Reversible Polymerization-like Kinetics for Programmable Self-Assembly of DNA-Encoded Nanoparticles with Limited Valence

Gu, Meng; Ma, Xiaodong; Zhang, Liangshun; Lin, Jiaping

doi:10.1021/jacs.9b07919

Cited by 22 publications

(24 citation statements)

References 65 publications

(99 reference statements)

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“…It is worth noting that using an exponential distribution to describe the length of multimer chains is equivalent to assume that multimerization of G4s complies with a step-growth mechanism. This is analogous to the case of the self-assembly of DNA-encoded nanoparticles into chain-like superstructures [40], and at variance with the chain-growth mechanism which is less commonly applied to supramolecular biopolymers [41,42]. In addition, as Tel22 multimers follow an exponential distribution, we can easily estimate the spread of their molecular mass distribution as quantified by the ratio between the weight average molecular weight and the number average molecular weight, i.e.…”

Section: Comparison Between Saxs Data and Simulationsmentioning

confidence: 88%

Connecting Structure, Conformation and Energetics of Human Telomere G-quadruplex Multimers

Rosi¹,

Libera²,

Orecchini³

et al. 2022

Preprint

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G-quadruplexes (G4s) are helical four-stranded structures forming from guanine-rich nucleic acid sequences, which are thought to play a role in cancer development and malignant transformation. Most current studies focus on G4 monomers, yet under suitable and biologically relevant conditions G4s undergo multimerization. Here, we address the structural, conformational and energetic features of G4 multimers formed in solutions by the human telomere sequence. A novel multi-technique approach is used combining Small Angle X-ray Scattering (SAXS) and circular dichroism experiments with coarse-grained simulations, to provide quantitative information about large-scale structural features and the stability of G4 multimers. The latter show a significant polydispersity with an exponential distribution of contour lengths, suggesting a step-growth polymerization. On increasing DNA concentration, the strength of G4 stacking interaction increases, as well as the number of the units in the aggregates, with dimers and trimers as the most probable forms. At the same time, a variation of G4 conformation is observed. Our findings provide a quantitative picture of human telomere G4 multimers, which must be accounted for to achieve a rational design of anticancer drugs targeting DNA structures.

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Section: Comparison Between Saxs Data and Simulationsmentioning

confidence: 88%

Connecting Structure, Conformation and Energetics of Human Telomere G-quadruplex Multimers

Rosi¹,

Libera²,

Orecchini³

et al. 2022

Preprint

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“…The DMSO solution of NRh-G (1.0 mM) was dripped into water. Next, the mixture was stirred for 2 h 30 - 33 and DMSO was then removed by dialysis. As synthesized nanoparticles were characterized by transmission electron microscope (TEM), dynamic light scattering (DLS), and Zeta potential analyzer.…”

Section: Methodsmentioning

confidence: 99%

γ-Glutamyl transpeptidase-activatable near-infrared nanoassembly for tumor fluorescence imaging-guided photothermal therapy

Zhou¹,

Yang²,

Zhao³

et al. 2021

Theranostics

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Rationale: Precise treatment of tumors is attracting increasing attention. Molecular probes simultaneously demonstrating the diagnostic signal and pharmacological effect in response to tumor microenvironment are highly desired. γ-glutamyl transpeptidase (GGT) is a biomarker with significantly up-regulated expression in the tumor area. We developed a GGT responsive near-infrared (NIR) nanoassembly for tumor-specific fluorescence imaging-guided photothermal therapy. Methods: The GGT responsive NIR probe was constructed by conjugating GGT-specific substrate γ-glutamic acid (γ-Glu) with cyanine fluorophore (NRh-NH 2 ) via amide reaction. The resulting NRh-G spontaneously assembled into nanoparticles (NRh-G-NPs) around 50 nm. The NPs were characterized and the properties evaluated in the presence or absence of GGT. Subsequently, we studied fluorescence imaging and photothermal therapy of NRh-G-NPs in vitro and in vivo . Results: NRh-G-NPs, upon specific reaction with GGT, turned into NRh-NH 2 -NPs, showing a ~180-fold fluorescence enhancement and excellent photothermal effect recovery. NRh-G-NPs could selectively light up U87MG tumor cells while their fluorescence was weak in L02 human normal liver cells. The NPs also showed excellent tumor cell ablation upon laser irradiation. After intravenous injection into tumor-bearing mice, NRh-G-NPs could arrive in the tumor area and specifically light up the tumor. Following laser irradiation, the tumor could be completely erased with no tumor reoccurrence for up to 40 days. Conclusions: NRh-G-NPs were specifically responsive to GGT overexpressed in U87MG tumor cells and selectively lit up the tumor for imaging-guided therapy. Besides, the recovery of photothermal property in the tumor area could improve cancer therapy precision and decreased side effects in normal tissues.

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“…We would like to calculate the rate at which the distribution parameter p changes with time. A generalization of this problem was discussed in the context of self-assembling nanoparticles by Gu et al [34] (SI 2).…”

Section: Reduction To One Dimensionmentioning

confidence: 99%

A Polyaddition Model for the Prebiotic Polymerization of RNA and RNA-Like Polymers

Spaeth

Hargrave

2020

Life

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Implicit in the RNA world hypothesis is that prebiotic RNA synthesis, despite occurring in an environment without biochemical catalysts, produced the long RNA polymers which are essential to the formation of life. In order to investigate the prebiotic formation of long RNA polymers, we consider a general solution of functionally identical monomer units that are capable of bonding to form linear polymers by a step-growth process. Under the assumptions that (1) the solution is well-mixed and (2) bonding/unbonding rates are independent of polymerization state, the concentration of each length of polymer follows the geometric Flory-Schulz distribution. We consider the rate dynamics that produce this equilibrium; connect the rate dynamics, Gibbs free energy of bond formation, and the bonding probability; solve the dynamics in closed form for the representative special case of a Flory-Schulz initial condition; and demonstrate the effects of imposing a maximum polymer length. Afterwards, we derive a lower bound on the error introduced by truncation and compare this lower bound to the actual error found in our simulation. Finally, we suggest methods to connect these theoretical predictions to experimental results.

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Reversible Polymerization-like Kinetics for Programmable Self-Assembly of DNA-Encoded Nanoparticles with Limited Valence

Cited by 22 publications

References 65 publications

Connecting Structure, Conformation and Energetics of Human Telomere G-quadruplex Multimers

Connecting Structure, Conformation and Energetics of Human Telomere G-quadruplex Multimers

γ-Glutamyl transpeptidase-activatable near-infrared nanoassembly for tumor fluorescence imaging-guided photothermal therapy

A Polyaddition Model for the Prebiotic Polymerization of RNA and RNA-Like Polymers

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