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. Author manuscript; available in PMC: 2008 Aug 22.
Published in final edited form as: ACS Chem Biol. 2007 Oct 19;2(10):674–684. doi: 10.1021/cb7001472

Table 1.

Physical properties of Yn-DNP3 ligands depicted in Figure 1a

Namea L (nm)b D (nm)c Kd (sol; nM)d Kd (cell; nM)e
Y16-DNP3 2.7 5.2 (±0.9) 3.0 ± 1.0 1.5 ± 0.5
Y26-DNP3 4.4 6.9(±1.3) 4.0 ± 1.0 1.2 ± 1.0
Y36-DNP3 6.1 10.4(±1.6) 4.0 ± 1.0 1.5 ± 1.0
Y46-DNP3 7.8 13.1(±2.5) 4.0 ± 1.0 1.6 ± 0.5
a

Y-shaped, trivalent (DNP3) ligand with n (= 16, 26, 36, or 46) bases in each of three single DNA strands that are annealed into the double stranded structure. Sequences of respective single strands are shown in Supplemental Table S1.

b

Estimated length (L) of each double-stranded arm of respective Yn-DNP3, based on length per base pair (0.34 nm).

c

Average rigid distances (D) between 5′ termini of Yn scaffolds for Yn-DNP3 ligands as determined by fluorescence resonance energy transfer measurements; numbers in parentheses indicate the range of distances between different termini due to some aplanarity and asymmetry in the rigid scaffolds (JB Lee, D Luo, in preparation).

d

Apparent dissociation constant for Yn-DNP3 ligands binding to IgE in solution, averaged from three experiments for each ligand (± standard deviation).

e

Apparent dissociation constant for Yn-DNP3 ligands binding to IgE-FcεRI on RBL cells, averaged from three experiments for each ligand (± standard deviation).