 RNA cyclic phosphate end

An RNA cyclic phosphate end is an RNA terminus in which a phosphate group links the $2^{\prime }$ and $3^{\prime }$ oxygens of the terminal ribose, forming a small cyclic phosphodiester bond arrangement. The ring is local to the terminal nucleotide; the whole RNA chain need not be circular. This end chemistry differs from both a free $3^{\prime }$ hydroxyl group and an ordinary terminal $3^{\prime }$ phosphate.^[ref]

The difference matters for RNA ligation. A 2012 study showed that RtcB opens the cyclic end to a $3^{\prime }$ phosphate before joining it to an RNA $5^{\prime }$ hydroxyl group. The reactions depended on GTP and enzyme guanylylation. Researchers followed labelled products over time using denaturing polyacrylamide gel electrophoresis, distinguishing starting cyclic ends, transient products and joined RNA.^[ref]

As a measurement example, two four-nucleotide RNA molecules could both spell AUGC while one ends in a free $3^{\prime }$ hydroxyl group and the other in a cyclic phosphate. A readout reporting only their letters would merge them, even though a reaction requiring the free hydroxyl group could distinguish them. Nucleotide sequence therefore does not completely specify terminal chemistry, and terminal chemistry can determine which RNA molecules an assay records.