Sedimentation Analysis of Novel DNA Structures Formed by Homo-Oligonucleotides

Abstract

Sedimentation velocity analysis has been used to examine the base-specific structural conformations and unusual hydrogen bonding patterns of model oligonucleotides. Homo-oligonucleotides composed of 8-28 residues of dA, dT, or dC nucleotides in 100 mM sodium phosphate, pH 7.4, at 20 degrees C behave as extended monomers. Comparison of experimentally determined sedimentation coefficients with theoretical values calculated for assumed helical structures show that dT and dC oligonucleotides are more compact than dA oligonucleotides. For dA oligonucleotides, the average width (1.7 nm), assuming a cylindrical model, is smaller than for control duplex DNA whereas the average rise per base (0.34 nm) is similar to that of B-DNA. For dC and dT oligonucleotides, there is an increase in the average widths (1.8 nm and 2.1 nm, respectively) whereas the average rise per base is smaller (0.28 nm and 0.23 nm, respectively). A significant shape change is observed for oligo dC(28) at lower temperatures (10 degrees C), corresponding to a fourfold decrease in axial ratio. Optical density, circular dichroism, and differential scanning calorimetry data confirm this shape change, attributable from nuclear magnetic resonance analysis to i-motif formation. Sedimentation equilibrium studies of oligo dG(8) and dG(16) reveal extensive self-association and the formation of G-quadruplexes. Continuous distribution analysis of sedimentation velocity data for oligo dG(16) identifies the presence of discrete dimers, tetramers, and dodecamers. These studies distinguish the conformational and colligative properties of the individual bases in DNA and their inherent capacity to promote specific folding pathways.

Phenomenological partial-specific volumes for G-quadruplex DNAs

“…Thus, these experiments do not establish a value of φ′ for a pure G-quartet structure, although they provide values for quadruplex-containing structures that may be biologically-relevant. The values of φ′ that we observe for G-quadruplex DNAs are similar to ones reported for populations of multimers of dG 8 and dG 16 ( φ′ ∼0.54 mL/g) that were likely to contain quadruplex structures (Hatters et al 2001). The values of φ′ obtained for the single-stranded 26-mer are the same, within-error, as that measured for a different single-stranded DNA by Chapman and Sturtevant (1969) and cited more recently (Durchschlag 1986).…”

The Macroscopic Rate of Nucleic Acid Translocation by Hepatitis C Virus Helicase NS3h Is Dependent on Both Sugar and Base Moieties

“…Partial specific volumes at temperatures different that 25 °C were calculated using the relationship ῡ T = ῡ 25 + 4.25 E −4 ( T − 25) 47. The value of the partial specific volume for 5′-dT 8 -Cy5-3′ and 5′-Cy5-18-mer-3′ was assumed to be equal to 0.61 ml/g and 0.58 ml/g, respectively based upon previously reported values for (dT) n , (dA) n , (dC) n , (dG) n 48…”

Fundamental aspects of the nucleic acid i-motif structures

“…Other techniques include sedimentation analysis 63 . It has been described that the C8 sequence adopts an Alike DNA structure at pH 7 and room temperature, whereas longer sequences containing 24 or 28 cytidine nucleotides assembled into an i-motif below ∼15-20°C.…”