Nucleic Acid Hybridization
Recently Published Documents


TOTAL DOCUMENTS

447
(FIVE YEARS 50)

H-INDEX

47
(FIVE YEARS 10)

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Bei Liu ◽  
Honglue Shi ◽  
Atul Rangadurai ◽  
Felix Nussbaumer ◽  
Chia-Chieh Chu ◽  
...  

ABSTRACTN6-methyladenosine (m6A) is a post-transcriptional modification that controls gene expression by recruiting proteins to RNA sites. The modification also slows biochemical processes through mechanisms that are not understood. Using temperature-dependent (20°C–65°C) NMR relaxation dispersion, we show that m6A pairs with uridine with the methylamino group in the anti conformation to form a Watson-Crick base pair that transiently exchanges on the millisecond timescale with a singly hydrogen-bonded low-populated (1%) mismatch-like conformation in which the methylamino group is syn. This ability to rapidly interchange between Watson-Crick or mismatch-like forms, combined with different syn:anti isomer preferences when paired (~1:100) versus unpaired (~10:1), explains how m6A robustly slows duplex annealing without affecting melting at elevated temperatures via two pathways in which isomerization occurs before or after duplex annealing. Our model quantitatively predicts how m6A reshapes the kinetic landscape of nucleic acid hybridization and conformational transitions, and provides an explanation for why the modification robustly slows diverse cellular processes.


Author(s):  
Yuan-I Chen ◽  
Manasa P. Sripati ◽  
Trung Duc Nguyen ◽  
Yin-Jui Chang ◽  
Yu-An Kuo ◽  
...  

Micromachines ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 390
Author(s):  
Maryia Drobysh ◽  
Almira Ramanaviciene ◽  
Roman Viter ◽  
Arunas Ramanavicius

The coronavirus disease 2019 (COVID-19) outbreak caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was proclaimed a global pandemic in March 2020. Reducing the dissemination rate, in particular by tracking the infected people and their contacts, is the main instrument against infection spreading. Therefore, the creation and implementation of fast, reliable and responsive methods suitable for the diagnosis of COVID-19 are required. These needs can be fulfilled using affinity sensors, which differ in applied detection methods and markers that are generating analytical signals. Recently, nucleic acid hybridization, antigen-antibody interaction, and change of reactive oxygen species (ROS) level are mostly used for the generation of analytical signals, which can be accurately measured by electrochemical, optical, surface plasmon resonance, field-effect transistors, and some other methods and transducers. Electrochemical biosensors are the most consistent with the general trend towards, acceleration, and simplification of the bioanalytical process. These biosensors mostly are based on the determination of antigen-antibody interaction and are robust, sensitive, accurate, and sometimes enable label-free detection of an analyte. Along with the specification of biosensors, we also provide a brief overview of generally used testing techniques, and the description of the structure, life cycle and immune host response to SARS-CoV-2, and some deeper details of analytical signal detection principles.


2021 ◽  
Vol 12 (5) ◽  
pp. 1656-1660
Author(s):  
Hiromu Kashida ◽  
Keiji Nishikawa ◽  
Wenjing Shi ◽  
Toshiki Miyagawa ◽  
Hayato Yamashita ◽  
...  

Herein we report an amplification system of helical excess triggered by nucleic acid hybridization for the first time.


Author(s):  
Bei Liu ◽  
Honglue Shi ◽  
Atul Rangadurai ◽  
Felix Nussbaumer ◽  
Chia-Chieh Chu ◽  
...  

ABSTRACTN6-methyladenosine (m6A) is a post-transcriptional modification that controls gene expression by recruiting proteins to RNA sites. The modification also slows biochemical processes through mechanisms that are not understood. Using NMR relaxation dispersion, we show that m6A pairs with uridine with the methylamino group in the anti conformation to form a Watson-Crick base pair that transiently exchanges on the millisecond timescale with a singly hydrogen-bonded low-populated (1%) mismatch-like conformation in which the methylamino group is syn. This ability to rapidly interchange between Watson-Crick or mismatch-like forms, combined with different syn:anti isomer preferences when paired (~1:100) versus unpaired (~10:1), explains how m6A robustly slows duplex annealing without affecting melting via two pathways in which isomerization occurs before or after duplex annealing. Our model quantitatively predicts how m6A reshapes the kinetic landscape of nucleic acid hybridization and conformational transitions, and provides an explanation for why the modification robustly slows diverse cellular processes.


Small ◽  
2020 ◽  
pp. 2006370
Author(s):  
Yi Zeng ◽  
Kevin M. Koo ◽  
Ai‐Guo Shen ◽  
Ji‐Ming Hu ◽  
Matt Trau

Small ◽  
2020 ◽  
Vol 16 (49) ◽  
pp. 2005476
Author(s):  
Marie L. Salva ◽  
Marco Rocca ◽  
Yong Hu ◽  
Emmanuel Delamarche ◽  
Christof M. Niemeyer

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Guan A. Wang ◽  
Xiaoyu Xie ◽  
Hayam Mansour ◽  
Fangfang Chen ◽  
Gabriela Matamoros ◽  
...  

Abstract Combining experimental and simulation strategies to facilitate the design and operation of nucleic acid hybridization probes are highly important to both fundamental DNA nanotechnology and diverse biological/biomedical applications. Herein, we introduce a DNA equalizer gate (DEG) approach, a class of simulation-guided nucleic acid hybridization probes that drastically expand detection windows for discriminating single nucleotide variants in double-stranded DNA (dsDNA) via the user-definable transformation of the quantitative relationship between the detection signal and target concentrations. A thermodynamic-driven theoretical model was also developed, which quantitatively simulates and predicts the performance of DEG. The effectiveness of DEG for expanding detection windows and improving sequence selectivity was demonstrated both in silico and experimentally. As DEG acts directly on dsDNA, it is readily adaptable to nucleic acid amplification techniques, such as polymerase chain reaction (PCR). The practical usefulness of DEG was demonstrated through the simultaneous detection of infections and the screening of drug-resistance in clinical parasitic worm samples collected from rural areas of Honduras.


2020 ◽  
Author(s):  
Georgina C. Gavins ◽  
Katharina Gröger ◽  
Michael D. Bartoschek ◽  
Philipp Wolf ◽  
Annette G. Beck-Sickinger ◽  
...  

AbstractDNA nanotechnology is an emerging field, which promises fascinating opportunities for the manipulation and imaging of proteins on a cell surface. The key to progress in the area is the ability to create the nucleic acid-protein junction in the context of living cells. Here we report a covalent labelling reaction, which installs a biostable peptide nucleic acid (PNA) tag. The reaction proceeds within minutes and is specific for proteins carrying a 2 kDa coiled coil peptide tag. Once installed the PNA label serves as a generic landing platform that enables the recruitment of fluorescent dyes via nucleic acid hybridization. We demonstrate the versatility of this approach by recruiting different fluorophores, assembling multiple fluorophores for increased brightness, and achieving reversible labelling by way of toehold mediated strand displacement. Additionally, we show that labelling can be carried out using two different coiled coil systems, with EGFR and ETBR, on both HEK293 and CHO cells. Finally, we apply the method to monitor internalization of EGFR on CHO cells.


2020 ◽  
pp. 385-397
Author(s):  
Lam-Kiu Fong ◽  
Ziwei Wang ◽  
George C. Schatz ◽  
Erik Luijten ◽  
Chad A. Mirkina

Sign in / Sign up

Export Citation Format

Share Document