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 ... more details
Summary author Sarah Bertino Jucker, M. and Pardi, A. 1995. Solution Structure of the CUUG Hairpin Loop A Novel RNA Tetraloop Motif. Biochemistry 34, 14416 14427. http pubs.acs.org doi pdf 10.1021 bi00044a019 PDB 1rng Licensing self cc by 3.0 ... more details
Orphan date January 2011 File STAXI RNA.svg right frame Consensus secondary structure of STAXI RNAs. This figure is adapted from a previous publication. ref name Weinberg2010 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 . References references 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, Barrick JE, Yao Z, et al. 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 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
Rfam box acc DHBV epsilon description Duck HBV RNA encapsidation signal epsilon abbreviation DHBV epsilon type Cis reg avg length 57 avg identity 00 ss Published PMID 9776740 se PMID 9776740 type Cis reg The Duck HBV RNA encapsidation signal epsilon is an RNA structure that is shown to facilitate encapsidation of the pregenomic RNA required for Viral replication replication . DHBV is used as a model to understand human HBV . DHBV epsilon consists of a stem structure, a bulge and an apical stem loop . The RNA structure was determined by chemical probing, NMR spectroscopy NMR analysis and by mutagenesis . ref cite journal doi 10.1093 nar 26.21.4818 last1 Smith Gj first1 3rd last2 Donello first2 JE last3 L ck first3 R last4 Steger first4 G last5 Hope first5 TJ title The hepatitis B virus post transcriptional regulatory element contains two conserved RNA stem loops which are required for function journal Nucleic acids research volume 26 issue 21 pages 4818 27 year 1998 pmid 9776740 pmc 147918 ref A recent NMR analysis of the DHBV epsilon have shown that the apical loop to be capped by a stable well structured UGUU tetraloop. ref cite journal last1 Girard first1 FC last2 Ottink first2 OM last3 Ampt first3 KA last4 Tessari first4 M last5 Wijmenga first5 SS title Thermodynamics and NMR studies on Duck, Heron and Human HBV encapsidation signals journal Nucleic acids research volume 35 issue 8 pages 2800 11 year 2007 pmid 17430968 pmc 1885660 doi 10.1093 nar gkm131 ref See also HBV RNA encapsidation signal epsilon Heron HBV RNA encapsidation signal epsilon References reflist 1 External links Rfam id DHBV epsilon name Duck HBV RNA encapsidation signal epsilon Category Cis regulatory RNA elements molecular cell biology stub ... more details
Rfam box acc HHBV epsilon description Heron HBV RNA encapsidation signal epsilon abbreviation HHBV epsilon type Cis reg avg length 57 avg identity 00 ss Published PMID 9188560 se PMID 9188560 type Cis reg The Heron HBV RNA encapsidation signal epsilon is an RNA structure that is shown to facilitate encapsidation of the pregenomic RNA required for replication. The HHBV epsilon consists of a stem structure, a bulge and an apical stem loop . The RNA structure has been determined by chemical probing and by mutagenesis . ref cite journal last1 Beck first1 J last2 Nassal first2 M title Sequence and structure specific determinants in the interaction between the RNA encapsidation signal and reverse transcriptase of avian hepatitis B viruses. journal Journal of virology volume 71 issue 7 pages 4971 80 year 1997 pmid 9188560 pmc 191728 ref A recent NMR spectroscopy NMR analysis of the HHBV epsilon have shown that the apical loop to be capped by a stable well structured UGUU tetraloop. ref cite journal last1 Girard first1 FC last2 Ottink first2 OM last3 Ampt first3 KA last4 Tessari first4 M last5 Wijmenga first5 SS title Thermodynamics and NMR studies on Duck, Heron and Human HBV encapsidation signals journal Nucleic acids research volume 35 issue 8 pages 2800 11 year 2007 pmid 17430968 pmc 1885660 doi 10.1093 nar gkm131 ref See also HBV RNA encapsidation signal epsilon Duck HBV RNA encapsidation signal epsilon References reflist 1 External links Rfam id HHBV epsilon name Heron hepatitis B virus epsilon Category Cis regulatory RNA elements molecular cell biology stub ... more details
File Cyano 2 RNA.svg right frame Consensus secondary structure of Cyano 2 RNAs. This figure is adapted from a previous publication. ref name Weinberg2010 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 Category Non coding RNA molecular cell biology stub ... more details
File Whalefall 1 RNA.svg right frame Consensus secondary structure of Whalefall 1 RNAs. This figure is adapted from a previous publication. ref name Weinberg2010 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 Category Non coding RNA molecular cell biology stub ... more details
302 issn 0028 0836 pmid 16541064 doi 10.1038 nature04586 ref Other motifs Tetraloop receptor interactions ... representation of a GAAA tetraloop an example from the GNRA tetraloop family. ref name pmid8781224 PDB ... 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 ... Tetraloop receptor interactions. image Tetraloop Receptor GAAA.png 200px thumb right alt Colored dice with checkered background GAAA Tetraloop and Receptor Stick representation of tetraloop yellow and its receptor, showing both Watson Crick and Hoogsteen base pairing. ref name pmid8781224 Tetraloop ... 85404 654 2 oclc doi url accessdate ref consisting of hydrogen bonding between the bases in the tetraloop ... journal author Jaeger L, Michel F, Westhof E title Involvement of a GNRA tetraloop in long range RNA ... interactions are an important component 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 ... on tetraloop receptor motifs for its structure and function. ref name Cate96 ref name Jaeger94 Specifically ... of the GAAA tetraloop. The third adenine forms a triple base pair. A minor motif Multiple image ... tetraloop, and metal ion binding to G A mismatches journal J. Mol. Biol. volume 295 issue 5 pages ... 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 lollipop shaped 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. Obviously, 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 struct ... more details
have been identified shown in the Figure in dark gray the 1 SRP54 binding motif, 2 Helix 6 GNAR tetraloop ... residue of the helix 6 GNAR tetraloop motif. ref name pmid15611297 cite journal author Zwieb C, van ... doi 10.1261 rna.7203605 url issn ref Helix 6 GNAR tetraloop The SRP RNAs of eukaryotes and Archaea have a GNAR tetraloop N is for any nucleotide , R is for a purine in helix 6. Its conserved adenosine ... more details
, as exemplified by the determination of an isolated tetraloop receptor motif structure published ... 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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