The Ssbp, Topoisomerase, Antirestriction, XerDC Integrase RNA motif (STAXI 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 ...

-like structure identified using

bioinformatics Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combi ...

. STAXI RNAs are located near to

gene In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a ba ...

s encoding

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respo ...

s that interact with DNA ( Ssbp,

topoisomerase DNA topoisomerases (or topoisomerases) are enzymes that catalyze changes in the topological state of DNA, interconverting relaxed and supercoiled forms, linked (catenated) and unlinked species, and knotted and unknotted DNA. Topological issues i ...

, XerDC

integrase Retroviral integrase (IN) is an enzyme produced by a retrovirus (such as HIV) that integrates—forms covalent links between—its genetic information into that of the host cell it infects. Retroviral INs are not to be confused with phage int ...

) or are associated with such proteins ( antirestriction proteins, which inhibit

restriction enzyme A restriction enzyme, restriction endonuclease, REase, ENase or'' restrictase '' is an enzyme that cleaves DNA into fragments at or near specific recognition sites within molecules known as restriction sites. Restriction enzymes are one class o ...

s). This observation raised the possibility that instances of the STAXI motif function as single-stranded DNA molecules, perhaps during

DNA replication In molecular biology, DNA replication is the biological process of producing two identical replicas of DNA from one original DNA molecule. DNA replication occurs in all living organisms acting as the most essential part for biological inheritanc ...

DNA repair DNA repair is a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome. In human cells, both normal metabolic activities and environmental factors such as radiation can cause DNA dam ...

. On the other hand, STAXI motifs often contain terminal loops conforming to the stable UNCG

tetraloop Tetraloops are a type of four-base hairpin loop motifs in RNA secondary structure that cap many double helices. There are many variants of the tetraloop. The published ones include ANYA, CUYG, GNRA, UNAC and UNCG. Three types of tetraloops are ...

, but the DNA version of this tetraloop (TNCG) is not especially stable. The STAXI motif consists of a simple

pseudoknot __NOTOC__ A pseudoknot is a nucleic acid secondary structure containing at least two stem-loop structures in which half of one stem is intercalated between the two halves of another stem. The pseudoknot was first recognized in the turnip yellow ...

structure that is repeated two or more times (see diagram). A number of other RNAs were identified in the same study, including: * Bacteroidales-1 RNA motif * Chlorobi-1 RNA motif * JUMPstart RNA motif * Lactis-plasmid RNA motif *

Ocean-V RNA motif The Ocean-V RNA motif is a conserved RNA structure discovered using bioinformatics. Only a few Ocean-V RNA sequences have been detected, all in sequences derived from DNA that was extracted from uncultivated bacteria found in ocean The ...

potC RNA motif The ''potC'' RNA motif is a conserved RNA structure discovered using bioinformatics. The RNA is detected only in genome sequences derived from DNA that was extracted from uncultivated marine bacteria. Thus, this RNA is present in environmen ...

psaA RNA motif The ''psaA'' RNA motif describes a class of RNAs with a common secondary structure. ''psaA'' RNAs are exclusively found in locations that presumably correspond to the 5' untranslated regions of operons formed of ''psaA'' and ''psaB'' genes. F ...

TwoAYGGAY RNA motif The TwoAYGGAY RNA motif is a conserved RNA structure identified by bioinformatics. Its name refers to the conserved AYGGAY nucleotide sequence (Y refers to either a C or U nucleotide) found in the motif's two terminal loops (see diagram). The R ...

ykkC-yxkD leader The ykkC/yxkD leader is a conserved sequence, conserved Cis-regulatory element, RNA structure found Upstream and downstream (DNA), upstream of the ykkC and yxkD genes in ''Bacillus subtilis'' and related genes in other bacteria. The function of t ...

References

External links

* Non-coding RNA {{molecular-cell-biology-stub