Doubly dangling DNA-DNA interactions for stitch ligation

[Albert Vilella]

Hi all,

I was searching for software to calculate the viability/stability of doubly dangling DNA-DNA interactions, and found out about MELTING. I am trying to figure out if I can use it for my specific purpose.

I would like to know how can I call MELTING (using v5.2) to calculate the viability/stability of double dangling ssDNA molecules (between 40-60bp long) where they have partial perfect overlaps as shown in the example below:

AGTTATATGATCTATAGTAAATCAGACACAAGGCACAAGGACAGGAAAATAGACAAATGT------------------------------

------------------------------TCCGTGTTCCTGTCCTTTTATCTGTTTACATTGTCTTTATCTTTCAGACTTTCGTCTAGG

Scanning through a template molecule, I am trying to find sticky ends (overlapping part) where each pair of oligos would have much higher propensity to hybridize with each other than form secondary structures with themselves or as dimers.

Looking forward to hearing from you,

Bests,

A.