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Showing content from https://pubmed.ncbi.nlm.nih.gov/20203007 below:

DNA as a universal substrate for chemical kinetics

Unimolecular module: DNA implementation of the formal unimolecular reaction

→

+

with reaction index

. Orange boxes highlight the DNA species that correspond to the formal species

(species identifier 1-2-3),

(4-5-6), and

(7-8-9). Domains identical or complementary to species identifiers for

,

, and

are colored red, green, and blue, respectively. Black domains (10 and 11) are unique to this formal reaction. To reduce rate constant

, toehold domain

may not be a full complement of domain 1. (

) Complex

undergoes a strand displacement reaction with strand

, with

displacing strand

. (

)

displaces

and

from complex

. Without buffer cancellation,

; with buffer cancellation,

. Reaction equations of type

–

are used in simulations (Figs. 5 and 6); simplified reaction equations

–

are useful for analysis.

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