Predicting oligonucleotide affinity to nucleic acid targets

RNA Secondary Structure Analysis Using RNAstructure

“…It is available for free and can be run using a web server or downloaded to run locally on Windows, Macintosh OS X, or Linux. The program includes several algorithms, including secondary structure prediction by free energy minimization or maximum expected accuracy structure prediction (Lu et al, 2009;, a partition function for predicting base pair probabilities (Mathews, 2004), ProbKnot for predicting structures including pseudoknots (Bellaousov and Mathews, 2010), stochastic sampling from the Boltzmann ensemble (Ding and Lawrence, 2003), OligoWalk for predicting binding affinity of oligonucleotides to a complementary RNA target (Lu and Mathews, 2007;Lu and Mathews, 2008a;Lu and Mathews, 2008b;Mathews et al, 1999a), methods for predicting the structure of interacting sequences (Piekna-Przybylska et al, 2009), and methods for predicting conserved structures common to two or more sequences (Harmanci et al, 2007;Harmanci et al, 2008;Harmanci et al, 2009;Harmanci et al, 2011;Mathews, 2005;Mathews and Turner, 2002;Uzilov et al, 2006;Xu and Mathews, 2011).Basic Protocol 1 provides instruction for predicting RNA secondary structure with the RNAstructure web server. Alternative protocol 1 provides instructions for using the graphical interface to predict lowest free energy structures and base pairing probabilities.…”

Inhibition of Escherichia coli RNase P by oligonucleotide directed misfolding of RNA

“…Oligonucleotide-based therapeutics can be rapidly designed and screened because much is known about molecular recognition between oligonucleotides and RNA, analogs are synthetically accessible (Freier and Altmann 1997), and their pharmacokinetic properties are likely to be similar (Crooke et al 1996). In principle, insight into regions that can be targeted by oligonucleotidedirected misfolding can be gained from secondary structure prediction (Banerjee and Turner 1995;Pan and Woodson 1998;Mathews et al 1999a;Chadalavada et al 2000;Childs et al 2002). Many RNAs function in RNA-protein complexes, however, and it is possible that the RNA-protein interaction could overcome an oligonucleotide strategy for inhibition.…”

Plasminogen activator inhibitor 1: Mechanisms of its synergistic regulation by growth factors

“…These algorithms were also used to predict the antisense sequences and their binding affinity to the RNA target. The data were analyzed by the Soligo program in the sFOLD package (Ding, Chan et al 2004), OligoWalk (Mathews, Burkard et al 1999), and Block-iT programs.…”

“…Computer algorithms that utilize minimum free energy calculations can predict secondary structures of RNA molecules and have been used to identify target accessibility and as a basis of rational design of antisense and nucleic acid probes (Mathews, Burkard et al 1999;Ding and Lawrence 2001;Ding, Chan et al 2004;Ding, Chan et al 2005). However, these computer programs do not predict tertiary structures that may influence target accessibility.…”