European Biophysics Journal

, Volume 39, Issue 3, pp 389–396 | Cite as

Phenomenological partial-specific volumes for G-quadruplex DNAs

  • Lance M. Hellman
  • David W. Rodgers
  • Michael Gregory Fried
Original Paper

Abstract

Accurate partial-specific volume (\( \overline{v} \)) values are required for sedimentation velocity and sedimentation equilibrium analyses. For nucleic acids, the estimation of these values is complicated by the fact that \( \overline{v} \) 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.

Keywords

Partial-specific volume Analytical ultracentrifugation G-quadruplex DNA Single-stranded DNA 

List of symbols

\( \overline{v} \)

Partial-specific volume

ϕ′

Apparent partial-specific volume

ϕ′(E–S)

Apparent partial-specific volume determined by Edelstein–Schachman equation

ϕ′(avg)

Averaged apparent partial-specific volume

ϕ′(extrap)

Extrapolated apparent partial-specific volume to [salt] = 0 M

Mb

Buoyant molecular weight

Mapp

Apparent molecular weight

sT,B

Sedimentation coefficient at experimental temperature and buffer

s20,w

Sedimentation coefficient at 20°C in water

f/f0

Frictional ratio

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Copyright information

© European Biophysical Societies' Association 2009

Authors and Affiliations

  • Lance M. Hellman
    • 1
  • David W. Rodgers
    • 1
  • Michael Gregory Fried
    • 1
  1. 1.Department of Molecular and Cellular Biochemistry, Center for Structural BiologyUniversity of KentuckyLexingtonUSA

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