Abstract
DNA or RNA aptamers have gained attention as the next generation antibody-like molecules for medical or diagnostic use. Conventional secondary structure prediction tools for nucleic acids play an important role to truncate or minimize sequence, or introduce limited chemical modifications without compromising or changing its binding affinity to targets in the design of improved aptamers selected by Systematic Evolution of Ligands by EXponential enrichment (SELEX). We describe a novel software package, ValFold, capable of predicting secondary structures with improved accuracy based on unique aptamer characteristics. ValFold predicts not only the canonical Watson-Crick pairs but also G-G pairs derived from G-quadruplex (known structure for many aptamers) using the stem candidate selection algorithm. The database is available for free at http://code.google.com/p/valfold/
Highlights
Aptamers are well-known nucleic acid molecules that tightly bind to their targets by recognizing their three-dimensional structures
Aptamers are usually obtained by the SELEX (Systematic Evolution of Ligands by EXponential enrichment) process [1, 2]
The aptamer sequence data show the following four unique characteristics compared to the usual genomic, RNA or other natural sequences analysis
Summary
Aptamers are well-known nucleic acid molecules that tightly bind to their targets by recognizing their three-dimensional structures. It is worthwhile in considering the third and the forth characteristics of aptamers to verify the strategy of a secondary structure prediction algorithm. The mainstream of ValFold is a secondary structure prediction algorithm to minimize the free energy.
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