arXiv subjects

Ching-Hwa Kiang

Publications and source records attributed to Ching-Hwa Kiang.

6 recordsLinked to original sources

arXiv2007

Defects Can Increase the Melting Temperature of DNA-Nanoparticle Assemblies

DNA-gold nanoparticle assemblies have shown promise as an alternative technology to DNA microarrays for DNA detection and RNA profiling. Understanding the effect of DNA sequences on the melting temperature of the system is central to developing reliable detection technology. We studied the effects of DNA base-pairing defects, such as mismatches and deletions, on the melting temperature of DNA-nanoparticle assemblies. We found that, contrary to the general assumption that defects lower the melting temperature of DNA, some defects increase the melting temperature of DNA-linked nanoparticle assemblies. The effects of mismatches and deletions were found to depend on the specific base pair, the sequence, and the location of the defects. Our results demonstrate that the surface-bound DNA exhibit hybridization behavior different from that of free DNA. Such findings indicate that a detailed understanding of DNA-nanoparticle assembly phase behavior is required for quantitative interpretation of DNA-nanoparticle aggregation.

physics.bio-ph↗

arXiv2007

Experimental Free Energy Surface Reconstruction From Single-Molecule Force Spectroscopy Using Jarzynski's Equality

We used the atomic force microscope to manipulate and unfold individual molecules of the titin I27 domain and reconstructed its free energy surface using Jarzynski's equality. The free energy surface for both stretching and unfolding was reconstructed using an exact formula that relates the nonequilibrium work fluctuations to the molecular free energy. In addition, the unfolding free energy barrier, i.e. the activation energy, was directly obtained from experimental data for the first time. This work demonstrates that Jarzynski's equality can be used to analyze nonequilibrium single-molecule experiments, and to obtain the free energy surfaces for molecular systems, including interactions for which only nonequilibrium work can be measured.

physics.bio-ph↗

arXiv2005

Disorder in DNA-Linked Gold Nanoparticle Assemblies

We report experimental observations on the effect of disorder on the phase behavior of DNA-linked nanoparticle assemblies. Variation in DNA linker lengths results in different melting temperatures of the DNA-linked nanoparticle assemblies. We observed an unusual trend of a non-monotonic ``zigzag'' pattern in the melting temperature as a function of DNAlinker length. Linker DNA resulting in unequal DNA duplex lengths introduces disorder and lowers the melting temperature of the nanoparticle system. Comparison with free DNA thermodynamics shows that such an anomalous zigzag pattern does not exist for free DNA duplex melting, which suggests that the disorder introduced by unequal DNA duplex lengths results in this unusual collective behavior of DNA-linked nanoparticle assemblies.

physics.bio-ph↗

arXiv2005

The Reversible Phase Transition of DNA-Linked Colloidal Gold Assemblies

We present direct evidence for a reversible phase transition of DNA-linked colloidal gold assemblies. Transmission electron microscopy and optical absorption spectroscopy are used to monitor the colloidal gold phase transition, whose behavior is dominated by DNA interactions. We use single-stranded DNA-capped colloidal gold that is linked by complementary linker DNA to form the assemblies. We found that, compared to free DNA, a sharp melting transition is observed for the DNA-linked colloidal gold assemblies. The structure of the assemblies is non-crystalline, much like a gel phase, consistent with theoretical predictions. Optical spectra and melting curves provide additional evidence of gelation of the colloidal system. The phase transition and separation are examples of percolation in a dilute solvent.

physics.bio-ph↗

arXiv2005

DNA-based Artificial Nanostructures: Fabrication, Properties, and Applications

Table of Content 1. Introduction 2. DNA fundamentals 3. Attachment of DNA to surface 4. Fabrication of nanostructures using DNA 4.1 Nanostructures of pure DNA 4.2 DNA-based assembly of metal nanoparticles 4.3 Construction of semiconductor particle arrays using DNA 4.4 DNA-directed nanowires 4.5 DNA-functionalized carbon nanotubes 4.6 Field-transistor based on DNA 4.7 Nanofabrication using artificial DNA 5. DNA-based nanostructures as biosensors 6. Properties of DNA-linked gold nanoparticles 6.1 Aggregation of DNA-modified gold nanoparticles 6.2 Melting of DNA-linked gold nanoparticle aggregations 6.3 Effects of external variables on the melting properties 7. Conclusion

physics.bio-ph↗

arXiv2002

Phase Transition of DNA-Linked Gold Nanoparticle

Melting and hybridization of DNA-capped gold nanoparticle networks are investigated with optical absorption spectroscopy. Single-stranded, 12-base DNA-capped gold nanoparticles are linked with complementary, single-stranded, 24-base linker DNA to form particle networks. Compared to free DNA, a sharp melting transition is seen in these networked DNA-nanoparticle systems. The sharpness is explained by percolation transition phenomena.

physics.bio-ph↗