Flanking A·T Basepairs Destabilize the B∗ Conformation of DNA A-Tracts

Abstract

Capillary electrophoresis has been used to characterize the interaction of monovalent cations with 26-basepair DNA oligomers containing A-tracts embedded in flanking sequences with different basepair compositions. A 26-basepair random-sequence oligomer was used as the reference; lithium and tetrabutylammonium (TBA(+)) ions were used as the probe ions. The free solution mobilities of the A-tract and random-sequence oligomers were identical in solutions containing <∼ 100 mM cation. At higher cation concentrations, the A-tract oligomers migrated faster than the reference oligomer in TBA(+) and slower than the reference in Li(+). Hence, cations of different sizes can interact very differently with DNA A-tracts. The increased mobilities observed in TBA(+) suggest that the large hydrophobic TBA(+) ions are preferentially excluded from the vicinity of the A-tract minor groove, increasing the effective net charge of the A-tract oligomers and increasing the mobility. By contrast, Li(+) ions decrease the mobility of A-tract oligomers because of the preferential localization of Li(+) ions in the narrow A-tract minor groove. Embedding the A-tracts in AT-rich flanking sequences markedly alters preferential interactions of monovalent cations with the B(∗) conformation. Hence, A-tracts embedded in genomic DNA may or may not interact preferentially with monovalent cations, depending on the relative number of A · T basepairs in the flanking sequences.

Ml proteins from Mesorhizobium loti and MucR from Brucella abortus: an AT-rich core DNA-target site and oligomerization ability

“…AT-rich sequences have a lower persistence length (the quantitative term for the stiffeness of a polymer) and they are more bendable than GC-rich sequences 16 . However, repetitive runs of four or more consecutive adenines (A-tracts) increases the rigidity of DNA strand and narrow the minor groove 16 , 28 , 29 . The T-A step is a flexible element of DNA that can serve to interrupt A-tracts and widen the minor groove 24 , 30 .…”

Using capillary electrophoresis to characterize the hydrodynamic and electrostatic properties of DNA in solutions containing various monovalent cations

“…Additional studies of monovalent cation localization were carried out using 20-and 26-bp dsDNA oligomers containing one or two A n -or A n T m -tracts. The results showed that (a) preferential localization of monovalent cations occurred in the A-tract minor groove because localization could be blocked by netropsin, a minor-groove binding drug [34]; (b) each A-tract localized monovalent cations independently, since cation localization was independent of A-tract phasing [31]; (c) single A 4or A 5 -tracts did not exhibit preferential cation localization when embedded in AT-rich flanking sequences [34,79]; (d) more monovalent cations were localized in A 2n -tracts than in A n T n -tracts, even though the total length of the A-tract was the same [79]; and (e), upon preferential counterion localization, the effective charge of an Atract was reduced, on average, by about one-third charge [78]. Recent molecular dynamics simulations have led to similar conclusions [80].…”

Electrophoretic Mobility of DNA in Solutions of High Ionic Strength

“…We have been using free-solution capillary electrophoresis (CE) to evaluate the properties of small ssDNA and dsDNA in solutions containing various monovalent cations. Our previous studies have addressed the dependence of the electrophoretic mobility of DNA on molecular weight (22)(23)(24), ionic strength (25,26), curvature (27)(28)(29)(30), charge density (23,(30)(31)(32), and solution viscosity (33). Here, we have used CE to determine the dependence of the electrophoretic mobility of ssDNA and dsDNA on ionic strength in solutions containing high concentrations of Na þ ions.…”