Leveraging Steric Moieties for Kinetic Control of DNA Strand Displacement Reactions

DNA strand displacement networks are a critical partof dynamicDNA nanotechnology and are proven primitives for implementing chemicalreaction networks. Precise kinetic control of these networks is importantfor their use in a range of applications. Among the better understoodand widely leveraged kinetic properties of these networks are toeholdsequence, length, composition, and location. While steric hindrancehas been recognized as an important factor in such systems, a clearunderstanding of its impact and role is lacking. Here, a systematicinvestigation of steric hindrance within a DNA toehold-mediated stranddisplacement network was performed through tracking kinetic reactionsof reporter complexes with incremental concatenation of steric moietiesnear the toehold. Two subsets of steric moieties were tested withsystematic variation of structures and reaction conditions to isolatesterics from electrostatics. Thermodynamic and coarse-grained computationalmodeling was performed to gain further insight into the impacts ofsteric hindrance. Steric factors yielded up to 3 orders of magnitudedecrease in the reaction rate constant. This pronounced effect demonstratesthat steric moieties can be a powerful tool for kinetic control instrand displacement networks while also being more broadly informativeof DNA structural assembly in both DNA-based therapeutic and diagnosticapplications that possess elements of steric hindrance through DNAfunctionalization with an assortment of chemistries.

Automated summary

DNA strand displacement networks are crucial to dynamic DNA nanotechnology and are widely used in chemical reaction networks. The precise kinetic control of these networks is important for various applications. Although the effects of factors such as toehold sequence, length, composition, and location are well understood, the impact of steric hindrance in these networks is not fully understood.