Coupling Transcriptional State to Large-Scale Repeat Expansions in Yeast

SummaryExpansions of simple DNA repeats cause numerous hereditary disorders in humans. Replication, repair, and transcription are implicated in the expansion process, but their relative contributions are yet to be distinguished. To separate the roles of replication and transcription in the expansion of Friedreich’s ataxia (GAA)n repeats, we designed two yeast genetic systems that utilize a galactose-inducible GAL1 promoter but contain these repeats in either the transcribed or nontranscribed region of a selectable cassette. We found that large-scale repeat expansions can occur in the lack of transcription. Induction of transcription strongly elevated the rate of expansions in both systems, indicating that active transcriptional state rather than transcription through the repeat per se affects this process. Furthermore, replication defects increased the rate of repeat expansions irrespective of transcriptional state. We present a model in which transcriptional state, linked to the nucleosomal density of a region, acts as a modulator of large-scale repeat expansions

Epitaxy: Programmable Atom Equivalents

The programmability of DNA makes it an attractive structure-directing ligand for the assembly of nanoparticle (NP) superlattices in a manner that mimics many aspects of atomic crystallization. However, the synthesis of multilayer single crystals of defined size remains a challenge. Though previous studies considered lattice mismatch as the major limiting factor for multilayer assembly, thin film growth depends on many interlinked variables. Here, a more comprehensive approach is taken to study fundamental elements, such as the growth temperature and the thermodynamics of interfacial energetics, to achieve epitaxial growth of NP thin films. Both surface morphology and internal thin film structure are examined to provide an understanding of particle attachment and reorganization during growth. Under equilibrium conditions, single crystalline, multilayer thin films can be synthesized over 500 × 500 μm² areas on lithographically patterned templates, whereas deposition under kinetic conditions leads to the rapid growth of glassy films. Importantly, these superlattices follow the same patterns of crystal growth demonstrated in atomic thin film deposition, allowing these processes to be understood in the context of well-studied atomic epitaxy and enabling a nanoscale model to study fundamental crystallization processes. Through understanding the role of epitaxy as a driving force for NP assembly, we are able to realize 3D architectures of arbitrary domain geometry and size.United States. Air Force Office of Scientific Research (AFOSR FA9550-11-1-0275)United States. Air Force Office of Scientific Research (FA9550-12-1-0280)United States. Department of Defense (N00014-15-1-0043)United States. Department of Energy (Grant DE-SC0000989-0002)National Science Foundation (U.S.) (Award DMR-1121262

Field-effect transistors assembled from functionalized carbon nanotubes

We have fabricated field effect transistors from carbon nanotubes using a novel selective placement scheme. We use carbon nanotubes that are covalently bound to molecules containing hydroxamic acid functionality. The functionalized nanotubes bind strongly to basic metal oxide surfaces, but not to silicon dioxide. Upon annealing, the functionalization is removed, restoring the electronic properties of the nanotubes. The devices we have fabricated show excellent electrical characteristics.Comment: 5 pages, 6 figure

Applied Plasma Research

Contains reports on three research projects.National Science Foundation (Grant GK-18185)M. I. T. Lincoln Laboratory Purchase Order No. CC-55

Structural correlations in heterogeneous electron transfer at monolayer and multilayer graphene electrodes

As a new form of carbon, graphene is attracting intense interest as an electrode material with widespread applications. In the present study, the heterogeneous electron transfer (ET) activity of graphene is investigated using scanning electrochemical cell microscopy (SECCM), which allows electrochemical currents to be mapped at high spatial resolution across a surface for correlation with the corresponding structure and properties of the graphene surface. We establish that the rate of heterogeneous ET at graphene increases systematically with the number of graphene layers, and show that the stacking in multilayers also has a subtle influence on ET kinetics. © 2012 American Chemical Society

A Defective mRNA Cleavage and Polyadenylation Complex Facilitates Expansions of Transcribed (GAA) n Repeats Associated with Friedreich’s Ataxia

Expansions of microsatellite repeats are responsible for numerous hereditary diseases in humans, including myotonic dystrophy and Friedreich's ataxia. Whereas the length of an expandable repeat is the main factor determining disease inheritance, recent data point to genomic trans modifiers that can impact the likelihood of expansions and disease progression. Detection of these modifiers may lead to understanding and treating repeat expansion diseases. Here, we describe a method for the rapid, genome-wide identification of trans modifiers for repeat expansion in a yeast experimental system. Using this method, we found that missense mutations in the endoribonuclease subunit (Ysh1) of the mRNA cleavage and polyadenylation complex dramatically increase the rate of (GAA) n repeat expansions but only when they are actively transcribed. These expansions correlate with slower transcription elongation caused by the ysh1 mutation. These results reveal an interplay between RNA processing and repeat-mediated genome instability, confirming the validity of our approach. Keywords: genome instability; repeat expansion; RNA polyadenylation; RNA processing; transcription-replication conflicts; Friedreich’s ataxia; DNA double-strand breaks; trans-modifiers of repeat expansions; genetic screen; whole-genome sequencin

Giant conductivity switching of LaAlO3/SrTiO3 heterointerfaces governed by surface protonation

Complex-oxide interfaces host a diversity of phenomena not present in traditional semiconductor heterostructures. Despite intense interest, many basic questions remain about the mechanisms that give rise to interfacial conductivity and the role of surface chemistry in dictating these properties. Here we demonstrate a fully reversible >4 order of magnitude conductance change at LaAlO3/SrTiO3 (LAO/STO) interfaces, regulated by LAO surface protonation. Nominally conductive interfaces are rendered insulating by solvent immersion, which deprotonates the hydroxylated LAO surface; interface conductivity is restored by exposure to light, which induces reprotonation via photocatalytic oxidation of adsorbed water. The proposed mechanisms are supported by a coordinated series of electrical measurements, optical/solvent exposures, and X-ray photoelectron spectroscopy. This intimate connection between LAO surface chemistry and LAO/STO interface physics bears far-reaching implications for reconfigurable oxide nanoelectronics and raises the possibility of novel applications in which electronic properties of these materials can be locally tuned using synthetic chemistry

Tunable anisotropy in inverse opals and emerging optical properties

Using self-assembly, nanoscale materials can be fabricated from the bottom up. Opals and inverse opals are examples of self-assembled nanomaterials made from crystallizing colloidal particles. As self-assembly requires a high level of control, it is challenging to use building blocks with anisotropic geometry to form complex opals, which limits the realizable structures. Typically, spherical colloids are employed as building blocks, leading to symmetric, isotropic superstructures. However, a significantly richer palette of directionally dependent properties are expected if less symmetric, anisotropic structures can be created, especially originating from the assembly of regular, spherical particles. Here we show a simple method to introduce anisotropy into inverse opals by subjecting them to a post-assembly thermal treatment that results in directional shrinkage of the silica matrix caused by condensation of partially hydrated sol-gel silica structures. In this way, we can tailor the shape of the pores, and the anisotropy of the final inverse opal preserves the order and uniformity of the self-assembled structure, while completely avoiding the need to synthesize complex oval-shaped particles and crystallize them into such target geometries. Detailed X-ray photoelectron spectroscopy (XPS) and infrared (IR) spectroscopy studies clearly identify increasing degrees of sol-gel condensation in confinement as a mechanism for the structure change. A computer simulation of structure changes resulting from the condensation-induced shrinkage further confirmed this mechanism. As an example of property changes induced by the introduction of anisotropy, we characterized the optical spectra of the anisotropic inverse opals and found that the optical properties can be controlled in a precise way using calcination temperature