Generally a gene knockdown agent should achieve high sequence specificity and should lack off-target effects (non-antisense effects due to interactions with structures other than gene transcripts). Three major gene knockdown types are compared with respect to offtarget effects and sequence specificities: 1) phosphorothioate-linked DNA (S-DNA); 2) short interfering RNA (siRNA); and, 3) Morpholino.
S-DNAs cause multiple off-target effects, largely because their backbone sulfurs bind to many different proteins. S-DNAs also achieve poor sequence specificity because S-DNA/RNA duplexes as short as 7 base-pairs are cleaved by RNase H.
siRNAs cause several off-target effects, but improved designs may soon avoid such effects. siRNAs also provide only limited sequence specificity because their short guide sequences largely determine which gene transcripts will be blocked or cleaved, and those guide sequences appear to recognize insufficient sequence information to uniquely target a selected gene transcript. This specificity limitation is inherent in their mechanism of action and so probably cannot be greatly improved.
Morpholinos are virtually free of off-target effects - probably because they cannot interact electrostatically with proteins. Morpholinos also achieve exquisite sequence specificity - in large part because they must bind at least about 14 to 15 contiguous bases to block a gene transcript, and this constitutes sufficient sequence information to uniquely target a selected gene transcript. Because of their freedom from off-target effects, exquisite sequence specificity, complete stability in biological systems, and highly predictable targeting, Morpholinos dominate the most demanding of all gene knockdown applications, studies in developing embryos.