scholarly journals A last-in first-out stack data structure implemented in DNA

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Annunziata Lopiccolo ◽  
Ben Shirt-Ediss ◽  
Emanuela Torelli ◽  
Abimbola Feyisara Adedeji Olulana ◽  
Matteo Castronovo ◽  
...  
Keyword(s):  
Data Structure ◽  
Nucleic Acid ◽  
Data Structures ◽  
Memory Systems ◽  
Chemical Data ◽  
Successive Reaction ◽  
Open Problems ◽  
Rule Based ◽  
History Of

AbstractDNA-based memory systems are being reported with increasing frequency. However, dynamic DNA data structures able to store and recall information in an ordered way, and able to be interfaced with external nucleic acid computing circuits, have so far received little attention. Here we present an in vitro implementation of a stack data structure using DNA polymers. The stack is able to record combinations of two different DNA signals, release the signals into solution in reverse order, and then re-record. We explore the accuracy limits of the stack data structure through a stochastic rule-based model of the underlying polymerisation chemistry. We derive how the performance of the stack increases with the efficiency of washing steps between successive reaction stages, and report how stack performance depends on the history of stack operations under inefficient washing. Finally, we discuss refinements to improve molecular synchronisation and future open problems in implementing an autonomous chemical data structure.

High resolution mapping of nucleic acid containing complexes in vitro and in situ

1996 ◽  
Vol 54 ◽  
pp. 48-49
Author(s):  
D. P. Bazett-Jones ◽  
M. J. Hendzel
Keyword(s):  
Nucleic Acid ◽  
High Resolution ◽  
Transcription Initiation ◽  
Molecular Mechanisms ◽  
Heavy Atom ◽  
Regulation Of Transcription ◽  
High Exposure ◽  
Resolution Mapping ◽  
Tata Sequence

Structural analysis of combinations of nucleosomes and transcription factors on promoter and enhancer elements is necessary in order to understand the molecular mechanisms responsible for the regulation of transcription initiation. Such complexes are often not amenable to study by high resolution crystallographic techniques. We have been applying electron spectroscopic imaging (ESI) to specific problems in molecular biology related to transcription regulation. There are several advantages that this technique offers in studies of nucleoprotein complexes. First, an intermediate level of spatial resolution can be achieved because heavy atom contrast agents are not necessary. Second, mass and stoichiometric relationships of protein and nucleic acid can be estimated by phosphorus detection, an element in much higher proportions in nucleic acid than protein. Third, wrapping or bending of the DNA by the protein constituents can be observed by phosphorus mapping of the complexes. Even when ESI is used with high exposure of electrons to the specimen, important macromolecular information may be provided. For example, an image of the TATA binding protein (TBP) bound to DNA is shown in the Figure (top panel). It can be seen that the protein distorts the DNA away from itself and much of its mass sits off the DNA helix axis. Moreover, phosphorus and mass estimates demonstrate whether one or two TBP molecules interact with this particular promoter TATA sequence.

In vitro evaluation of hexitol nucleic acid antisense oligonucleotides

1999 ◽  
Author(s):  
Arthur Van Aerschot ◽  
Mark Vandermeeren ◽  
Johan Geysen ◽  
Walter Luyten ◽  
Marc Miller ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Antisense Oligonucleotides ◽  
In Vitro Evaluation

Genetically Encoded RNA Nanodevices for Cellular Imaging and Regulation

Nanoscale ◽  
2021 ◽  
Author(s):  
Qikun Yu ◽  
Kewei Ren ◽  
Mingxu You
Keyword(s):  
Nucleic Acid ◽  
Cellular Imaging ◽  
Synthetic Dna

Nucleic acid-based nanodevices have been widely used in the fields of biosensing and nanomedicine. Traditionally, the majority of these nanodevices were first constructed in vitro using synthetic DNA or RNA...

scholarly journals Representations, Affordances, and Interactive Systems

2021 ◽  
Vol 5 (5) ◽  
pp. 23
Author(s):  
Robert Rowe
Keyword(s):  
Artificial Intelligence ◽  
Cognitive Science ◽  
Data Structures ◽  
Digital Computer ◽  
Mental Representations ◽  
Interactive Systems ◽  
Algorithmic Composition ◽  
The World ◽  
History Of

The history of algorithmic composition using a digital computer has undergone many representations—data structures that encode some aspects of the outside world, or processes and entities within the program itself. Parallel histories in cognitive science and artificial intelligence have (of necessity) confronted their own notions of representations, including the ecological perception view of J.J. Gibson, who claims that mental representations are redundant to the affordances apparent in the world, its objects, and their relations. This review tracks these parallel histories and how the orientations and designs of multimodal interactive systems give rise to their own affordances: the representations and models used expose parameters and controls to a creator that determine how a system can be used and, thus, what it can mean.

scholarly journals Are RNA-Based Tests Sufficient for COVID-19 Diagnosis? An Inspiration of Three Asymptomatic Cases

2021 ◽  
Vol 30 ◽  
pp. 096368972098545
Author(s):  
Tao Hu ◽  
Xiao Liu ◽  
Qinan Yin ◽  
Xingting Duan ◽  
Li Yan
Keyword(s):  
Computed Tomography ◽  
Nucleic Acid ◽  
Virus Infection ◽  
Severe Acute Respiratory Syndrome ◽  
The Other ◽  
Computed Tomography Scan ◽  
Health Authorities ◽  
History Of ◽  
Tomography Scan ◽  
Nucleic Acid Tests

In this work, we discovered a new phenomenon—asymptomatic COVID-19 infection, or covert case, during the pandemic. All the 3 patients had a history of exposure, with no symptoms, and no abnormalities were found in computed tomography scan or lab tests. Except for case 2, the other patients’ severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) nucleic acid tests were negative. But their anti-SARS-COV-2 nucleocapsid antibody showed a dynamic trend, consistent with the process of virus infection and clearance. A growing number of asymptomatic or covert cases need more attention. Lack of surveillance may lead to another outbreak. We hope to demonstrate our cases to attract the attention of governments or health authorities that covert cases should be the focus as well.

scholarly journals Neither a Novel Tau Proteinopathy nor an Expansion of a Phenotype: Reappraising Clinicopathology-Based Nosology

2021 ◽  
Vol 22 (14) ◽  
pp. 7292
Author(s):  
Luca Marsili ◽  
Jennifer Sharma ◽  
Alberto J. Espay ◽  
Alice Migazzi ◽  
Elhusseini Abdelghany ◽  
...  
Keyword(s):  
Spinocerebellar Ataxia Type ◽  
Niemann Pick Disease ◽  
Whole Exome ◽  
Heterozygous Variant ◽  
History Of ◽  
Ataxia Syndrome ◽  
Niemann Pick

The gold standard for classification of neurodegenerative diseases is postmortem histopathology; however, the diagnostic odyssey of this case challenges such a clinicopathologic model. We evaluated a 60-year-old woman with a 7-year history of a progressive dystonia–ataxia syndrome with supranuclear gaze palsy, suspected to represent Niemann–Pick disease Type C. Postmortem evaluation unexpectedly demonstrated neurodegeneration with 4-repeat tau deposition in a distribution diagnostic of progressive supranuclear palsy (PSP). Whole-exome sequencing revealed a new heterozygous variant in TGM6, associated with spinocerebellar ataxia type 35 (SCA35). This novel TGM6 variant reduced transglutaminase activity in vitro, suggesting it was pathogenic. This case could be interpreted as expanding: (1) the PSP phenotype to include a spinocerebellar variant; (2) SCA35 as a tau proteinopathy; or (3) TGM6 as a novel genetic variant underlying a SCA35 phenotype with PSP pathology. None of these interpretations seem adequate. We instead hypothesize that impairment in the crosslinking of tau by the TGM6-encoded transglutaminase enzyme may compromise tau functionally and structurally, leading to its aggregation in a pattern currently classified as PSP. The lessons from this case study encourage a reassessment of our clinicopathology-based nosology.

scholarly journals Hybrid-Type SELEX for the Selection of Artificial Nucleic Acid Aptamers Exhibiting Cell Internalization Activity

Pharmaceutics ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 888
Author(s):  
Hiro Uemachi ◽  
Yuuya Kasahara ◽  
Keisuke Tanaka ◽  
Takumi Okuda ◽  
Yoshihiro Yoneda ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Surface Protein ◽  
Functional Screening ◽  
Nucleic Acid Aptamers ◽  
Hybrid Type ◽  
Cell Internalization ◽  
Promising Target ◽  
A Cell ◽  
Exponential Enrichment

Nucleic acid aptamers have attracted considerable attention as next-generation pharmaceutical agents and delivery vehicles for small molecule drugs and therapeutic oligonucleotides. Chemical modification is an effective approach for improving the functionality of aptamers. However, the process of selecting appropriately modified aptamers is laborious because of many possible modification patterns. Here, we describe a hybrid-type systematic evolution of ligands by exponential enrichment (SELEX) approach for the generation of the artificial nucleic acid aptamers effective against human TROP2, a cell surface protein identified by drug discovery as a promising target for cancer therapy. Capillary electrophoresis SELEX was used for the pre-screening of multiple modified nucleic acid libraries and enrichment of TROP2 binding aptamers in the first step, followed by functional screening using cell-SELEX in the second step for the generation of cell-internalizing aptamers. One representative aptamer, Tac-B1, had a nanomolar-level affinity to human TROP2 and exhibited elevated capacity for internalization by cells. Because of the growing interest in the application of aptamers for drug delivery, our hybrid selection approach has great potential for the generation of functional artificial nucleic acid aptamers with ideal modification patterns in vitro.

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