Detection of DNA oligonucleotides with base mutations by terahertz spectroscopy and microstructures

<div><p>DNA oligonucleotides with a 5-base mutation at the 3'-terminus were investigated by terahertz (THz) spectroscopy in a marker-free manner. The four single-stranded oligonucleotides with 17nt have been detected with specificity on a microfluidic chip, and corroborated by spectral measurements with split-ring resonators. The number of hydrogen bonds formed between the oligonucleotide and its surrounding water molecules, deemed a key contribution to the THz absorption of biological solutions, was explored by molecular dynamics simulations to explain the experimental findings. Our work underlies the feasibility of THz spectroscopy combined with microstructures for marker-free detection of DNA, which may form the basis of a prospective diagnostic tool for studying genic mutation.</p></div

Absorption coefficients of TE buffer and the concentration dependence of the Ter-5A at 0.6–1.4 THz.

<p>The inset shows the amplified spectra at a narrow frequency band of 0.78–0.83 THz to highlight the error bars and the frequency resolution clearly.</p

Sequences of oligonucleotides investigated in this study.

<p>Sequences of oligonucleotides investigated in this study.</p

An optical microscope image of the SRRs.

<p>There are 20 nm thick Cr (Chromium) and 200 nm thick Au (gold) metal films on the Si substrate. The SRRs have a period of 60 μm. The gap size between two adjacent open square rings is equivalently 2.5 μm. The linewidth of the open square ring is 2 μm and the line length for the maximum open square ring is 50 μm.</p

THz transmission spectra of the SRRs and the dry oligonucleotides on SRRs.

<p>The resonant frequency peak for each spectrum is marked with a vertical dash.</p

A schematic presentation of the microfluidic chip.

<p>The chip involves a 17-mm-long filleted rhombus with a depth of 50 μm on one of the two quartz plates was fabricated by lithography. The inlet/outlet circular holes with a diameter of 1 mm were fabricated by laser drilling.</p

Comparative Analysis of Genome-Wide Chromosomal Histone Modification Patterns in Maize Cultivars and Their Wild Relatives

<div><p>Recent advances demonstrate that epigenome changes can also cause phenotypic diversity and can be heritable across generations, indicating that they may play an important role in evolutionary processes. In this study, we analyzed the chromosomal distribution of several histone modifications in five elite maize cultivars (B73, Mo17, Chang7-2, Zheng58, ZD958) and their two wild relatives (<i>Zea mays</i> L. ssp. <i>parviglumis</i> and <i>Zea nicaraguensis</i>) using a three-dimensional (3D) epigenome karyotyping approach by combining immunostaining and 3D reconstruction with deconvolution techniques. The distribution of these histone modifications along chromosomes demonstrated that the histone modification patterns are conserved at the chromosomal level and have not changed significantly following domestication. The comparison of histone modification patterns between metaphase chromosomes and interphase nuclei showed that some of the histone modifications were retained as the cell progressed from interphase into metaphase, although remodelling existed. This study will increase comprehension of the function of epigenetic modifications in the structure and evolution of the maize genome.</p></div

Ideogram of FISH karyotype of four maize lines.

<p>The four maize lines include B73, Mo17, Zheng58 and ZD958 (Chang7-2×Zheng58). Assignments of pseudo-colors to each probe: TAG as white, CentC as green, 45S rDNA as yellow and knob 180-bp as red.</p

List of primary antibodies used in the present study.

<p>List of primary antibodies used in the present study.</p

Comparison of H3K4me3 distribution of across interphase nuclei and metaphase chromosomes in B73.

<p>Immunolabelled metaphase chromosomes (DAPI staining signals in blue and immunosignals in green) by H3K4me3 are aligned with the distribution of H3K4me3 and DNA methylation in the equivalent interphase nuclei assembled from ChIP-seq data <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097364#pone.0097364-Wang1" target="_blank">[31]</a>. Each chromosome was divided into 10 Mb intervals. The left vertical axis indicates the number of unique reads per 10 Mb of H3K4me3 (blue curve), and the right vertical axis indicates the number of unique reads per 10 Mb of DNA methylation (red curve).</p