Constraint-guided equal-strut growth generates a tunable family of DNA-realizable wireframe filaments

Wireframe DNA nanostructures are built from edges of prescribed length meeting at vertices of prescribed valency, which makes their design space a geometric one: which equal-edge frameworks can be built at all, given a maximum vertex degree, a minimum edge angle and a steric clearance. We apply a constrained growth construction—each new vertex placed by trilateration at a fixed strut length from at least three placed vertices, accepted only if the resulting framework still satisfies the design constraints—and report three results. First, under a degree cap of six the construction is extremely selective: of all periodic face-choice patterns tested, only the Boerdijk–Coxeter tetrahelix grows without stalling, and it does so because its interior vertices have degree exactly six, saturating the budget. Second, raising the cap to seven unlocks a one-parameter family of kinked variants indexed by the defect spacing k, whose radius is programmable from 0.52 to 1.13 strut lengths and whose handedness alternates with k, while straightness stays above 0.99. Values k ∈ {3, 5, 8} stall for an identifiable reason—the capped vertex lands at unit distance from a fourth earlier vertex—and run freely at a cap of eight. Both caps are within demonstrated multi-arm junction capability. Third, two members of the family, the pure tetrahelix and a k = 6 variant, were routed into DNA, energy-minimised and run for 5×105 oxDNA steps at 30◦C: both are stable, with second-half mean energies −1.4919±0.0017 and −1.5004 ± 0.0019 per nucleotide and shape changes under 4%. The kinked variant routes into 8 strand cycles against the tetrahelix’s 22. We also report what did not survive checking: a twist–stretch coupling that vanished under length convergence, and a circular-dichroism sign rule that its own descriptor failed to predict.

Authors

Publication Details

Journal
ChemRxiv
Published
2026-11-01
DOI
https://doi.org/10.26434/chemrxiv.15011427/v1
Primary Topic
Advanced biosensing and bioanalysis techniques
Type
preprint
Controls
|||
ALL TIME
JAN
FEB
MAR
APR
MAY
JUN
JUL
AUG
SEP
OCT
preprint

Constraint-guided equal-strut growth generates a tunable family of DNA-realizable wireframe filaments

Chandan Shukla
ChemRxiv
Advanced biosensing and bioanalysis techniques
preprint

Constraint-guided equal-strut growth generates a tunable family of DNA-realizable wireframe filaments

Chandan Shukla
preprint en

Abstract

Wireframe DNA nanostructures are built from edges of prescribed length meeting at vertices of prescribed valency, which makes their design space a geometric one: which equal-edge frameworks can be built at all, given a maximum vertex degree, a minimum edge angle and a steric clearance. We apply a constrained growth construction—each new vertex placed by trilateration at a fixed strut length from at least three placed vertices, accepted only if the resulting framework still satisfies the design constraints—and report three results. First, under a degree cap of six the construction is extremely selective: of all periodic face-choice patterns tested, only the Boerdijk–Coxeter tetrahelix grows without stalling, and it does so because its interior vertices have degree exactly six, saturating the budget. Second, raising the cap to seven unlocks a one-parameter family of kinked variants indexed by the defect spacing k, whose radius is programmable from 0.52 to 1.13 strut lengths and whose handedness alternates with k, while straightness stays above 0.99. Values k ∈ {3, 5, 8} stall for an identifiable reason—the capped vertex lands at unit distance from a fourth earlier vertex—and run freely at a cap of eight. Both caps are within demonstrated multi-arm junction capability. Third, two members of the family, the pure tetrahelix and a k = 6 variant, were routed into DNA, energy-minimised and run for 5×105 oxDNA steps at 30◦C: both are stable, with second-half mean energies −1.4919±0.0017 and −1.5004 ± 0.0019 per nucleotide and shape changes under 4%. The kinked variant routes into 8 strand cycles against the tetrahelix’s 22. We also report what did not survive checking: a twist–stretch coupling that vanished under length convergence, and a circular-dichroism sign rule that its own descriptor failed to predict.

ChemRxiv
Advanced biosensing and bioanalysis techniques
AI Navigator

Ask Laika to Summarize, Analyze, and Connect papers live on the map.

Summarize Papers & Methodologies

Extract key findings, datasets, and comparative methods across publications.

Benchmark Rankings & Visual Analytics

Rank top research institutions, authors, funders, topics, and journals by Field-Weighted Citation Impact (FWCI) and paper volume with instant charts.

Connect Distant Disciplines

Bridge topological clusters on the map to find hidden collaborative intersections.

Laika access coming soon
Constraint-guided equal-strut growth generates a tunable family of DNA-realizable wireframe filaments — Chandan Shukla · ChemRxiv (2026) | TGRS Research Map | TGRS