Direct Detection of Bacterial Genomic DNA at Sub-Femtomolar Concentrations Using Single Molecule Arrays

2013 ◽  
Vol 85 (3) ◽  
pp. 1932-1939 ◽  
Author(s):  
Linan Song ◽  
Dandan Shan ◽  
Mingwei Zhao ◽  
Brian A. Pink ◽  
Kaitlin A. Minnehan ◽  
...  
Keyword(s):  
Single Molecule ◽  
Genomic Dna ◽  
Direct Detection

scholarly journals Analysis of HLA-G long-read genomic sequences in mother–offspring pairs with preeclampsia

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Ayako Nishizawa ◽  
Kazuki Kumada ◽  
Keiko Tateno ◽  
Maiko Wagata ◽  
Sakae Saito ◽  
...  
Keyword(s):  
Single Molecule ◽  
Gene Polymorphisms ◽  
Genomic Dna ◽  
Genomic Sequences ◽  
Genomic Sequencing ◽  
Public Database ◽  
Coding Sequences ◽  
Pacbio Rs Ii ◽  
Potential Association ◽  
Long Read

AbstractPreeclampsia is a pregnancy-induced disorder that is characterized by hypertension and is a leading cause of perinatal and maternal–fetal morbidity and mortality. HLA-G is thought to play important roles in maternal–fetal immune tolerance, and the associations between HLA-G gene polymorphisms and the onset of pregnancy-related diseases have been explored extensively. Because contiguous genomic sequencing is difficult, the association between the HLA-G genotype and preeclampsia onset is controversial. In this study, genomic sequences of the HLA-G region (5.2 kb) from 31 pairs of mother–offspring genomic DNA samples (18 pairs from normal pregnancies/births and 13 from preeclampsia births) were obtained by single-molecule real-time sequencing using the PacBio RS II platform. The HLA-G alleles identified in our cohort matched seven known HLA-G alleles, but we also identified two new HLA-G alleles at the fourth-field resolution and compared them with nucleotide sequences from a public database that consisted of coding sequences that cover the 3.1-kb HLA-G gene span. Intriguingly, a potential association between preeclampsia onset and the poly T stretch within the downstream region of the HLA-G*01:01:01:01 allele was found. Our study suggests that long-read sequencing of HLA-G will provide clues for characterizing HLA-G variants that are involved in the pathophysiology of preeclampsia.

scholarly journals Multiplexed Detection of COVID-19 with Single-Molecule Technology

2021 ◽  
Author(s):  
Noa Furth ◽  
Shay Shilo ◽  
Niv Cohen ◽  
Nir Erez ◽  
Vadim Fedyuk ◽  
...  
Keyword(s):  
Immune Response ◽  
Viral Infection ◽  
Single Molecule ◽  
Direct Detection ◽  
Genetic Material ◽  
Diagnostic Tools ◽  
Proof Of Concept ◽  
Multiplexed Detection ◽  
Diagnostic Approaches ◽  
Quantitative Nature

The COVID-19 pandemic raises the need for diverse diagnostic approaches to rapidly detect different stages of viral infection. The flexible and quantitative nature of single-molecule imaging technology renders it optimal for development of new diagnostic tools. Here we present a proof-of-concept for a single-molecule based, enzyme-free assay for multiplexed detection of SARS-CoV-2. The unified platform we developed allows direct detection of the viral genetic material from patients' samples, as well as their immune response consisting of IgG and IgM antibodies. Thus, it establishes a platform for diagnostics of COVID-19, which could also be adjusted to diagnose additional pathogens.

Direct detection of unamplified genomic DNA based on photo-induced silver ion reduction by DNA molecules

2013 ◽  
Vol 49 (23) ◽  
pp. 2350 ◽  
Author(s):  
Ye Lim Jung ◽  
Cheulhee Jung ◽  
Jung Hun Park ◽  
Moon Il Kim ◽  
Hyun Gyu Park
Keyword(s):  
Genomic Dna ◽  
Direct Detection ◽  
Silver Ion ◽  
Dna Molecules

scholarly journals Single Molecule Investigation of Ag+ Interactions with Single Cytosine-, Methylcytosine- and Hydroxymethylcytosine-Cytosine Mismatches in a Nanopore

2014 ◽  
Vol 4 (1) ◽  
Author(s):  
Yong Wang ◽  
Bin-Quan Luan ◽  
Zhiyu Yang ◽  
Xinyue Zhang ◽  
Brandon Ritzo ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Binding Site ◽  
Single Molecule ◽  
Metal Ion ◽  
Detection Method ◽  
Direct Detection ◽  
Alpha Hemolysin ◽  
Duplex Stability ◽  
Dynamics Simulations ◽  
Direct Detection Method

Abstract Both cytosine-Ag-cytosine interactions and cytosine modifications in a DNA duplex have attracted great interest for research. Cytosine (C) modifications such as methylcytosine (mC) and hydroxymethylcytosine (hmC) are associated with tumorigenesis. However, a method for directly discriminating C, mC and hmC bases without labeling, modification and amplification is still missing. Additionally, the nature of coordination of Ag+ with cytosine-cytosine (C-C) mismatches is not clearly understood. Utilizing the alpha-hemolysin nanopore, we show that in the presence of Ag+, duplex stability is most increased for the cytosine-cytosine (C-C) pair, followed by the cytosine-methylcytosine (C-mC) pair and the cytosine-hydroxymethylcytosine (C-hmC) pair, which has no observable Ag+ induced stabilization. Molecular dynamics simulations reveal that the hydrogen-bond-mediated paring of a C-C mismatch results in a binding site for Ag+. Cytosine modifications (such as mC and hmC) disrupted the hydrogen bond, resulting in disruption of the Ag+ binding site. Our experimental method provides a novel platform to study the metal ion-DNA interactions and could also serve as a direct detection method for nucleobase modifications.

Direct detection of genomic DNA with fluidic force discrimination assays

2009 ◽  
Vol 392 (2) ◽  
pp. 139-144 ◽  
Author(s):  
S.P. Mulvaney ◽  
C.N. Ibe ◽  
C.R. Tamanaha ◽  
L.J. Whitman
Keyword(s):  
Genomic Dna ◽  
Direct Detection

scholarly journals Multisite EGFR phosphorylation is regulated by adaptor protein abundances and dimer lifetimes

2020 ◽  
Vol 31 (7) ◽  
pp. 695-708 ◽  
Author(s):  
Emanuel Salazar-Cavazos ◽  
Carolina Franco Nitta ◽  
Eshan D. Mitra ◽  
Bridget S. Wilson ◽  
Keith A. Lidke ◽  
...  
Keyword(s):  
Single Molecule ◽  
Direct Detection ◽  
Adaptor Protein ◽  
Egfr Signaling ◽  
Rule Based ◽  
Receptor Dimerization ◽  
Multisite Phosphorylation

Using a modified single-molecule pull-down (SiMPull) approach, the first direct detection of activation-dependent multisite phosphorylation on intact EGFR is provided. Integrating SiMPull data with rule-based modeling revealed roles for receptor dimerization dynamics and adaptor protein concentrations in directing EGFR signaling.

scholarly journals Direct Detection of Intramolecular Dynamics of Membrane Proteins using Time-resolved X-ray Single-molecule Tracking

2020 ◽  
Vol 118 (3) ◽  
pp. 170a
Author(s):  
Kazuhiro Mio ◽  
shoko fujimura ◽  
Masaki Ishihara ◽  
Muneyo Mio ◽  
Masahiro Kuramochi ◽  
...  
Keyword(s):  
Membrane Proteins ◽  
Single Molecule ◽  
Direct Detection ◽  
Intramolecular Dynamics ◽  
Time Resolved ◽  
Single Molecule Tracking ◽  
X Ray

Feasibility of Population Scale Comprehensive Identification and Analysis of Complex Structural Variations in Cancer Genome Using Nanochannel Array

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 476-476
Author(s):  
Alex Hastie ◽  
Ernest Lam ◽  
Heng Dai ◽  
Warren Andrews ◽  
Andy Pang ◽  
...  
Keyword(s):  
Single Molecule ◽  
Complex Traits ◽  
Genomic Dna ◽  
Genomic Sequence ◽  
Conflicts Of Interest ◽  
Large Population ◽  
Sequence Motif ◽  
Structural Variations ◽  
Hematological Cancers ◽  
Population Scale

Abstract Diseases with complex traits such as hematological cancer are known to be associated with large structural variations (SV > 1 kb). Techniques such as karyotyping, FISH and aCGH have been common tools for gross chromosomal lesion analysis. Yet population scale comprehensive SV analysis with these tools remains impractical, tedious or incomplete such as missing balanced lesions by aCGH. Recently, high throughput Next Generation Sequencing (NGS) has generated a large amount of sequencing reads that have rapidly reduced costs and are effective in detection of SNPs and small indels; however, complicated by the fact that large structural variations, often spanning tens to hundreds of thousands of base pairs or involving complex rearrangements throughout the genome, are hard for current short read sequencing technology to assemble or infer. Therefore, there is a blind spot in effectively detecting SVs within this range (1 kb ~ 1 Mb) due to insufficient tools. Here we demonstrate a technology that rapidly linearizes very long strands of genomic DNA (100 kb to Mbs) through NanoChannels to directly visualize large SVs and rearrangements preserved within intact genomic DNA at the single molecule level. Through specific sequence motif labeling, de novo genome physical maps are assembled within hours and hundreds to thousands of SV events, balanced or imbalanced, are called with no a priori knowledge of the samples. Preliminary testing data from a group of cancer samples and multiple trio families will be shown to demonstrate this highly comprehensive and cost effective approach, with results validated by direct single-molecule images and multiple orthogonal methods. We also show long spanning molecules would provide very valuable information of precise mapping of viral genomic sequence integration in human genomes that are potentially associated with malignant cell transformation. For the first time, it is now feasible to do large population-based comprehensive genome structural variation studies on a single platform. This innovations will transform the biomedical research, diagnosis and treatment of hematological cancers that result from structural variations and chromosomal lesions. Disclosures No relevant conflicts of interest to declare.

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