= RNA cyclic phosphate end
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An <RNA cyclic phosphate end> is an <RNA> terminus in which a <phosphate> group links the $2'$ and $3'$ 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 $3'$ <hydroxyl group> and an ordinary terminal $3'$ phosphate.<GTP-dependent RtcB RNA splicing by Anupam K. Chakravarty and Stewart Shuman>[Figure1, cyclic-phosphate and linear-phosphate end structures]{ref}
The difference matters for <RNA ligation>. A 2012 study showed that <RtcB> opens the cyclic end to a $3'$ phosphate before joining it to an <RNA> $5'$ <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>.<GTP-dependent RtcB RNA splicing by Anupam K. Chakravarty and Stewart Shuman>[Abstract and Figures2–3, sequential end processing and labelled-product analysis]{ref}
As a measurement example, two four-<nucleotide> <RNA> molecules could both spell `AUGC` while one ends in a free $3'$ <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.
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