5	+10.0	+0.5	+1.5	-6.0	+1.0	+3.5
B4	3′-CAC BAT ACG		+3.5	-0.5	+6.5	+10.5	+10.0	+0.5	+1.5	-6.0	+1.0	+3.5

D1	5′-GTG ATA TGC		+8.0	+2.5	+15.5	+19.5	+16.5	+6.5	+13.0	+4.0	+6.5	+11.5
B5	3′-CAC TAB ACG		+8.0	+2.5	+15.5	+19.5	+16.5	+6.5	+13.0	+4.0	+6.5	+11.5

ΔT_m = change in T_m’s relative to unmodified reference duplex D1:D2 (T_m ≡ 29.5 °C); T_m’s determined as the first derivative maximum of denaturation curves (A₂₆₀ vs T) recorded in medium salt buffer ([Na⁺] = 110 mM, [Cl^-] = 100 mM, pH 7.0 (NaH₂PO₄/Na₂HPO₄)), using 1.0 μM of each strand. T_m values are averages of at least two measurements within 1.0 °C; A = adenin-9-yl-DNA monomer, C = cytosin-1-yl-DNA monomer, G = guanin-9-yl-DNA monomer, T = thymin-1-yl-DNA monomer. See Figure 1 for structures of monomers. “-” = not determined.

Previously reported in reference 32.

Previously reported in reference 34.

Not previously reported.