Comprehensive thermodynamic analysis of 3' double-nucleotide overhangs neighboring Watson-Crick terminal base pairs

Abstract

Thermodynamic parameters are reported for duplex formation of 48 self-complementary RNA duplexes containing Watson–Crick terminal base pairs (GC, AU and UA) with all 16 possible 3′ double-nucleotide overhangs; mimicking the structures of short interfering RNAs (siRNA) and microRNAs (miRNA). Based on nearest-neighbor analysis, the addition of a second dangling nucleotide to a single 3′ dangling nucleotide increases stability of duplex formation up to 0.8 kcal/mol in a sequence dependent manner. Results from this study in conjunction with data from a previous study [A. S. O'Toole, S. Miller and M. J. Serra (2005) RNA, 11, 512.] allows for the development of a refined nearest-neighbor model to predict the influence of 3′ double-nucleotide overhangs on the stability of duplex formation. The model improves the prediction of free energy and melting temperature when tested against five oligomers with various core duplex sequences. Phylogenetic analysis of naturally occurring miRNAs was performed to support our results. Selection of the effector miR strand of the mature miRNA duplex appears to be dependent upon the identity of the 3′ double-nucleotide overhang. Thermodynamic parameters for 3′ single terminal overhangs adjacent to a UA pair are also presented.

Structural dynamics of a single-stranded RNA–helix junction using NMR

“…This indicates that A25 and U26 stack onto the adjoined helix rather than forming flexible terminal-like residues. Prior studies have shown that ssRNA nucleotides that overhang the 3 ′ or 5 ′ termini stabilize the adjacent helix (O'Toole et al 2005(O'Toole et al , 2006. Much smaller (<0.1 ppm) CS perturbations are observed at other residues in the ssRNA tail, including the adenine core (A30-A32), which also suggests a more helical conformation (Fig.…”

“…′ termini stabilize the adjacent helix, ignoring the conformation and dynamics of the ssRNA residues themselves (O'Toole et al 2005(O'Toole et al , 2006. Recently, Herschlag and coworkers studied the sequence dependence of an ssRNA adjoining the group I ribozyme to a duplex.…”

Resveratrol Alters microRNA Expression Profiles in A549 Human Non-Small Cell Lung Cancer Cells

“…These observations strongly indicate that resveratrol is able to influence the expression of specific miRNAs in a lung cancer A549 cells. The asterisk following the name indicates non-functional miRNA or passenger strand that is released from the miRNA duplex (biologically active miRNA: passenger miRNA) during miRNA biogenesis (O'Toole et al, 2006). Recent studies have suggested that miRNA* affords potential opportunities for contributing to the regulation network (Guo et al, 2010).…”

Rat mir-155 generated from the lncRNA Bic is ‘hidden’ in the alternate genomic assembly and reveals the existence of novel mammalian miRNAs and clusters

“…Following the export of premiRNAs to the cytoplasm by Exportin-5, the loop region of the hairpin is removed by the Dicer endonuclease to produce a short, double-stranded RNA (dsRNA) (Cullen 2004). Based on the thermodynamic stability of each end of this duplex (O'Toole et al 2006), one of the strands is preferentially incorporated in the RNA-induced silencing complex (RISC), producing a biologically active mature miRNA (generally the -5p miR), while the inactive strand (the -3p miR) is degraded (Kim 2005). The RISC complex inhibits translation elongation or triggers mRNA degradation, depending upon the degree of complementarity of the miRNA with its target (Carrington and Ambros 2003;Bartel 2004;Djuranovic et al 2012).…”