Imparting the unique properties of DNA into complex material architectures and functions

Xu, Phyllis F.; Noh, Hyunwoo; Lee, Ju Hun; Domaille, Dylan W.; Nakatsuka, Matthew A.; Goodwin, Andrew P.; Jennifer, N.

doi:10.1016/j.mattod.2013.07.001

Cited by 10 publications

(9 citation statements)

References 93 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Accordingly, large scale implementation of these techniques requires reliable algorithms, generally based on nearest-neighbors statistical thermodynamics, to predict the oligomers melting profiles in various ambient conditions [3][4][5][6]. Starting from the peculiar Watson-Crick hybridization rule, uncountable DNA molecules and architectures have been designed over the last years for application in functional nanodevices and drug deliveries [7][8][9][10][11].…”

Section: Introductionmentioning

confidence: 99%

“…[3][4][5][6] Starting from the peculiar Watson-Crick hybridization rule, uncountable DNA molecules and architectures have been designed over the last few years for application in functional nanodevices and drug deliveries. [7][8][9][10][11] Curved molecules can be identied by their slow electrophoretic mobility. 12,13 Being common to the control regions of transcription, the bending of the double helix is essential for gene regulation and to the compaction of genomic DNA into chromatin.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Twisting and bending stress in DNA minicircles

Zoli

2014

Soft Matter

View full text Add to dashboard Cite

The interplay between bending of the molecule axis and appearance of disruptions in circular DNA molecules, with ∼100 base pairs, is addressed. Three minicircles with different radii and almost equal contents of AT and GC pairs are investigated. The DNA sequences are modeled by a mesoscopic Hamiltonian which describes the essential interactions in the helix at the level of the base pair and incorporates twisting and bending degrees of freedom. Helix unwinding and bubble formation patterns are consistently computed by a path integral method that sums over a large number of molecule configurations compatible with the model potential. The path ensembles are determined, as a function of temperature, by minimizing the free energy of the system. Fluctuational openings appear along the helix to release the stress due to the bending of the molecule backbone. In agreement with the experimental findings, base pair disruptions are found with larger probability in the smallest minicircle of 66 bps whose bending angle is ∼6°. For this minicircle, a sizeable untwisting is obtained with the helical repeat showing a step-like increase at T = 315 K. The method can be generalized to determine the bubble probability profiles of open ends linear sequences.

show abstract

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Twisting and bending stress in DNA minicircles

Zoli

2014

Soft Matter

View full text Add to dashboard Cite

show abstract

“…In biomedical applications, aptamers have found the greatest utility as either surface capture or detection agents, or as targeting groups for imaging contrast or drug delivery . However, the ability to easily incorporate competitive binding into aptamer design has allowed their implementation as molecular switches, in which the binding of an aptamer to its target causes its dehybridization from a complement strand and a change in detectable properties …”

Section: Design Of Thrombin‐sensitive Microbubbles Using Competitive mentioning

confidence: 99%

Stimulus–responsive ultrasound contrast agents for clinical imaging: motivations, demonstrations, and future directions

Goodwin

Nakatsuka

Mattrey

2014

WIREs Nanomed Nanobiotechnol

Self Cite

View full text Add to dashboard Cite

Microbubble ultrasound contrast agents allow imaging of the vasculature with excellent resolution and signal-to-noise ratios. Contrast in microbubbles derives from their interaction with an ultrasound wave to generate signal at harmonic frequencies of the stimulating pulse; subtracting the elastic echo caused by the surrounding tissue can enhance the specificity of these harmonic signals significantly. The nonlinear acoustic emission is caused by pressure-driven microbubble size fluctuations, which in both theoretical descriptions and empirical measurements was found to depend on the mechanical properties of the shell that encapsulates the microbubble as well as stabilizes it against the surrounding aqueous environment. Thus biochemically-induced switching between a rigid “off” state and a flexible “on” state provides a mechanism for sensing chemical markers for disease. In our research, we coupled DNA oligonucleotides to a stabilizing lipid monolayer to modulate stiffness of the shell and thereby induce stimulus-responsive behavior. In initial proof-of-principle studies, it was found that signal modulation came primarily from DNA crosslinks preventing the microbubble size oscillations rather than merely damping the signal. Next, these microbubbles were redesigned to include an aptamer sequence in the crosslinking strand, which not only allowed the sensing of the clotting enzyme thrombin but also provided a general strategy for sensing other soluble biomarkers in the bloodstream. Finally, the thrombin-sensitive microbubbles were validated in a rabbit model, presenting the first example of an ultrasound contrast agent that could differentiate between active and inactive clots for the diagnosis of Deep Venous Thrombosis.

show abstract

“…These special characteristics arise due to the varying composition and order of four different nucleotide subunits in DNA sequences; adenine (A), cytosine (C), guanine (G), and thymine (T). Predictable and sequence-dependent structure formation is mediated by hybridization between complementary nucleic acid base-pairing, allowing construction of programmable self-assemblies and combination of multiple functional units on a single nano-assembly with high precision 3-5. Most of all, the unique and remarkable physiochemical properties of nucleic acids resulting from its chemical composition has provided a basis for rational design of materials with programmable size, shape, and function.…”

Section: Introductionmentioning

confidence: 99%

Antitumor therapeutic application of self-assembled RNAi-AuNP nanoconstructs: Combination of VEGF-RNAi and photothermal ablation

Son¹,

Kim²,

You³

et al. 2017

Theranostics

View full text Add to dashboard Cite

Nucleic acid-directed self-assembly provides an attractive method to fabricate prerequisite nanoscale structures for a wide range of technological applications due to the remarkable programmability of DNA/RNA molecules. In this study, exquisite RNAi-AuNP nanoconstructs with various geometries were developed by utilizing anti-VEGF siRNA molecules as RNAi-based therapeutics in addition to their role as building blocks for programmed self-assembly. In particular, the anti-VEGF siRNA-functionalized AuNP nanoconstructs can take additional advantage of gold-nanoclusters for photothermal cancer therapeutic agent. A noticeable technical aspect of self-assembled RNAi-AuNP nanoconstructs in this study is the precise conjugation and separation of designated numbers of therapeutic siRNA onto AuNP to develop highly sophisticated RNA-based building blocks capable of creating various geometries of RNAi-AuNP nano-assemblies. The therapeutic potential of RNAi-AuNP nanoconstructs was validated in vivo as well as in vitro by combining heat generation capability of AuNP and anti-angiogenesis mechanism of siRNA. This strategy of combining anti-VEGF mechanism for depleting angiogenesis process at initial tumor progression and complete ablation of residual tumors with photothermal activity of AuNP at later tumor stage showed effective tumor growth inhibition and tumor ablation with PC-3 tumor bearing mice.

show abstract

Imparting the unique properties of DNA into complex material architectures and functions

Cited by 10 publications

References 93 publications

Twisting and bending stress in DNA minicircles

Twisting and bending stress in DNA minicircles

Stimulus–responsive ultrasound contrast agents for clinical imaging: motivations, demonstrations, and future directions

Antitumor therapeutic application of self-assembled RNAi-AuNP nanoconstructs: Combination of VEGF-RNAi and photothermal ablation

Contact Info

Product

Resources

About