1. Punctuated Evolution Caused by Selection of Rare Beneficial Mutations
2. Let i j k and l denote positions of bases in the linear sequence and ( i j ) denote a base pair. The secondary structure of an RNA sequence is defined as the set P of allowed base pairs (here Watson-Crick pairs plus GU) that minimize free energy subject to a no-knot condition requiring that if ( i j ) and ( k l ) are both in P then i < k < j implies i < l < j (that is base pairs do not cross). The secondary structure is computed with our implementation (10) of a dynamic programming algorithm originally from (21) which is widely used in laboratories to assist in the prediction of secondary structures. The procedure is based on empirical energy parameters (22).
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4. Systematic Evolution of Ligands by Exponential Enrichment: RNA Ligands to Bacteriophage T4 DNA Polymerase
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