| pubmed-article:19485416 | rdf:type | pubmed:Citation | lld:pubmed |
| pubmed-article:19485416 | lifeskim:mentions | umls-concept:C0205102 | lld:lifeskim |
| pubmed-article:19485416 | lifeskim:mentions | umls-concept:C0035668 | lld:lifeskim |
| pubmed-article:19485416 | lifeskim:mentions | umls-concept:C0184512 | lld:lifeskim |
| pubmed-article:19485416 | lifeskim:mentions | umls-concept:C0181687 | lld:lifeskim |
| pubmed-article:19485416 | lifeskim:mentions | umls-concept:C0205117 | lld:lifeskim |
| pubmed-article:19485416 | lifeskim:mentions | umls-concept:C1709450 | lld:lifeskim |
| pubmed-article:19485416 | pubmed:issue | 24 | lld:pubmed |
| pubmed-article:19485416 | pubmed:dateCreated | 2009-6-16 | lld:pubmed |
| pubmed-article:19485416 | pubmed:abstractText | RNA internal loops are often important sites for folding and function. Residues in internal loops can have pKa values shifted close to neutral pH because of the local structural environment. A series of RNA internal loops were studied at different pH by UV absorbance versus temperature melting experiments and imino proton nuclear magnetic resonance (NMR). A stabilizing CA pair forms at pH 7 in the CG/AA and CA/AA nearest neighbors when the CA pair is the first noncanonical pair (loop-terminal pair) in 3 x 3 nucleotide and larger size-symmetric internal loops. These CG/AA and CA/AA nearest neighbors, with CA adjacent to a closing Watson-Crick pair, are further stabilized when the pH is lowered from 7 to 5.5. The results are consistent with a significantly larger fraction (from approximately 20% at pH 7 to approximately 90% at pH 5.5) of adenines being protonated at the N1 position to form stabilizing wobble CA+ pairs adjacent to a sheared GA or AA pair. The noncanonical pair adjacent to the GA pair in CG/AA can either stabilize or destabilize the loop, consistent with the sequence-dependent thermodynamics of GA pairs. No significant pH-dependent stabilization is found for most of the other nearest neighbor combinations involving CA pairs (e.g., CA/AG and AG/CA), which is consistent with the formation of various nonwobble pairs observed in different local sequence contexts in crystal and NMR structures. A revised free-energy model, including stabilization by wobble CA+ pairs, is derived for predicting stabilities of medium-size RNA internal loops. | lld:pubmed |
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| pubmed-article:19485416 | pubmed:language | eng | lld:pubmed |
| pubmed-article:19485416 | pubmed:journal | http://linkedlifedata.com/r... | lld:pubmed |
| pubmed-article:19485416 | pubmed:citationSubset | IM | lld:pubmed |
| pubmed-article:19485416 | pubmed:chemical | http://linkedlifedata.com/r... | lld:pubmed |
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| pubmed-article:19485416 | pubmed:status | MEDLINE | lld:pubmed |
| pubmed-article:19485416 | pubmed:month | Jun | lld:pubmed |
| pubmed-article:19485416 | pubmed:issn | 1520-4995 | lld:pubmed |
| pubmed-article:19485416 | pubmed:author | pubmed-author:RamA BAB | lld:pubmed |
| pubmed-article:19485416 | pubmed:author | pubmed-author:TurnerDouglas... | lld:pubmed |
| pubmed-article:19485416 | pubmed:author | pubmed-author:KennedyScott... | lld:pubmed |
| pubmed-article:19485416 | pubmed:issnType | Electronic | lld:pubmed |
| pubmed-article:19485416 | pubmed:day | 23 | lld:pubmed |
| pubmed-article:19485416 | pubmed:volume | 48 | lld:pubmed |
| pubmed-article:19485416 | pubmed:owner | NLM | lld:pubmed |
| pubmed-article:19485416 | pubmed:authorsComplete | Y | lld:pubmed |
| pubmed-article:19485416 | pubmed:pagination | 5738-52 | lld:pubmed |
| pubmed-article:19485416 | pubmed:dateRevised | 2009-11-18 | lld:pubmed |
| pubmed-article:19485416 | pubmed:meshHeading | pubmed-meshheading:19485416... | lld:pubmed |
