A coarse-grained model captures the temporal evolution of DNA nanotube length distributions

Mardanlou, Vahid; Yaghoubi, Kimia C.; Green, Leopold N.; Subramanian, Hari K. K.; Hariadi, Rizal F.; Kim, Jongmin; Franco, Elisa

doi:10.1007/s11047-017-9657-7

Cited by 6 publications

(10 citation statements)

References 22 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Fitted rates are generally different than those obtained in earlier work [13], which focused on a different type of nanotubes. We attribute the discrepancies to the following reasons: a) nanotubes used for these experiments include a toehold domain (in contrast to the tiles considered in [13]), which affects stacking interactions among neighboring tiles and thus polymerization/depolymerization rates; b) here invader and anti-invader reactions are modeled and fitted simultaneously with the nanotube model; c) nanotube growth experiments in [13] were conducted on a two-tile system, in which nucleation can be controlled more precisely. We compare the rates fitted here to prior results in the literature.…”

Section: Fitted Model Parameters: Invasion and Anti-invasion By Dna Mcontrasting

confidence: 85%

“…This reaction rate is three orders of magnitude higher than the joining rate estimate for DNA ribbons in [21], which is 3.5 × 10 4 /M/s, and is higher than hybridization rates for DNA and RNA; this indicates that we may be overestimating the actual joining rate due to our choice of fitting constraints. Further, because we are simultaneously fitting numerous parameters with non stringent constraints, it is reasonable to expect fits falling in a broad range of values, as we showed in recent work on this model (but different nanotube type) by comparing the results of 350 fitting campaigns [13]. Finally, our fragmentation rate is in the order of 10 −4 /s, suggesting that breakage events are rare.…”

Section: Fitted Model Parameters: Invasion and Anti-invasion By Dna Msupporting

confidence: 60%

“…In some sections, we indicate molecular species and their concentration with the same (capital) letters to simplify the notation. The model is built based on the results published in [13].…”

Section: Modeling the Dynamics Of Nanotube Length Distributionsmentioning

confidence: 99%

“…First, one needs to model several processes that are known to affect nanotube length: nucleation, polymerization and depolymerization, end-joining, and fragmentation. These processes were modeled in detail in [13], and here we only report a brief summary; the model was fitted to the data collected in this paper as they are generated by a different type of DNA nanotubes relative to [13]. Further, we focus on the inclusion of additional reactions modeling invasion, anti-invasion, and transcription and degradation processes that generate…”

Section: Modeling the Dynamics Of Nanotube Length Distributionsmentioning

confidence: 99%

“…Finally, we note that fitted rates depend on the chosen level of granularity of the model (number of bins) [13]. Table 13: Non-fitted parameters for model equations (38)-(46).…”

Section: Fitted Model Parameters: Invasion and Anti-invasion By Dna Mmentioning

confidence: 99%

See 4 more Smart Citations

Autonomous dynamic control of DNA nanostructure self-assembly

et al. 2019

Self Cite

View full text Add to dashboard Cite

Section: Fitted Model Parameters: Invasion and Anti-invasion By Dna Mcontrasting

confidence: 85%

Section: Fitted Model Parameters: Invasion and Anti-invasion By Dna Msupporting

confidence: 60%

Section: Modeling the Dynamics Of Nanotube Length Distributionsmentioning

confidence: 99%

Section: Modeling the Dynamics Of Nanotube Length Distributionsmentioning

confidence: 99%

“…Finally, we note that fitted rates depend on the chosen level of granularity of the model (number of bins) [13]. Table 13: Non-fitted parameters for model equations (38)-(46).…”

Section: Fitted Model Parameters: Invasion and Anti-invasion By Dna Mmentioning

confidence: 99%

See 3 more Smart Citations

Autonomous dynamic control of DNA nanostructure self-assembly

et al. 2019

Self Cite

View full text Add to dashboard Cite

Rapid self‐assembly of γPNA nanofibers at constant temperature

et al. 2021

View full text Add to dashboard Cite

Peptide nucleic acids (PNAs) have primarily been used to achieve therapeutic gene modulation through antisense strategies since their design in the 1990s. However, the application of PNAs as a functional nanomaterial has been more recent. We recently reported that γ-modified peptide nucleic acids (γPNAs) could be used to enable formation of complex, self-assembling nanofibers in select polar aprotic organic solvent mixtures. Here we demonstrate that distinct γPNA strands, each with a high density of γ-modifications can form complex nanostructures at constant temperatures within 30 minutes. Additionally, we demonstrate DNA-assisted isothermal growth of γPNA nanofibers, thereby overcoming a key hurdle for future scale-up of applications related to nanofiber growth and micropatterning.

show abstract

DNA Nanostructures that Self-Heal in Serum

Schulman

2019

Nano Lett.

View full text Add to dashboard Cite

Self-assembled DNA nanostructures have potential applications in therapeutics, diagnostics, and synthetic biology. A challenge in using DNA nanostructures in biological environments or cell culture, however, is that they may be degraded by enzymes found in these environments, such as nucleases. Such degradation can be slowed by introducing alternative substrates for nucleases, or by coating nanostructures with membranes or peptides. Here we demonstrate a means by which degradation can be reversed in situ through the repair of nanostructure defects. To demonstrate this effect, we show that degradation rates of DNA nanotubes, micron-scale self-assembled structures, are at least 4-fold lower in the presence of tiles that can repair nanotube defects during the degradation process. Micrographs of nanotubes show that tiles from solution incorporate into nanotubes and that this incorporation increases nanotube lifetime to several days in serum. We use experimental data to formulate a simple model of nanostructure self-healing. This model suggests how introducing even a relatively low rate of repair could allow a nanostructure to survive almost indefinitely because of a dynamic equilibrium between microscale repair and degradation processes. The ability to repair nanostructures could thus allow particular structures or devices to operate for long periods of time and might offer a single means to resist different types of chemical degradation.

show abstract

A coarse-grained model captures the temporal evolution of DNA nanotube length distributions

Cited by 6 publications

References 22 publications

Autonomous dynamic control of DNA nanostructure self-assembly

Autonomous dynamic control of DNA nanostructure self-assembly

Rapid self‐assembly of γPNA nanofibers at constant temperature

DNA Nanostructures that Self-Heal in Serum

Contact Info

Product

Resources

About