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. Author manuscript; available in PMC: 2013 Apr 1.
Published in final edited form as: Anal Biochem. 2012 Jan 28;423(1):178–183. doi: 10.1016/j.ab.2012.01.017

Table 1.

Summary of Polyamide-DNA Interactions Observed by Fluorescence Spectroscopy

# Sequence Site Dye locn % Δ int Kd, nM
1 dImImPyγImPyPyβDp head T37 10 ± 5 7.8 ± 1.6
2 dImImPyPyγPyImPyPyβDp head T37 34 ± 2 2.3 ± 0.3
3 dImImPyImγPyPyβPyβDp tail T37 25 ± 3 50 ± 15
4 dImImβImγPyPyPyPyβDp tail T37 38 ± 3 140 ± 30
5 dImPyPyPyγPyImImPyβDp head T34 22 ± 4 11.4 ± 1
6 dImPyPyβPyPyPyγ-PyPyβPyPyPyPyβTab n/a T3 5.5 ± 1.5 4.8 ± 0.6
a

Im = imidazole, dIm = desamino-imidazole, Py = pyrrole, β= beta alanine, γ= gamma turn, Ta = 3,3’-diamino-N-methyldipropylamine, Dp = N,N-dimethylaminopropylamine. Site refers to the expected binding location based on recognition rules. Dye locn refers to the position of the TAMRA dye. % Δ int refers to the percent change in fluorescence intensity between the free DNA and PA-bound DNA. Unless otherwise noted, DNA binding to all PAs was measured with HP1 in 10 mM HEPES, 50 mM NaCl, pH 7.4, 25°C.

b

Kds were measured with HP2 and 200 µM nt calf thymus DNA, an additive carrier necessary to achieve reliable isotherms with this PA. Such carriers are used frequently in the literature and are known to decrease non-specific interactions between nucleic acids and proteins or small molecules [38; 39].