Antisense DNA parameters derived from next-nearest-neighbor analysis of experimental data |
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Authors: | Donald M Gray Carla W Gray Byong-Hoon Yoo Tzu-Fang Lou |
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Affiliation: | (1) Department of Molecular and Cell Biology, The University of Texas at Dallas, 800 W. Campbell Road, Richardson, Texas 75080, USA;(2) Departments of Pediatrics and Biochemistry and Molecular Biology, Atlantic Research Center, Room C-302, Dalhousie University, 5849 University Avenue, Halifax, Nova Scotia, B3H 4H7, Canada |
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Abstract: | Background The enumeration of tetrameric and other sequence motifs that are positively or negatively correlated with in vivo antisense DNA effects has been a useful addition to the arsenal of information needed to predict effective targets for antisense DNA control of gene expression. Such retrospective information derived from in vivo cellular experiments characterizes aspects of the sequence dependence of antisense inhibition that are not predicted by nearest-neighbor (NN) thermodynamic parameters derived from in vitro experiments. However, quantitation of the antisense contributions of motifs is problematic, since individual motifs are not isolated from the effects of neighboring nucleotides, and motifs may be overlapping. These problems are circumvented by a next-nearest-neighbor (NNN) analysis of antisense DNA effects in which the overlapping nature of nearest-neighbors is taken into account. |
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