scholarly journals Modular protein-oligonucleotide signal exchange

2019 ◽  
Author(s):  
Deepak K. Agrawal
Keyword(s):  
Real Time ◽  
Output Signal ◽  
Point Of Care ◽  
Specific Protein ◽  
Dna Oligonucleotides ◽  
Exchange Processes ◽  
Dna Strand Displacement ◽  
Displacement Reactions ◽  
Biochemical Systems ◽  
Output Characteristics

ABSTRACTThe ability to detect a protein selectively and produce a predicted signal in real time is a long-lasting engineering challenge in the field of biochemistry. Such a mechanism typically requires a sensing module to recognize the input protein and a translation module to produce a programmable output signal that reflects the concentration of the input. Here we present a generic biomolecular reaction process that exchanges the concentration of an input protein with a DNA oligonucleotide. This approach uses the unique characteristic of DNA oligonucleotide aptamer that can either bind to a specific protein or to a complementary DNA oligonucleotide reversibly. We then pass the information of the protein concentration to the output signal through DNA strand displacement reactions. Using this strategy, we design and characterize four different exchange processes that can produce modular DNA oligonucleotides in response to different proteins such as clinically important human α-thrombin and vascular endothelial growth factor (VEGF). These exchange processes are capable of real time sensing and are modular such that they can be used for concurrent detection of different proteins with well-defined input-output characteristics. The novelty and simplicity of our approach encourage to develop advanced biochemical systems for point-of-care testing of infectious diseases and treatments.

scholarly journals Modular protein-oligonucleotide signal exchange

2020 ◽  
Vol 48 (12) ◽  
pp. 6431-6444
Author(s):  
Deepak K Agrawal ◽  
Rebecca Schulman
Keyword(s):  
Specific Protein ◽  
Vascular Endothelial ◽  
Complementary Dna ◽  
Exchange Processes ◽  
Dna Strand Displacement ◽  
Specific Proteins ◽  
Dna Strand ◽  
Endothelial Growth Factor ◽  
Signal Exchange

Abstract While many methods are available to measure the concentrations of proteins in solution, the development of a method to quantitatively report both increases and decreases in different protein concentrations in real-time using changes in the concentrations of other molecules, such as DNA outputs, has remained a challenge. Here, we present a biomolecular reaction process that reports the concentration of an input protein in situ as the concentration of an output DNA oligonucleotide strand. This method uses DNA oligonucleotide aptamers that bind either to a specific protein selectively or to a complementary DNA oligonucleotide reversibly using toehold-mediated DNA strand-displacement. It is possible to choose the sequence of output strand almost independent of the sensing protein. Using this strategy, we implemented four different exchange processes to report the concentrations of clinically relevant human α-thrombin and vascular endothelial growth factor using changes in concentrations of DNA oligonucleotide outputs. These exchange processes can operate in tandem such that the same or different output signals can indicate changes in concentration of distinct or identical input proteins. The simplicity of our approach suggests a pathway to build devices that can direct diverse output responses in response to changes in concentrations of specific proteins.

scholarly journals Probabilistic switching circuits in DNA

2018 ◽  
Vol 115 (5) ◽  
pp. 903-908 ◽  
Author(s):  
Daniel Wilhelm ◽  
Jehoshua Bruck ◽  
Lulu Qian
Keyword(s):  
Input Signal ◽  
Building Block ◽  
Output Signal ◽  
Single Type ◽  
Dna Molecules ◽  
Switching Circuits ◽  
Molecular Building Block ◽  
Molecular Events ◽  
Dna Strand Displacement ◽  
Displacement Reactions

A natural feature of molecular systems is their inherent stochastic behavior. A fundamental challenge related to the programming of molecular information processing systems is to develop a circuit architecture that controls the stochastic states of individual molecular events. Here we present a systematic implementation of probabilistic switching circuits, using DNA strand displacement reactions. Exploiting the intrinsic stochasticity of molecular interactions, we developed a simple, unbiased DNA switch: An input signal strand binds to the switch and releases an output signal strand with probability one-half. Using this unbiased switch as a molecular building block, we designed DNA circuits that convert an input signal to an output signal with any desired probability. Further, this probability can be switched between 2n different values by simply varying the presence or absence of n distinct DNA molecules. We demonstrated several DNA circuits that have multiple layers and feedback, including a circuit that converts an input strand to an output strand with eight different probabilities, controlled by the combination of three DNA molecules. These circuits combine the advantages of digital and analog computation: They allow a small number of distinct input molecules to control a diverse signal range of output molecules, while keeping the inputs robust to noise and the outputs at precise values. Moreover, arbitrarily complex circuit behaviors can be implemented with just a single type of molecular building block.

scholarly journals A miniaturized optoelectronic biosensor for real-time point-of-care total protein analysis.

MethodsX ◽  
2021 ◽  
pp. 101414
Author(s):  
Ophir Vermesh ◽  
Fariah Mahzabeen ◽  
Jelena Levi ◽  
Marilyn Tan ◽  
Israt S. Alam ◽  
...  
Keyword(s):  
Real Time ◽  
Total Protein ◽  
Point Of Care ◽  
Protein Analysis ◽  
Time Point

scholarly journals Training an asymmetric signal perceptron through reinforcement in an artificial chemistry

2014 ◽  
Vol 11 (93) ◽  
pp. 20131100 ◽  
Author(s):  
Peter Banda ◽  
Christof Teuscher ◽  
Darko Stefanovic
Keyword(s):  
State Of The Art ◽  
Chemical Species ◽  
Mass Action ◽  
Mass Action Kinetics ◽  
Dna Strand Displacement ◽  
Autonomous Adaptation ◽  
Biochemical Systems ◽  
Dna Strand ◽  
Logic Functions ◽  
Application Specific

State-of-the-art biochemical systems for medical applications and chemical computing are application-specific and cannot be reprogrammed or trained once fabricated. The implementation of adaptive biochemical systems that would offer flexibility through programmability and autonomous adaptation faces major challenges because of the large number of required chemical species as well as the timing-sensitive feedback loops required for learning. In this paper, we begin addressing these challenges with a novel chemical perceptron that can solve all 14 linearly separable logic functions. The system performs asymmetric chemical arithmetic, learns through reinforcement and supports both Michaelis–Menten as well as mass-action kinetics. To enable cascading of the chemical perceptrons, we introduce thresholds that amplify the outputs. The simplicity of our model makes an actual wet implementation, in particular by DNA-strand displacement, possible.

scholarly journals Evaluation of mobile real-time polymerase chain reaction tests for the detection of severe acute respiratory syndrome coronavirus 2

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Chukwunonso Onyilagha ◽  
Henna Mistry ◽  
Peter Marszal ◽  
Mathieu Pinette ◽  
Darwyn Kobasa ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Real Time ◽  
Point Of Care ◽  
Middle Eastern ◽  
Turnaround Time ◽  
Cross Reactivity ◽  
Clinical Samples ◽  
Diarrhea Virus ◽  
Highly Sensitive ◽  
Transmissible Gastroenteritis

AbstractThe coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), calls for prompt and accurate diagnosis and rapid turnaround time for test results to limit transmission. Here, we evaluated two independent molecular assays, the Biomeme SARS-CoV-2 test, and the Precision Biomonitoring TripleLock SARS-CoV-2 test on a field-deployable point-of-care real-time PCR instrument, Franklin three9, in combination with Biomeme M1 Sample Prep Cartridge Kit for RNA 2.0 (M1) manual extraction system for rapid, specific, and sensitive detection of SARS-COV-2 in cell culture, human, and animal clinical samples. The Biomeme SARS-CoV-2 assay, which simultaneously detects two viral targets, the orf1ab and S genes, and the Precision Biomonitoring TripleLock SARS-CoV-2 assay that targets the 5′ untranslated region (5′ UTR) and the envelope (E) gene of SARS-CoV-2 were highly sensitive and detected as low as 15 SARS-CoV-2 genome copies per reaction. In addition, the two assays were specific and showed no cross-reactivity with Middle Eastern respiratory syndrome coronavirus (MERS-CoV), infectious bronchitis virus (IBV), porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis (TGE) virus, and other common human respiratory viruses and bacterial pathogens. Also, both assays were highly reproducible across different operators and instruments. When used to test animal samples, both assays equally detected SARS-CoV-2 genetic materials in the swabs from SARS-CoV-2-infected hamsters. The M1 lysis buffer completely inactivated SARS-CoV-2 within 10 min at room temperature enabling safe handling of clinical samples. Collectively, these results show that the Biomeme and Precision Biomonitoring TripleLock SARS-CoV-2 mobile testing platforms could reliably and promptly detect SARS-CoV-2 in both human and animal clinical samples in approximately an hour and can be used in remote areas or health care settings not traditionally serviced by a microbiology laboratory.

Real-time medication prices at the point of care: Experiences of prescribers

2021 ◽  
Author(s):  
Foster R Goss ◽  
Anna Sinaiko ◽  
Tim Podhajsky ◽  
Chen-Tan Lin
Keyword(s):  
Real Time ◽  
Point Of Care

Biocomputing based on DNA strand displacement reactions

ChemPhysChem ◽  
2021 ◽  
Author(s):  
Hui Lv ◽  
Qian Li ◽  
Jiye Shi ◽  
Fei Wang ◽  
Chunhai Fan
Keyword(s):  
Strand Displacement ◽  
Dna Strand Displacement ◽  
Displacement Reactions ◽  
Dna Strand

scholarly journals Haemophilus influenzae Meningitis Direct Diagnosis by Metagenomic Next-Generation Sequencing: A Case Report

Pathogens ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 461
Author(s):  
Madjid Morsli ◽  
Quentin Kerharo ◽  
Jeremy Delerce ◽  
Pierre-Hugues Roche ◽  
Lucas Troude ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Haemophilus Influenzae ◽  
Real Time ◽  
Real Time Pcr ◽  
Point Of Care ◽  
Next Generation ◽  
Oxford Nanopore ◽  
Sequence Encoding ◽  
Oxford Nanopore Technologies ◽  
Generation Sequencing

Current routine real-time PCR methods used for the point-of-care diagnosis of infectious meningitis do not allow for one-shot genotyping of the pathogen, as in the case of deadly Haemophilus influenzae meningitis. Real-time PCR diagnosed H. influenzae meningitis in a 22-year-old male patient, during his hospitalisation following a more than six-metre fall. Using an Oxford Nanopore Technologies real-time sequencing run in parallel to real-time PCR, we detected the H. influenzae genome directly from the cerebrospinal fluid sample in six hours. Furthermore, BLAST analysis of the sequence encoding for a partial DUF417 domain-containing protein diagnosed a non-b serotype, non-typeable H.influenzae belonging to lineage H. influenzae 22.1-21. The Oxford Nanopore metagenomic next-generation sequencing approach could be considered for the point-of-care diagnosis of infectious meningitis, by direct identification of pathogenic genomes and their genotypes/serotypes.

scholarly journals Real-time point of care microcirculatory assessment of shock: design, rationale and application of the point of care microcirculation (POEM) tool

Critical Care ◽  
2016 ◽  
Vol 20 (1) ◽  
Author(s):  
David N. Naumann ◽  
Clare Mellis ◽  
Shamus L. G. Husheer ◽  
Philip Hopkins ◽  
Jon Bishop ◽  
...  
Keyword(s):  
Real Time ◽  
Point Of Care ◽  
Design Rationale ◽  
Time Point
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