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Detecting respiratory viral RNA using expanded genetic alphabets and self-avoiding DNA.

Identifieur interne : 000E32 ( PubMed/Checkpoint ); précédent : 000E31; suivant : 000E33

Detecting respiratory viral RNA using expanded genetic alphabets and self-avoiding DNA.

Auteurs : Lyudmyla G. Glushakova [États-Unis] ; Nidhi Sharma [États-Unis] ; Shuichi Hoshika [États-Unis] ; Andrea C. Bradley [États-Unis] ; Kevin M. Bradley [États-Unis] ; Zunyi Yang [États-Unis] ; Steven A. Benner [États-Unis]

Source :

Analytical biochemistry [ 1096-0309 ] ; 2015.

RBID : pubmed:26299645

Descripteurs français

English descriptors

KwdEn :
- Coronaviridae (classification), Coronaviridae (isolation & purification), Coronaviridae (metabolism), DNA (metabolism), DNA, Single-Stranded (metabolism), DNA-Directed RNA Polymerases (metabolism), Deoxyribonucleosides (metabolism), Fluorescent Dyes (chemistry), Hydrogen Bonding, Immobilized Nucleic Acids (metabolism), Limit of Detection, Microspheres, Molecular Typing (methods), Multiplex Polymerase Chain Reaction (methods), Nucleic Acid Heteroduplexes, Nucleic Acid Hybridization (methods), Orthomyxoviridae (classification), Orthomyxoviridae (isolation & purification), Orthomyxoviridae (metabolism), Phycoerythrin (chemistry), Pyridones (metabolism), RNA, Viral (isolation & purification), RNA, Viral (metabolism), Respiratory Syncytial Viruses (classification), Respiratory Syncytial Viruses (isolation & purification), Respiratory Syncytial Viruses (metabolism), Respiratory Tract Infections (diagnosis), Respiratory Tract Infections (virology), Reverse Transcriptase Polymerase Chain Reaction, Synthetic Biology (methods), Triazines (metabolism), Viral Proteins (metabolism).
MESH :
- chemical , chemistry : Fluorescent Dyes, Phycoerythrin.
- chemical , isolation & purification : RNA, Viral.
- chemical , metabolism : DNA, DNA, Single-Stranded, DNA-Directed RNA Polymerases, Deoxyribonucleosides, Immobilized Nucleic Acids, Pyridones, RNA, Viral, Triazines, Viral Proteins.
- classification : Coronaviridae, Orthomyxoviridae, Respiratory Syncytial Viruses.
- diagnosis : Respiratory Tract Infections.
- isolation & purification : Coronaviridae, Orthomyxoviridae, Respiratory Syncytial Viruses.
- metabolism : Coronaviridae, Orthomyxoviridae, Respiratory Syncytial Viruses.
- methods : Molecular Typing, Multiplex Polymerase Chain Reaction, Nucleic Acid Hybridization, Synthetic Biology.
- virology : Respiratory Tract Infections.
- Hydrogen Bonding, Limit of Detection, Microspheres, Nucleic Acid Heteroduplexes, Reverse Transcriptase Polymerase Chain Reaction.

Abstract

Nucleic acid (NA)-targeted tests detect and quantify viral DNA and RNA (collectively xNA) to support epidemiological surveillance and, in individual patients, to guide therapy. They commonly use polymerase chain reaction (PCR) and reverse transcription PCR. Although these all have rapid turnaround, they are expensive to run. Multiplexing would allow their cost to be spread over multiple targets, but often only with lower sensitivity and accuracy, noise, false positives, and false negatives; these arise by interactions between the multiple nucleic acid primers and probes in a multiplexed kit. Here we offer a multiplexed assay for a panel of respiratory viruses that mitigates these problems by combining several nucleic acid analogs from the emerging field of synthetic biology: (i) self-avoiding molecular recognition systems (SAMRSs), which facilitate multiplexing, and (ii) artificially expanded genetic information systems (AEGISs), which enable low-noise PCR. These are supplemented by "transliteration" technology, which converts standard nucleotides in a target to AEGIS nucleotides in a product, improving hybridization. The combination supports a multiplexed Luminex-based respiratory panel that potentially differentiates influenza viruses A and B, respiratory syncytial virus, severe acute respiratory syndrome coronavirus (SARS), and Middle East respiratory syndrome (MERS) coronavirus, detecting as few as 10 MERS virions in a 20-μl sample.

DOI: 10.1016/j.ab.2015.08.015
PubMed: 26299645

Affiliations:

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<front><div type="abstract" xml:lang="en">Nucleic acid (NA)-targeted tests detect and quantify viral DNA and RNA (collectively xNA) to support epidemiological surveillance and, in individual patients, to guide therapy. They commonly use polymerase chain reaction (PCR) and reverse transcription PCR. Although these all have rapid turnaround, they are expensive to run. Multiplexing would allow their cost to be spread over multiple targets, but often only with lower sensitivity and accuracy, noise, false positives, and false negatives; these arise by interactions between the multiple nucleic acid primers and probes in a multiplexed kit. Here we offer a multiplexed assay for a panel of respiratory viruses that mitigates these problems by combining several nucleic acid analogs from the emerging field of synthetic biology: (i) self-avoiding molecular recognition systems (SAMRSs), which facilitate multiplexing, and (ii) artificially expanded genetic information systems (AEGISs), which enable low-noise PCR. These are supplemented by "transliteration" technology, which converts standard nucleotides in a target to AEGIS nucleotides in a product, improving hybridization. The combination supports a multiplexed Luminex-based respiratory panel that potentially differentiates influenza viruses A and B, respiratory syncytial virus, severe acute respiratory syndrome coronavirus (SARS), and Middle East respiratory syndrome (MERS) coronavirus, detecting as few as 10 MERS virions in a 20-μl sample. </div>
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<Abstract><AbstractText>Nucleic acid (NA)-targeted tests detect and quantify viral DNA and RNA (collectively xNA) to support epidemiological surveillance and, in individual patients, to guide therapy. They commonly use polymerase chain reaction (PCR) and reverse transcription PCR. Although these all have rapid turnaround, they are expensive to run. Multiplexing would allow their cost to be spread over multiple targets, but often only with lower sensitivity and accuracy, noise, false positives, and false negatives; these arise by interactions between the multiple nucleic acid primers and probes in a multiplexed kit. Here we offer a multiplexed assay for a panel of respiratory viruses that mitigates these problems by combining several nucleic acid analogs from the emerging field of synthetic biology: (i) self-avoiding molecular recognition systems (SAMRSs), which facilitate multiplexing, and (ii) artificially expanded genetic information systems (AEGISs), which enable low-noise PCR. These are supplemented by "transliteration" technology, which converts standard nucleotides in a target to AEGIS nucleotides in a product, improving hybridization. The combination supports a multiplexed Luminex-based respiratory panel that potentially differentiates influenza viruses A and B, respiratory syncytial virus, severe acute respiratory syndrome coronavirus (SARS), and Middle East respiratory syndrome (MERS) coronavirus, detecting as few as 10 MERS virions in a 20-μl sample. </AbstractText>
<CopyrightInformation>Copyright © 2015 Elsevier Inc. All rights reserved.</CopyrightInformation>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Glushakova</LastName>
<ForeName>Lyudmyla G</ForeName>
<Initials>LG</Initials>
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Detecting respiratory viral RNA using expanded genetic alphabets and self-avoiding DNA.

Detecting respiratory viral RNA using expanded genetic alphabets and self-avoiding DNA.

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