Analysis of Grain Boundary Dependent Memory Characteristics in Poly-Si One-Transistor Dynamic Random-Access Memory.

A capacitorless one-transistor dynamic random-access memory cell with a polysilicon body (poly-Si 1T-DRAM) has a cost-effective fabrication process and allows a three-dimensional stacked architecture that increases the integration density of memory cells. Also, since this device uses grain boundaries (GBs) as a storage region, it can be operated as a memory cell even in a thin body device. GBs are important to the memory characteristics of poly-Si 1T-DRAM because the amount of trapped charge in the GBs determines the memory's data state. In this paper, we report on a statistical analysis of the memory characteristics of poly-Si 1T-DRAM cells according to the number and location of GBs using TCAD simulation. As the number of GBs increases, the sensing margin and retention time of memory cells deteriorate due to increasing trapped electron charge. Also, "0" state current increases and memory performance degrades in cells where all GBs are adjacent to the source or drain junction side in a strong electric field. These results mean that in poly-Si 1T-DRAM design, the number and location of GBs in a channel should be considered for optimal memory performance.

Ultrafast generation of fundamental and multiple-order phonon excitations in highly enriched (6,5) single-wall carbon nanotubes.

Using a macroscopic ensemble of highly enriched (6,5) single-wall carbon nanotubes, combined with high signal-to-noise ratio and time-dependent differential transmission spectroscopy, we have generated vibrational modes in an ultrawide spectral range (10-3000 cm(-1)). A total of 14 modes were clearly resolved and identified, including fundamental modes of A, E1, and E2 symmetries and their combinational modes involving two and three phonons. Through comparison with continuous wave Raman spectra as well as calculations based on an extended tight-binding model, we were able to identify all the observed peaks and determine the frequencies of the individual and combined modes. We provide a full summary of phonon frequencies for (6,5) nanotubes that can serve as a basic reference with which to refine our understanding of nanotube phonon spectra as well as a testbed for new theoretical models.

NMR study on the B-Z junction formation of DNA duplexes induced by Z-DNA binding domain of human ADAR1.

Z-DNA is produced in a long genomic DNA by Z-DNA binding proteins, through formation of two B-Z junctions with the extrusion of one base pair from each junction. To answer the question of how Z-DNA binding proteins induce B-Z transitions in CG-rich segments while maintaining the B-conformation of surrounding segments, we investigated the kinetics and thermodynamics of base-pair openings of a 13-bp DNA in complex with the Z-DNA binding protein, Zα(ADAR1). We also studied perturbations in the backbone of Zα(ADAR1) upon binding to DNA. Our study demonstrates the initial contact conformation as an intermediate structure during B-Z junction formation induced by Zα(ADAR1), in which the Zα(ADAR1) protein displays unique backbone conformational changes, but the 13-bp DNA duplex maintains the B-form helix. We also found the unique structural features of the 13-bp DNA duplex in the initial contact conformation: (i) instability of the AT-rich region II and (ii) longer lifetime for the opening state of the CG-rich region I. Our findings suggest a three-step mechanism of B-Z junction formation: (i) Zα(ADAR1) specifically interacts with a CG-rich DNA segment maintaining B-form helix via a unique conformation; (ii) the neighboring AT-rich region becomes very unstable, and the CG-rich DNA segment is easily converted to Z-DNA; and (iii) the AT-rich regions are base-paired again, and the B-Z junction structure is formed.

Base pair opening kinetics and dynamics in the DNA duplexes that specifically recognized by very short patch repair protein (Vsr).

In Escherichia coli, the very short patch (VSP) repair system is a major pathway for removal of T.G mismatches in Dcm target sequences. In the VSP repair pathway, the very short patch repair (Vsr) endonuclease selectively recognizes a T.G mismatch in Dcm target sequences and hydrolyzes the 5'-phosphate group of the mismatched thymine. The hydrogen exchange NMR studies here revealed that the T5.G18 mismatch in the Dcm target sequence significantly stabilizes own base pair but destabilizes the two neighboring G4.C19 and A6.T17 base pairs compare to other T.G mismatches. These unusual patterns of base pair stability in the Dcm target sequence can explain how the Vsr endonuclease specifically recognizes the mismatched Dcm target sequence and intercalates into the DNA.

Solution structure and backbone dynamics of the XPC-binding domain of the human DNA repair protein hHR23B.

Human cells contain two homologs of the yeast RAD23 protein, hHR23A and hHR23B, which participate in the DNA repair process. hHR23B houses a domain (residues 277-332, called XPCB) that binds specifically and directly to the xeroderma pigmentosum group C protein (XPC) to initiate nucleotide excision repair (NER). This domain shares sequence homology with a heat shock chaperonin-binding motif that is also found in the stress-inducible yeast phosphoprotein STI1. We determined the solution structure of a protein fragment containing amino acids 275-342 of hHR23B (termed XPCB-hHR23B) and compared it with the previously reported solution structures of the corresponding domain of hHR23A. The periodic positioning of proline residues in XPCB-hHR23B produced kinked alpha helices and assisted in the formation of a compact domain. Although the overall structure of the XPCB domain was similar in both XPCB-hHR23B and XPCB-hHR23A, the N-terminal part (residues 275-283) of XPCB-hHR23B was more flexible than the corresponding part of hHR23A. We tried to infer the characteristics of this flexibility through (15)N-relaxation studies. The hydrophobic surface of XPCB-hHR23B, which results from the diverse distribution of N-terminal region, might give rise to the functional pleiotropy observed in vivo for hHR23B, but not for hHR23A.

Structural insights into the monosaccharide specificity of Escherichia coli rhamnose mutarotase.

The crystal structure of Escherichia coli rhamnose mutarotase (YiiL) is completely different from the previously reported structures of the Lactococcus lactis galactose mutarotase and the Bacillus subtilis RbsD (pyranase). YiiL exists as a locally asymmetric dimer, which is stabilized by an intermolecular beta-sheet, various hydrophobic interactions, and a cation-pi interaction with a salt-bridge. The protein folds of YiiL are similar to those of a Streptomyces coelicolor mono-oxygenase and a hypothetical Arabidopsis thaliana protein At3g17210. By assaying the enzymatic activity of six active-site mutants and by comparing the crystal structure-derived active site conformations of YiiL, RbsD, and a galactose mutarotase, we were able to define the amino acid residues required for catalysis and suggest a possible catalytic mechanism for YiiL. Although the active-site amino acid residues of YiiL (His, Tyr, and Trp) differ greatly from those of galactose mutarotase (His, Glu, and Asp), their geometries, which determine the structures of the preferred monosaccharide substrates, are conserved. In addition, the in vivo function of YiiL was assessed by constructing a mutant E.coli strain that carries a yiiL deletion. The presence of the yiiL gene is critical for efficient cell growth only when concentrations of l-rhamnose are limited.