The binding of poly(rA) and poly(rU) to denatured DNA.I. Model studies with homopolymers.

Abstract

We have compared the properties of the poly(rA).oligo(dT) complex with those of the poly(rU).oligo(dA)n complex. Three main differences were found. First, poly(rA) and oligo(dT)n do not form a complex in concentrations of CsCl exceeding 2 M because the poly(rA) is insoluble in high salt. If the complex is made in low salt, it is destabilized if the CsCl concentration is raised. Complexes between poly(rU) and oligo(dA)n, on the other hand, can be formed in CsCl concentrations up to 6.6 M. Second, complexes between poly(rA) and oligo(dT)n are more rapidly destabilized with decreasing chain length than complexes between poly(rU) and oligo(dA)n. Third, the density of the complex between poly(rA) and poly(dT) in CsCl is slightly lower than that of poly(dT), whereas the density of the complex between poly(rU) and poly(dA) in CsCl is at least 300 g/cm3 higher than that of poly(dA). These results explain why denatured natural DNAs that bind poly(rU) in a CsCl gradient usually do not bind poly(rA).

Electrophoretic strand separation of long DNAs with poly (U,G) in agarose gels

“…It is possible that further improvements in separation could be obtained by altering the ionic conditions or by adding Mg2+ ions. It should also be possible to separate strands in gels with polymers that cannot be used in CsCl gradients, like poly(C) which does not self-aggregate [1,18] or poly(A), which is insoluble at high Cs concentrations (see [20,21]). Poly(C), for instance, should preferentially bind to the 1-strand of phage lambda DNA, making it the slower-moving band in agarose and reversing the mobility found with poly(U,G).…”