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-HIV RNA aptamers have been described based on conserved signature motifs, including family 1 pseudoknots (F1Pk), family 2 pseudoknots (F2Pk), 6/5 asymmetric loop motif ((6/5)AL) and UCAA-bulge motif ...
the 2 ′- hydroxyl and the N3 atom of the purine base may stabilize purine bases in the anti conformation in A- RNA (PDB ID: 315D). Figure 1 . View largeDownload slide Hoogsteen base pairs in DNA and RNA ...
. Of the 24 sequences, 13 are from orientation 1 and 11 from orientation 2 . The most productive design comes when atomic fragments from ribosomal RNAs (42% of the 24 sequences) and glycine riboswitches (42 ...
coli release factor 2 are linked through residue 246. RNA , 6, 1704–1713. Google Scholar 3982–3987 Nucleic Acids Research, 2001, Vol. 29, No. 19 © 2001 Oxford University Press Class- 1 translation ...
is oriented towards the phosphate backbone group connecting G40 and G41 suggesting a favorable electrostatic interaction between the RNA and the ligand at this position. Ligand stacking with the C7:G41 base ...
. Google Scholar CrossRef Search ADS PubMed Damgaard CK, Andersen ES, Knudsen B, Gorodkin J, Kjems J. 2004. RNA interactions in the 5’ region of the HIV- 1 genome. J Mol Biol . 336( 2 ): 369– 379. Google ...
in hybridization strength, are the replacement of cytosine by 5-methylcytosine and the replacement of adenine by 2 -aminoadenine (or diaminopurine) (4). Introduction of a methyl group in the 5 position of uracil ...
–protein binding. Indeed, the predominant single-stranded nature and additional 2 ′-hydroxy group may make such interactions more important, and yet distinct, for RNA compared to DNA and carbohydrates ...
at transcriptional and post-transcriptional level by a variety of mechanisms [ 1 ]. Advancement in high-throughput RNA -seq technologies with increased sequencing depth has unveiled the true glimpse of a diverse ...
on duplex structure and stability, thereby providing better rules for RNA structure prediction and validation. The crystal structure of an RNA duplex containing the sequence r(GGUAUUGCGGUACC) 2 has been solved ...
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