File GNRA tetraloop.jpg thumb right 250 px Structure of a GNRA tetraloop from a group I self splicing intron . ref cite journal author Cate, J.H., Gooding, A.R., Podell, E., Zhou, K., Golden, B.L., Kundrot, C.E., Cech, T.R., Doudna, J.A. title Crystal structure of a group I ribozyme domain principles of RNA packing. journal Science year 1996 volume 273 pages 1676 1685 pmid 8781224 doi 10.1126 science.273.5282.1678 issue 5282 ref Tetraloops are a type of four base hairpin loop structural motif motif s in Nucleic acid secondary structure RNA secondary structure that cap many double helices ref cite journal author Woese CR, Winkers S, Gutell RR title Architecture of ribosomal RNA Constraints on the sequence of tetra loops journal Proc. Nati. Acad. Sci. USA year 1990 volume 87 pages 8467 71 pmid 2236056 doi 10.1073 pnas.87.21.8467 issue 21 pmc 54977 ref . Three types of tetraloops are common in ribosomal RNA GNRA, UNCG and CUUG. The GNRA tetraloop has a guanine adenine base pair where the guanine is 5 to the helix and the adenine is 3 to the helix. See also RNA Tertiary Structure section RNA Tertiary Structure Tetraloop receptor interactions Tetraloop receptor interactions References references molecular biology stub Category RNA fa fr T traboucle ... more details
Infobox rfam Name STAXI RNA image STAXI RNA.svg width 330 caption Consensus secondary structure of STAXI RNAs Symbol STAXI AltSymbols Rfam RF01728 miRBase miRBase family RNA type sRNA Tax domain Enterobacteriales GO SO CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The Ssbp, Topoisomerase, Antirestriction, XerDC Integrase RNA motif STAXI RNA motif is a conserved RNA like structure identified using bioinformatics . ref name Weinberg2010 cite journal author Weinberg Z, Wang JX, Bogue J, et al. title Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea and their metagenomes journal Genome Biol volume 11 issue 3 pages R31 year 2010 month March pmid 20230605 doi 10.1186 gb 2010 11 3 r31 url pmc 2864571 ref STAXI RNAs are located near to gene s encoding protein s that interact with DNA Single strand binding protein Ssbp , topoisomerase , XerDC integrase or are associated with such proteins antirestriction proteins, which inhibit restriction enzyme s . This observation raised the possibility that instances of the STAXI motif function as single stranded DNA molecules, perhaps during DNA replication or DNA repair . On the other hand, STAXI motifs often contain terminal loops conforming to the stable UNCG tetraloop , but the DNA version of this tetraloop TNCG is not especially stable. The STAXI motif consists of a simple pseudoknot 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 PotC RNA motif PsaA RNA motif TwoAYGGAY RNA motif YkkC yxkD leader References references External links Rfam id RF01728 name STAXI RNA Category Non coding RNA molecular cell biology stub ... more details
The TD 2 RNA motif is a conserved RNA structure found in Treponema denticola , ref cite journal author Weinberg Z title Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline journal Nucleic Acids Res. volume 35 issue 14 pages 4809 19 year 2007 pmid 17621584 pmc 1950547 doi 10.1093 nar gkm487 url author separator , author2 Barrick JE author3 Yao Z display authors 3 last4 Roth first4 A. last5 Kim first5 J. N. last6 Gore first6 J. last7 Wang first7 J. X. last8 Lee first8 E. R. last9 Block first9 K. F. ref as well as metagenome sequences extracted from a termite hindgut , which is known to be enriched for Spirochaete s. Since TD 2 RNAs are not typically positioned in 5 UTR s, the motif is presumed to correspond to a non coding RNA . The TD 2 RNA s secondary structure is supported by covariation see secondary structure prediction , and one stem typically has terminal GNRA tetraloop s, which are known to be especially stable. Surprisingly, however, the motif has an unusual number of stems containing runs of adenosine s that base pair with coordinate runs of uridine s. The lengths of these runs do correspond, thus comprising part of the covariation evidence in support of the motif s assignment as a conserved RNA. The first 5 most stem in the TD 2 RNA motif exhibits covariation, but also appears to be lost in some TD 2 RNAs. Seven TD 2 RNAs overlap predicted representatives of the TD 1 RNA motif , but it is unknown whether these two motifs can somehow be merged. References references Category Non coding RNA molecular cell biology stub ... more details
Infobox rfam Name Cyano 2 RNA motif image Cyano 2 RNA.svg width 350 caption Consensus secondary structure of Cyano 2 RNAs Symbol Cyano 2 AltSymbols Rfam RF01702 miRBase miRBase family RNA type sRNA Tax domain Synechococcus GO SO The Cyano 2 RNA motif is a conserved RNA structure identified by bioinformatics . ref name Weinberg2010 cite journal author Weinberg Z, Wang JX, Bogue J, et al. title Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea and their metagenomes journal Genome Biol volume 11 issue 3 pages R31 year 2010 month March pmid 20230605 doi 10.1186 gb 2010 11 3 r31 url pmc 2864571 ref Cyano 2 RNAs are found in Cyanobacteria l species classified within the genus Synechococcus . Many terminal loops in the two conserved stem loop s contain the nucleotide sequecne GCGA, and these sequences might in some cases form stable GNRA tetraloop s. Since the two stem loops are somewhat distant from one another it is possible that they represent two independent non coding RNA s that are often or always co transcription genetics transcribed . The region one thousand base pair s upstream of predicted Cyano 2 RNAs is usually devoid of annotated features such as RNA or protein coding gene s. This absence of annotated genes within one thousand base pairs is relatively unusual within bacteria . See also Yfr1 Yfr2 Cyano S1 RNA motif References references External links Rfam id RF01702 name Cyano 2 RNA Category Non coding RNA molecular cell biology stub ... more details
Infobox rfam Name Whalefall 1 RNA motif image Whalefall 1 RNA.svg width caption Consensus secondary structure of Whalefall 1 RNAs Symbol wf 1 AltSymbols Rfam RF01762 miRBase miRBase family RNA type sRNA Tax domain Whale fall metagenome GO SO CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The Whalefall 1 RNA motif also called wf 1 refers to a conserved RNA structure that was discovered using bioinformatics . ref name Weinberg2010 cite journal author Weinberg Z, Wang JX, Bogue J, et al. title Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea and their metagenomes journal Genome Biol volume 11 issue 3 pages R31 year 2010 month March pmid 20230605 doi 10.1186 gb 2010 11 3 r31 url pmc 2864571 ref ref name Weinberg2009 cite journal author Weinberg Z, Perreault J, Meyer MM, Breaker RR title Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis journal Nature volume 462 issue 7273 pages 656 9 year 2009 month December pmid 19956260 doi 10.1038 nature08586 url ref Structurally, the motif consists of two stem loop s see diagram , the second of which is often terminated by a CUUG tetraloop , which is an energetically favorable RNA sequence. Whalefall 1 RNAs are found only in DNA extracted from uncultivated bacteria found on whale fall , i.e., a whale carcass. As of 2010, Whalefall 1 RNAs have not been detected in any known, cultivated species of bacteria, and are thus one of several RNAs present in environmental samples . References references External links Rfam id RF01762 name Whalefall 1 RNA Category Non coding RNA molecular cell biology stub ... more details
ref Other motifs Tetraloop receptor interactions image GAAA Tetraloop.png 200px thumb left alt Stick representation of a GAAA tetraloop an example from the GNRA tetraloop family. ref name pmid8781224 ... url issn rendered with http pymol.sourceforge.net PyMOL ref Tetraloop receptor interactions combine base pairing and stacking interactions between the loop nucleotides of a tetraloop motif ... tetraloop receptor interaction journal J. Mol. Biol. volume 266 issue 3 pages 493 506 year 1997 month February pmid 9067606 doi 10.1006 jmbi.1996.0810 url issn ref In each of these tetraloop families ... of the tetraloop depends on the composition of bases within the loop and on the composition ..., Bevilacqua PC title Evidence that folding of an RNA tetraloop hairpin is less cooperative than its ... within Tetraloop receptor interactions. image Tetraloop Receptor GAAA.png 200px thumb right alt GAAA Tetraloop and Receptor Stick representation of tetraloop yellow and its receptor, showing both Watson Crick and Hoogsteen base pairing. ref name pmid8781224 Tetraloop receptor motifs are long range tertiary ... consisting of hydrogen bonding between the bases in the tetraloop to stemloop sequences in distal ... E title Involvement of a GNRA tetraloop in long range RNA tertiary interactions journal J. Mol ... of these tertiary interactions. For example, in GNRA tetraloop interactions, the second nucleotide of the tetraloop stacks directly on an A platform motif see above within the receptor. ref name Cate96 The sequence of the tetraloop and its receptor often covary so that the same type of tertiary contact can be made with different isoforms of the tetraloop and its cognate receptor. ref name pmid2258934 ... issn ref For example, the self splicing group I intron relies on tetraloop receptor motifs for its structure ... its 2 OH with the receptor and via interactions with the guanine of the GAAA tetraloop. The third ... R disser S, Tinoco I title Solution structure of Cobalt III hexammine complexed to the GAAA tetraloop ... more details
Image Stem loop.svg frame An example of an RNA stem loop Refimprove date May 2010 Stem loop intramolecular base pair ing is a pattern that can occur in single stranded DNA or, more commonly, in RNA . The structure is also known as a hairpin or hairpin loop. It occurs when two regions of the same strand, usually complementary in nucleotide sequence when read in opposite directions, base pair to form a double helix that ends in an unpaired loop. The resulting structure is a key building block of many RNA biomolecular structure Secondary structure secondary structure s. Formation and stability The formation of a stem loop structure is dependent on the stability of the resulting helix and loop regions. The first prerequisite is the presence of a sequence that can fold back on itself to form a paired double helix. The stability of this helix is determined by its length, the number of mismatches or bulges it contains a small number are tolerable, especially in a long helix and the base composition of the paired region. Pairings between guanine and cytosine have three hydrogen bond s and are more stable compared to adenine uracil pairings, which have only two. In RNA, guanine uracil pairings featuring two hydrogen bonds are as well common and favorable. Base stacking interactions, which align the pi bond pi orbitals of the bases aromatic rings in a favorable orientation, also promote helix formation. The stability of the loop also influences the formation of the stem loop structure. Loops that are less than three bases long are steric effects sterically impossible and do not form. Large loops with no secondary structure of their own such as pseudoknot pairing are also unstable. Optimal loop length tends to be about 4 8 bases long. One common loop with the sequence UUCG is known as the tetraloop and is particularly stable due to the base stacking interactions of its component nucleotides. Structural contexts Stem loops occur in pre microRNA structures and most famously in t ... more details
the 1 SRP54 binding motif, 2 Helix 6 GNAR tetraloop motif, 3 5e motif, and 4 UGU NR motif. Citation ... GNAR tetraloop motif. ref name pmid15611297 cite journal author Zwieb C, van Nues RW, Rosenblad MA ... url issn ref Helix 6 GNAR tetraloop The SRP RNAs of eukaryotes and Archaea have a GNAR tetraloop N ... more details
, as exemplified by the determination of an isolated tetraloop receptor motif structure published ... structure of a GAAA tetraloop receptor RNA journal EMBO J. volume 16 issue 24 pages 7490 9 year 1997 ... the tetraloop motif ..it should not come as a surprise if self folding RNA molecules were to make ... more details
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