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. Author manuscript; available in PMC: 2009 Dec 3.
Published in final edited form as: Biochemistry. 2008 Dec 2;47(48):12670–12679. doi: 10.1021/bi8012615

Figure 2.

Figure 2

Oligonucleotides used to identify the RNA hairpin-ligand interactions via 2DCS. Oligonucleotide 5 is an RNA hairpin library with six randomized positions (N). The library has 4096 unique members. Oligonucleotides 6-8 were used at 1,000 times the concentration of 1 in selection experiments to ensure that interactions occurred to loop nucleotides and not to the cassette. The oligonucleotides that comprise 6 are a mimic of the stem in 5; the sequence was altered such that it does not compete for RT-PCR primers. Oligonucleotides 7 and 8 are DNA competitors. Oligonucleotide 9 was used to study the binding of 6′-acylated neamine to 5′CG and 5′GC steps.