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

@article{citeulike:742093, 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.}, address = {Department of Chemistry, Allegheny College, 520 N. Main Street, Meadville, PA 16335, USA.}, author = {O'Toole, A. S. and Miller, S. and Haines, N. and Zink, M. C. and Serra, M. J.}, citeulike-article-id = {742093}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/nar/gkl428}, citeulike-linkout-1 = {http://nar.oxfordjournals.org/cgi/content/abstract/34/11/3338}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/16820533}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=16820533}, doi = {10.1093/nar/gkl428}, issn = {1362-4962}, journal = {Nucleic Acids Res}, keywords = {3, analysis, mirna, overhang, thermodynamic}, number = {11}, pages = {3338--3344}, posted-at = {2006-07-06 15:39:59}, priority = {0}, title = {Comprehensive thermodynamic analysis of 3' double-nucleotide overhangs neighboring Watson-Crick terminal base pairs.}, url = {http://dx.doi.org/10.1093/nar/gkl428}, volume = {34}, year = {2006} }

TY - JOUR ID - citeulike:742093 L3 - citeulike-article-id:742093 N2 - 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. IS - 11 JF - Nucleic Acids Res SN - 1362-4962 AD - Department of Chemistry, Allegheny College, 520 N. Main Street, Meadville, PA 16335, USA. EP - 3344 TI - Comprehensive thermodynamic analysis of 3' double-nucleotide overhangs neighboring Watson-Crick terminal base pairs. VL - 34 SP - 3338 KW - 3 KW - analysis KW - mirna KW - overhang KW - thermodynamic AU - O'Toole, AS AU - Miller, S AU - Haines, N AU - Zink, MC AU - Serra, MJ PY - 2006/// UR - http://dx.doi.org/10.1093/nar/gkl428 ER -