Folding of rna-dna hybrid molecules ?
First of all I was going to thank for making mfold available over the website. I have been using the program in analyses of possible structures of viruses and related molecules. Provided the interests focus on specific group of reverse transcribing elements , I came up with the specific question , I thought I would share. Presently the server offers separate forms for folding the RNA and DNA. While it is clearly 'demand driven concept' the molecules involved in the replication of the group of retroviruses do include RNA-DNA hybrids such us primer tRNA::cDNA 5'3' hybrid molecule. Provided above I started to wonder if perhaps it wouldn't be impossible to formulate a merge RNA-DNA folding form able to fold possible structures and evaluate the energies?