Watson-Crick pairing, the Heisenberg group and Milnor invariants

DOI10.1007/S00285-008-0223-XMaRDI QIDQ843289zbMATH OpenOpenAlexWikidataFDO

Authors Siddhartha Gadgil

Publication date 12 October 2009

Published in Journal of Mathematical Biology (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/0809.3110

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40)

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 emph{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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Cited in

(4)

• Homogeneous length functions on groups
• Homogeneous length functions on groups: intertwined computer and human proofs
• Random words in free groups, non-crossing matchings and RNA secondary structures
• Conjugacy invariant pseudo-norms, representability and RNA secondary structures

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