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.Comment: 12 pages, 3 figure

Polyyne Ring Nucleus Growth Model for Single-Layer Carbon Nanotubes

We propose, based on recent experimental results, a polyyne ring nucleus (PRN) growth model for the synthesis of single-layer nanotubes (SLN's). The PRN model assumes that (i) the critical nuclei are the planar carbon polyyne rings that are observed to be most stable for sizes in the range C10 to C40; (ii) ComCn clusters (possibly charged) play the role of a catalyst by serving to add C2 or other gas phase species into the growing tube; (iii) promoters such as S, Bi, and Pb serve to modify the rates for these processes by stabilizing the ring structure. We suggest experiments to test and amplify this PRN model, including a flow tube arrangement that might be useful for synthesizing more uniform SLN's

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.Comment: 4 pages, 4 figures, Phys.Rev.Lett. (2005), to appea

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.Comment: 9 pages, 4 figures, submitte

Multiscale mechanobiology: mechanics at the molecular, cellular, and tissue levels

Mechanical force is present in all aspects of living systems. It affects the conformation of molecules, the shape of cells, and the morphology of tissues. All of these are crucial in architecture-dependent biological functions. Nanoscience of advanced materials has provided knowledge and techniques that can be used to understand how mechanical force is involved in biological systems, as well as to open new avenues to tailor-made bio-mimetic materials with desirable properties. In this article, we describe models and show examples of how force is involved in molecular functioning, cell shape patterning, and tissue morphology

Single molecule force measurements of perlecan/HSPG2: A key component of the osteocyte pericellular matrix

Perlecan/HSPG2, a large, monomeric heparan sulfate proteoglycan (HSPG), is a key component of the lacunar canalicular system (LCS) of cortical bone, where it is part of the mechanosensing pericellular matrix (PCM) surrounding the osteocytic processes and serves as a tethering element that connects the osteocyte cell body to the bone matrix. Within the pericellular space surrounding the osteocyte cell body, perlecan can experience physiological fluid flow drag force and in that capacity function as a sensor to relay external stimuli to the osteocyte cell membrane. We previously showed that a reduction in perlecan secretion alters the PCM fiber composition and interferes with bone's response to a mechanical loading in vivo. To test our hypothesis that perlecan core protein can sustain tensile forces without unfolding under physiological loading conditions, atomic force microscopy (AFM) was used to capture images of perlecan monomers at nanoscale resolution and to perform single molecule force measurement (SMFMs). We found that the core protein of purified full-length human perlecan is of suitable size to span the pericellular space of the LCS, with a measured end-to-end length of 170 ± 20 nm and a diameter of 2–4 nm. Force pulling revealed a strong protein core that can withstand over 100 pN of tension well over the drag forces that are estimated to be exerted on the individual osteocyte tethers. Data fitting with an extensible worm-like chain model showed that the perlecan protein core has a mean elastic constant of 890 pN and a corresponding Young's modulus of 71 MPa. We conclude that perlecan has physical properties that would allow it to act as a strong but elastic tether in the LCS

Introduction of a strong temperature-sensitive phenotype into enterovirus 71 by altering an amino acid of virus 3D polymerase

AbstractIn 1998, an enterovirus 71 (EV71) epidemic in Taiwan resulted in 78 deaths; however, the molecular basis of EV71 pathogenicity remains poorly understood. Comparison of the deduced amino acid sequences in 3D polymerases of EV71clinical isolates showed the T251V or T251I substitution from 1986 and 1998 outbreaks. An EV71 replicon system showed that introducing an I251T mutation did not affect luciferase activities at 35 °C when compared with wild type; however, lower luciferase activities were observed when they were incubated at 39.5 °C. In addition, the I251T mutation in the EV71 infectious clone not only reduced viral replication at 39.5 °C in vitro but also decreased the virulence of the mouse adaptive strain MP4 in neonatal mice in an i.p. infection model. Therefore, these results suggested that the threonine at position 251 results in a temperature sensitivity phenotype of EV71 which may contribute to the attenuation of circulating strains

Mechanical Activation of a Multimeric Adhesive Protein Through Domain Conformational Change

The mechanical force-induced activation of the adhesive protein von Willebrand factor (VWF), which experiences high hydrodynamic forces, is essential in initiating platelet adhesion. The importance of the mechanical force-induced functional change is manifested in the multimeric VWF's crucial role in blood coagulation, when high fluid shear stress activates plasma VWF (PVWF) multimers to bind platelets. Here, we showed that a pathological level of high shear stress exposure of PVWF multimers results in domain conformational changes, and the subsequent shifts in the unfolding force allow us to use force as a marker to track the dynamic states of the multimeric VWF. We found that shear-activated PVWF multimers are more resistant to mechanical unfolding than nonsheared PVWF multimers, as indicated in the higher peak unfolding force. These results provide insight into the mechanism of shear-induced activation of PVWF multimers