Size, constant sequences, and optimal selection Export

@article{citeulike:3015780, abstract = {Because the abundance of functional molecules in RNA sequence space has many unexplored aspects, we compared the outcome of 11 independent selections, performed using the same affinity selection protocol and contiguous randomized regions of 16, 22, 26, 50, 70, and 90 nucleotides. All affinity selections targeted the simplest isoleucine aptamer, an asymmetric internal loop. This loop should be abundant in all selections, so that it can be compared across all experiments. In some cases, two primer sets intended to favor selection of different structures have also been compared. The simplest isoleucine aptamer dominates all selections except with the shortest tract, 16 contiguous randomized nucleotides. Here the isoleucine aptamer cannot be accommodated and no other motif can be selected. Our results suggest an optimum length for selection; surprisingly, both the shortest and the longest randomized tracts make it more difficult to recover the motif. Estimated apparent initial abundances suggest that the simplest isoleucine motif was 20- to 40-fold more frequent in selection with 50- or 70-nucleotide randomized regions than with any other length. Considering primer sets, a pre-formed stable stem within fixed flanking sequences had a five-to 10-fold negative effect on apparent motif abundance at all lengths. Differing random tract lengths also determined the probable motif permutation and the most abundant helix lengths. These data support a significant but lesser role for primer sequences in the outcome of selections. 10.1261/rna.2161305}, author = {Legiewicz, Michal and Lozupone, Catherine and Knight, R. O. B. and Yarus, Michael}, citeulike-article-id = {3015780}, citeulike-linkout-0 = {http://dx.doi.org/10.1261/rna.2161305}, citeulike-linkout-1 = {http://www.rnajournal.org/cgi/content/abstract/11/11/1701}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/16177137}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=16177137}, day = {1}, doi = {10.1261/rna.2161305}, journal = {RNA}, keywords = {aptamer, dna, evolution, rna, selex, structure}, month = {November}, number = {11}, pages = {1701--1709}, posted-at = {2008-07-17 21:50:32}, priority = {5}, title = {Size, constant sequences, and optimal selection}, url = {http://dx.doi.org/10.1261/rna.2161305}, volume = {11}, year = {2005} }

TY - JOUR ID - citeulike:3015780 L3 - citeulike-article-id:3015780 N2 - Because the abundance of functional molecules in RNA sequence space has many unexplored aspects, we compared the outcome of 11 independent selections, performed using the same affinity selection protocol and contiguous randomized regions of 16, 22, 26, 50, 70, and 90 nucleotides. All affinity selections targeted the simplest isoleucine aptamer, an asymmetric internal loop. This loop should be abundant in all selections, so that it can be compared across all experiments. In some cases, two primer sets intended to favor selection of different structures have also been compared. The simplest isoleucine aptamer dominates all selections except with the shortest tract, 16 contiguous randomized nucleotides. Here the isoleucine aptamer cannot be accommodated and no other motif can be selected. Our results suggest an optimum length for selection; surprisingly, both the shortest and the longest randomized tracts make it more difficult to recover the motif. Estimated apparent initial abundances suggest that the simplest isoleucine motif was 20- to 40-fold more frequent in selection with 50- or 70-nucleotide randomized regions than with any other length. Considering primer sets, a pre-formed stable stem within fixed flanking sequences had a five-to 10-fold negative effect on apparent motif abundance at all lengths. Differing random tract lengths also determined the probable motif permutation and the most abundant helix lengths. These data support a significant but lesser role for primer sequences in the outcome of selections. 10.1261/rna.2161305 IS - 11 JF - RNA EP - 1709 TI - Size, constant sequences, and optimal selection VL - 11 SP - 1701 KW - aptamer KW - dna KW - evolution KW - rna KW - selex KW - structure AU - Legiewicz, Michal AU - Lozupone, Catherine AU - Knight, ROB AU - Yarus, Michael PY - 2005/11/01/ UR - http://dx.doi.org/10.1261/rna.2161305 ER -