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Watson–Crick pairing, the Heisenberg group and Milnor invariants

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Abstract

We study the secondary structure of RNA determined by Watson–Crick pairing without pseudo-knots using Milnor invariants of links. We focus on the first non-trivial invariant, which we call the Heisenberg invariant. The Heisenberg invariant, which is an integer, can be interpreted in terms of the Heisenberg group as well as in terms of lattice paths. We show that the Heisenberg invariant gives a lower bound on the number of unpaired bases in an RNA secondary structure. We also show that the Heisenberg invariant can predict allosteric structures for RNA. Namely, if the Heisenberg invariant is large, then there are widely separated local maxima (i.e., allosteric structures) for the number of Watson–Crick pairs found.

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Authors and Affiliations

  1. Department of Mathematics, Indian Institute of Science, Bangalore, 560003, India

    Siddhartha Gadgil

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  1. Siddhartha Gadgil
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Correspondence to Siddhartha Gadgil.

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Partially supported by DST (under grant DSTO773) and UGC (under SAP-DSA Phase IV).

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Gadgil, S. Watson–Crick pairing, the Heisenberg group and Milnor invariants. J. Math. Biol. 59, 123–142 (2009). https://doi.org/10.1007/s00285-008-0223-x

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  • DOI: https://doi.org/10.1007/s00285-008-0223-x

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