Size, constant sequences, and optimal selection
Open accessAbstract
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.
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Template-directed ligation would shift the pool toward longer sequences.
“In addition, our simulations indicate that template-directed ligation would shift the pool toward longer sequences, another important factor for activity (31,32).”
From Prebiotically plausible mechanisms increase compositional diversity of nucleic acid sequences (2012) · cites this paper as [32]
No aptamers were isolated at the shortest length (16 bases) in selections for isoleucine aptamers that differed only by the length of the random region.
“This was demonstrated by a series of selections for isoleucine aptamers that differed only by the length of the random region; no aptamers were isolated at the shortest length (16 bases) (32).”
From Prebiotically plausible mechanisms increase compositional diversity of nucleic acid sequences (2012) · cites this paper as [32]
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- Authors
- LEGIEWICZ, M., LOZUPONE, C., KNIGHT, R., & YARUS, M.
- Affiliations
- University of Colorado Boulder (US)
- Venue
- RNA
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2005-09-21
- Volume
- 11
- Issue
- 11
- Pages
- 1701-1709
- ISSN
- 1355-8382 (ISSN-L)
- 1469-9001
- PMC
- PMC1370856
- OpenAlex
- W2019123725
- Cited by
- 69
- References
- 30
- Citations by year
- 2026: 4 · 2025: 4 · 2024: 1 · 2023: 3 · 2022: 4 · 2021: 2 · 2019: 3 · 2018: 5 · 2017: 3 · 2016: 4 · 2015: 2 · 2014: 3 · 2013: 2 · 2012: 4
- FWCI
- 1.38
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- RNA (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Aeronautics and Space Administration (NCC21052)
- National Institutes of Health
- National Institute of General Medical Sciences (GM48080, R01GM048080, T32GM008759, T32GM142607)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Advanced biosensing and bioanalysis techniques
- Keywords
- RNA aptamers, affinity selection, RNA secondary structure, helix length
- MeSH terms
- Base Sequence, Binding Sites, Chromatography, Affinity, Isoleucine, Molecular Sequence Data, Nucleic Acid Conformation, Oligoribonucleotides, Protein Binding, RNA
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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