The ARRPOF RNA motif is a conserved
RNA
Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and deoxyribonucleic acid ( DNA) are nucleic acids. Along with lipids, proteins, and carbohydra ...
structure that was
discovered by bioinformatics.
Most ARRPOF motif examples are found in environmental DNA samples, and the host organism is unknown. The only classified organism with an ARRPOF motif is
Fusobacterium nucleatum
''Fusobacterium nucleatum'' is a Gram negative, anaerobic oral bacterium, commensal to the human oral cavity, that plays a role in periodontal disease. This organism is commonly recovered from different monocultured microbial and mixed infection ...
, and the ARRPOF motif instance is found in the
pKH9 plasmid.
It is hypothesized that the ARRPOF motif is associated with
plasmid
A plasmid is a small, extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently. They are most commonly found as small circular, double-stranded DNA molecules in bacteria; how ...
replication.
The pKH9 plasmid has a ''rep'' gene. Although these genes are known to be necessary for the replication of some plasmids, when this ''rep'' gene was eliminated from the pKH9 plasmid, the plasmid was still able to replicate.
Another region of the pKH9 plasmid was found that was necessary for replication,
and an ARRPOF motif occurs in part of this region.
Because plasmid replication involves
DNA molecules that are transiently single-stranded, it was also suggested
that it is possible that the ARRPOF motif functions as single-stranded DNA and not as RNA. In terms of
secondary structure
Protein secondary structure is the three dimensional conformational isomerism, form of ''local segments'' of proteins. The two most common Protein structure#Secondary structure, secondary structural elements are alpha helix, alpha helices and beta ...
, RNA and
DNA are difficult to distinguish when only sequence information is available.
References
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Non-coding RNA