RNA STRAND

[…] erformance of our algorithms, namely HK-PK, HK-PK-free, IP-pk168 and DK-pk16. HK-PK (with 88 pseudoknotted structures) and HK-PK-free (with 337 pseudoknot-free structures) datasets were compiled from RNA STRAND database and were used as test datasets in evaluating HotKnots V2.0 []; IP-pk168 (with 168 pseudoknotted structures) contains 16 categories of pseudoknotted structures with at most 85% sequ […]

[…] the 5′ adaptor ligation step. This also reduces undesired products caused by excess unligated 3′ adaptor.Alternatively, the 5′ adaptor can be ligated to the first strand cDNA after degradation of the RNA strand, for instance through alkaline treatment () or RNase H digestion (Figure ). Provided that the 5′ adaptor (DNA) is 5′ adenylated and 3′ blocked, the ATP-independent thermostable Mth K97A (so […]

[…] to all dm3 transcriptomes from FlyBase (downloaded January 2016, versions r5.57): with the same bowtie2 parameters, but also first forcing sense strandedness as bridge orientation should preserve the RNA strand information, and then for reads that did not align in the sense direction, permitting antisense alignment. Reads that aligned with equal alignment score to more than one transcriptome were […]

[…] ys163) in the conserved motif (Tyr-Xaa3-Lys-Xaa(9–11)-Gln-Xaa(21–33)-Lys) of the PIWI domain that are believed to be involved in binding to the 5’ phosphate group of the first nucleotide of the guide RNA strand [] are all present in WCR Argonautes ().Also illustrated in , WCR Argonautes possess conserved metal chelating residues (Asp, Asp and His [DDH]) that are found in the catalytic motif of PIW […]

[…] vitamin B12 uptake is lower in S. Typhimurium than E. coli). Also, we have recently observed that conjugation of PNA with the (KFF)3K peptide hinders PNA hybridization efficiency with a complementary RNA strand. To determine if the attachment of vitamin B12 affects hybridization of a PNA oligomer with complementary RNA, we performed polyacrylamide gel electrophoresis (PAGE) experiments. We used th […]

[…] n the middle of the C-terminal helix (). The hexameric model of EV71 2C 116–329 suggests that the C-terminal RNA binding motif may be located on the rim of the ring structure. It is possible that one RNA strand simultaneously interacts with multiple RNA binding sites on the hexamer and plays an essential role in stabilizing the 2C hexamer. This hypothesis is supported by a biochemical and structur […]