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. Author manuscript; available in PMC: 2017 Mar 15.
Published in final edited form as: J Am Chem Soc. 2017 Jan 20;139(4):1372–1375. doi: 10.1021/jacs.6b10410

Table 1.

Properties of Single- and Double-Stranded Oligonucleotides Containing 8-DEA-tC in 1× PBS buffer pH 7.4a

Sequence Nameb Sequence ss Φem ds Φem ds λmax,abs/nm (ss) ds λmax,em/nm (ss) Tm (°C) ΔTm (°C)c
GA 5′-CGC-AGX-ATC-G-3′ 0.020 0.050 422 (425) 499 (499) 50.7 −5.1
CT 5′-CGC-ACX-TTC-G-3′ 0.020 0.025 414 (413) 492 (495) 54.7 +2.0
GC 5′-CGC-AGX-CTC-G-3′ 0.032 0.12 348 (425) 500 (499) 49.1 −14.5
CA 5′-CGC-ACX-ATC-G-3′ 0.014 0.017 410 (420) 494 (493) 57.4 +2.1
GG 5′-CGC-AGX-GTC-G-3′ 0.027 0.056 400 (415) 499 (498) 58.2 −7.0
CC 5′-CGC-ACX-CTC-G-3′ 0.013 0.024 413 (421) 496 (496) 60.2 +6.7
TA 5′-CGC-ATX-ATC-G-3′ 0.014 0.026 420 (417) 495 (495) 48.7 −1.6
TT 5′-CGC-ATX-TTC-G-3′ 0.025 0.041 416 (413) 495 (495) 48.5 +0.2
AA 5′-CGC-AAX-ATC-G-3′ 0.008 0.042 410 (415) 498 (497) 48.4 −2.6
AA mismatchd 5′-CGC-AAX-ATC-G-3′ 0.008 0.015 417 (415) 501 (497) 33.1 +9.6
AA AP sitee 5′-CGC-AAX-ATC-G-3′ 0.008 0.007 421 (415) 466 (497) 36.9 n.d.f
tC parent AAg 5′-CGC-AAtC-ATC-G-3′ 0.11 0.11 389 (390) 501 (502) 55.3 +4.3
a

Detailed procedures for photophysical measurements are given in the Supporting Information. Quantum yield measurements were performed at least in duplicate and the reported numbers are averaged. Typical errors based on standard deviation are approximately ±15%. ds = double-stranded; ss = single-stranded.

b

Sequences named for neighboring bases.

c

Tm for natural DNA duplex subtracted from Tm for the 8-DEA-tC-containing duplex.

d

AA sequenced annealed to 5′-CGA-TAT-TGC-G-3′ (8-DEA-tC opposite A).

e

AA sequenced annealed to 5′-CGA-T(dSpacer)T-TGC-G-3′ (8-DEA-tC opposite the dSpacer surrogate for an abasic site, AP).

f

Temperature-dependent CD changes were nonsigmoidal for the natural DNA strand and Tm could not be determined.

g

Sequence AA made with parent tC in place of 8-DEA-tC.