A new approach to the study of sequence‐dependent properties of polynucleotides

Abstract

Abstract A sequence‐dependent properly of any long polynucleotide can be related to the properties of a limited number of other polynucleotides. The properties of the constituent sequence subunits need not be individually known. Only the properties of a set of linearly independent sequence combinations in polymers need be known. The number of independent sequences depends on the number of neighboring bases (or base pairs) contributing to the property and on the number of different bases (or base pairs) allowed. General formulae are derived. If only nearest neighbors contribute to a property, there are 13 linearly independent single‐strand sequences with four different bases and there are 8 linearly independent double‐strand sequences with two different base pairs. The study of independent sequences in polymers should be especially useful with double‐stranded polynucleotides. It should be possible by this polymer approach to estimate nearest‐neighbor frequencies from the circular dichroism of double strands and also to investigate the relation between solution conformation and double‐strand sequence.