Phenomenological partial-specific volumes for G-quadruplex DNAs |
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Authors: | Lance M Hellman David W Rodgers Michael Gregory Fried |
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Institution: | (1) Department of Molecular and Cellular Biochemistry, Center for Structural Biology, University of Kentucky, 741 South Limestone, Lexington, KY 40536-0509, USA; |
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Abstract: | Accurate partial-specific volume (`(v)] \overline{v} ) values are required for sedimentation velocity and sedimentation equilibrium analyses. For nucleic acids, the estimation
of these values is complicated by the fact that `(v)] \overline{v} depends on base composition, secondary structure, solvation and the concentrations and identities of ions in the surrounding
buffer. Here we describe sedimentation equilibrium measurements of the apparent isopotential partial-specific volume ϕ′ for two G-quadruplex DNAs and a single-stranded DNA of similar molecular weight and base composition. The G-quadruplex DNAs
are a 22 nucleotide fragment of the human telomere consensus sequence and a 27 nucleotide fragment from the human c-myc promoter.
The single-stranded DNA is 26 nucleotides long and is designed to have low propensity to form secondary structures. Parallel
measurements were made in buffers containing NaCl and in buffers containing KCl, spanning the range 0.09 M ≤ salt] ≤ 2.3 M.
Limiting values of ϕ′, extrapolated to salt] = 0 M, were: 22-mer (NaCl-form), 0.525 ± 0.004 mL/g; 22-mer (KCl-form), 0.531 ± 0.006 mL/g; 27-mer
(NaCl-form), 0.548 ± 0.005 mL/g; 27-mer (KCl-form), 0.557 ± 0.006 mL/g; 26-mer (NaCl-form), 0.555 ± 0.004 mL/g; 26-mer (KCl-form),
0.564 ± 0.006 mL/g. Small changes in ϕ′ with salt] suggest that large changes in counterion association or hydration are unlikely to take place over these concentration
ranges. |
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