Qiao W, Kalachikov S, Liu Y, Levicky R. Charge-Neutral Morpholino Microarrays for Nucleic Acid Analysis. Anal Biochem. 2012;[Epub ahead of print] doi:10.1016/j.ab.2012.12.001
Nice Information. Which one's are more stable duplexes? MO / DNA , DNA / DNA or RNA /DNA?
An MO/RNA heteruduplex is a bit more stable than a DNA/RNA heteroduplex and slightly less stable than an RNA/RNA duplex. Morpholinos invade natural RNA secondary structure because RNA duplexes need some mispairing to avoid processing by nucleases that recognize dsRNA; the overall stability of the perfectly-paired MO/RNA heteroduplex has lower energy than the mispaired RNA/RNA duplex.
I've not found the data on the relative stability of the DNA/DNA duplex vs. the Morpholino heteroduplexes, so I'm not sure where to fit that one in. It's less stable than the RNA duplex.