Table 2.

Sequences of 33 nt 2CNqA-ssDNAs and complementary qA_nitro-ssDNAs used in the DNA FRET study

Sequence namea	5′-3′ Sequence (X = 2CNqA, Y = qAnitro)
DNA-D0	CGA TCA AAA AAA ATT ACG ATT ATA AGG AGG AGG
DNA-D7	CGA TCA XAA AAA ATT ACG ATT ATA AGG AGG AGG
DNA-D9	CGA TCA AAX AAA ATT ACG ATT ATA AGG AGG AGG
DNA-D11	CGA TCA AAA AXA ATT ACG ATT ATA AGG AGG AGG
DNA-A0	CCT CCT CCT TAT AAT CGT AAT TTT TTT TGA TCG
DNA-A13	CCT CCT CCT TAT YAT CGT AAT TTT TTT TGA TCG
DNA-A14	CCT CCT CCT TAT AYT CGT AAT TTT TTT TGA TCG
DNA-A19	CCT CCT CCT TAT AAT CGT YAT TTT TTT TGA TCG
DNA-A20	CCT CCT CCT TAT AAT CGT AYT TTT TTT TGA TCG

^aSequence names indicate position of the donor (D) or the acceptor (A) in the oligonucleotide counted from its 5′ end, whereas DNA-D0 and DNA-A0 denote unmodified reference sequences.