Rates of formation and thermal stabilities of RNA:DNA and DNA:DNA duplexes at high concentrations of formamide

Abstract

The thermal stabilities of RNA:DNA hybrids are substantially greater than those of DNA:DNA duplexes in aqueous electrolyte solutions containing high concentrations of formamide. Association rates to form DNA:DNA duplexes and DNA:RNA hybrids have been measured in these solvents. There is a temperature range in which DNA:DNA rates are negligible and RNA:DNA rates close to optimal.

RNA:DNA hybrids are more stable than DNA:DNA duplexes in concentrated perchlorate and trichloroacetate solutions

“…In 4 M NaC104 at 700C (the Topt for RNA:DNA association in this system) the observed is 8. It has been reported that the DNA:DNA reassociation rate constant in 80% formamide, 0.4 M NaCl is about 1/3 to 1/3.6 of that in aqueous solution (8 There is a very clear decrease in the apparent limiting value of the degree of reaction in 4 M NaC104 as the temperature decreases from 70C to 40C. We believe that several factors may contribute to this phenomena.…”

“…The difference in stability between RNA:DNA hybrids and DNA:DNA duplexes in the usual aqueous solutions of non-denaturing salts (8,19,16) is much smaller than the differences observed for the above mentioned electrolytes and for formamide (8).…”

“…It is therefore possible to find conditions under which incubation of RNA with DNA duplexes leads to the formation of R-loops (7) and conditions under which RNA:DNA hybrids will form from the respective single strands but DNA:DNA duplexes are unstable and do not form (8). These conditions are useful for a number of applications (9,10).…”

RNA Hybridization to DNA Coupled with Cyanogen‐Bromide‐Activated Sephadex

“…In practical terms, this result indicates that the elution conditions required to recover acceptable yields of messenger-sized cRNA from DNA-Sephadex are 90% formamide, 0.2 M NaCl and 70°C, but the data also clearly show that ethanolamine-blocked CNBr-activated Sephadex is a reactive matrix, and therefore not ideal for nucleicacid-affinity chromatography. An improvement to the method described here is suggested by the work of Casey and Davidson [35] who have reported on the thermal stabilities of DNA . RNA duplexes in aqueous electrolyte solutions containing high concentrations of formamide.…”

Isolation and characterization of the glucose-6-phosphate dehydrogenase gene of Drosophila melanogaster

“…These DNA fragments (approx. 1 x 10m3 pg of coding sequence) were hybridized to adult polyribosomal poly(A) + RNA (30 pg) under conditions that allow RNA-DNA hybridization, but do not allow DNA-DNA reannealing (Casey and Davidson, 1977;Levy et al, 1982). The R,,t value achieved was 460, which is approx.…”