Circuit topology

Graph topology applied to electrical and communications circuits, or biomolecules

The circuit topology of a folded linear polymer refers to the arrangement of its intra-molecular contacts. Examples of linear polymers with intra-molecular contacts are nucleic acids and proteins. Proteins fold via the formation of contacts of various natures, including hydrogen bonds, disulfide bonds, and beta-beta interactions. RNA molecules fold by forming hydrogen bonds between nucleotides, forming nested or non-nested structures. Contacts in the genome are established via protein bridges including CTCF and cohesins and are measured by technologies including Hi-C. Circuit topology categorises the topological arrangement of these physical contacts, that are referred to as hard contacts. Furthermore, chains can fold via knotting. Circuit topology uses a similar language to categorise both "soft" and "hard" contacts, and provides a full description of a folded linear chain. In this framework, a "circuit" refers to a segment of the chain where each contact site within the segment forms connections with other contact sites within the same segment, and thus is not left unpaired. A folded chain can thus be studied based on its constituting circuits.

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