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The strand concentration was determined spectrophotometrically.
An analytical solution for the concentration distribution of mobile strands at intermediate hybridization times provides a convenient tool to calculate the mobile strand concentration profiles.
The model fit parameters provide a description of the network strand length distribution in the tight network and show that the network strand concentration increases and the network strand length decreases when a higher crosslinker concentration was used to prepare the tight network.
The nucleotide strand concentration parameter is implemented using a natural logarithmic function.
The equation to predict the melting temperature, without the use of nucleotide strand concentration (DNA) as one of the parameters is provided in the supporting information (Supporting Text S1).
In particular, the model introduced here accounts quantitatively and explicitly for disruption in stacking interactions, breakage of hydrogen bonding, salt effects and the nucleotide strand concentration in the melting of DNA.
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When the Cy3 and Cy5 dyes were attached to different oligonucleotide strands, the strand concentrations were 14 and 7 nM, respectively.
The single strand concentrations for rGACG AGCGUCA, rGACG AGUGUCA, rGACA AGUGUCA, rGACU AGAGUCA, and rGGU AGGCCA were each ∼2.0 mM, unless otherwise noted.
While preparing samples for crystallization, we noted an unusually slow CuAAC reaction at high concentrations of the 7-EAA-modified self-complementary 16 nt strand (∼1 mM), with an increase in reaction rate at lower strand concentrations.
Any side product is assumed to be contributed to a slight mismatch in strand concentrations loaded during assembly, preventing all nucleic acid strands from forming into the 3WJ complex.
A series of samples containing the M1/MC2 duplex only, and GNP M1/MC2s (with or without PEG modification, with ∼85 M1 strands per GNP) with identical effective final M1/MC2 strand concentrations (80 nM) and DNA strand loading per GNP (85) are mixed with YO-PRO-1 (400 nM, M1/MC2 YO-PRO-1 M1/MC2 YO-PRO-1:5) for 10 M1/MC2 YO-PRO-1e I (2 U/L) is introduced.
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