scholarly journals Mechanisms underlying sequence-dependent DNA hybridisation rates in the absence of secondary structure

2021 ◽  
Author(s):  
Sophie Hertel ◽  
Richard Spinney ◽  
Stephanie Xu ◽  
Thomas E Ouldridge ◽  
Richard Morris ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Dna Sequences ◽  
Physical Factors ◽  
Biological Processes ◽  
Physical Mechanisms ◽  
Mechanistic Insight ◽  
Sequence Dependent ◽  
Dna Hybridisation ◽  
Kinetics Of ◽  
Insight Into

The kinetics of DNA hybridisation are fundamental to biological processes and DNA-based technologies. However, the precise physical mechanisms that determine why different DNA sequences hybridise at different rates are not well understood. Secondary structure is one predictable factor that influences hybridisation rates but is not sufficient on its own to fully explain the observed sequence-dependent variance. Consequently, to achieve a good correlation with experimental data, current prediction algorithms require many parameters that provide little mechanistic insight into DNA hybridisation. In this context, we measured hybridisation rates of 43 different DNA sequences that are not predicted to form secondary structure and present a parsimonious physically justified model to quantify their hybridisation rates. Accounting only for the combinatorics of complementary nucleating interactions and their sequence-dependent stability, the model achieves good correlation with experiment with only two free parameters, thus providing new insight into the physical factors underpinning DNA hybridisation rates.

scholarly journals DNA hybridisation kinetics using single-molecule fluorescence imaging

2021 ◽  
Author(s):  
Rebecca Andrews
Keyword(s):  
Nucleic Acid ◽  
Single Molecule ◽  
Biological Processes ◽  
Single Molecule Fluorescence ◽  
Extrinsic Factors ◽  
Factors Affecting ◽  
Dna Hybridisation ◽  
Single Molecule Studies ◽  
Kinetics Of ◽  
Insight Into

Abstract Deoxyribonucleic acid (DNA) hybridisation plays a key role in many biological processes and nucleic acid biotechnologies, yet surprisingly there are many aspects about the process which are still unknown. Prior to the invention of single-molecule microscopy, DNA hybridisation experiments were conducted at the ensemble level, and thus it was impossible to directly observe individual hybridisation events and understand fully the kinetics of DNA hybridisation. In this mini-review, recent single-molecule fluorescence-based studies of DNA hybridisation are discussed, particularly for short nucleic acids, to gain more insight into the kinetics of DNA hybridisation. As well as looking at single-molecule studies of intrinsic and extrinsic factors affecting DNA hybridisation kinetics, the influence of the methods used to detect hybridisation of single DNAs is considered. Understanding the kinetics of DNA hybridisation not only gives insight into an important biological process but also allows for further advancements in the growing field of nucleic acid biotechnology.

Ion Channel Permeation and Selectivity

2019 ◽  
Author(s):  
Juan J. Nogueira ◽  
Ben Corry
Keyword(s):  
Ion Channels ◽  
Ion Channel ◽  
Ion Selectivity ◽  
Ionic Currents ◽  
Biological Processes ◽  
Ion Permeation ◽  
Voltage Gated ◽  
Physical Mechanisms ◽  
Theoretical Approaches ◽  
Mechanistic Insight

Many biological processes essential for life rely on the transport of specific ions at specific times across cell membranes. Such exquisite control of ionic currents, which is regulated by protein ion channels, is fundamental for the proper functioning of the cells. It is not surprising, therefore, that the mechanism of ion permeation and selectivity in ion channels has been extensively investigated by means of experimental and theoretical approaches. These studies have provided great mechanistic insight but have also raised new questions that are still unresolved. This chapter first summarizes the main techniques that have provided significant knowledge about ion permeation and selectivity. It then discusses the physical mechanisms leading to ion permeation and the explanations that have been proposed for ion selectivity in voltage-gated potassium, sodium, and calcium channels.

Mechanistic insight into active chlorine species mediated electrochemical degradation of recalcitrant phenolic polymers

RSC Advances ◽  
2014 ◽  
Vol 4 (104) ◽  
pp. 59821-59830 ◽  
Author(s):  
S. Sundarapandiyan ◽  
T. Shiny Renitha ◽  
J. Sridevi ◽  
B. Chandrasekaran ◽  
P. Saravanan ◽  
...  
Keyword(s):  
Active Chlorine ◽  
Electrochemical Degradation ◽  
Mechanistic Insight ◽  
Electro Oxidation ◽  
Kinetics Of ◽  
Insight Into

Degradation of recalcitrant phenolic syntan by electro-oxidation was investigated. The kinetics of mineralization of phenolic syntan was followed both in terms of TOC and COD measurements.

scholarly journals Renitence vacuoles facilitate protection against phagolysosomal damage in activated macrophages

2018 ◽  
Vol 29 (5) ◽  
pp. 657-668 ◽  
Author(s):  
Amanda O. Wong ◽  
Matangi Marthi ◽  
Zachary I. Mendel ◽  
Brian Gregorka ◽  
Michele S. Swanson ◽  
...  
Keyword(s):  
Membrane Damage ◽  
Morphological Features ◽  
Activated Macrophages ◽  
Membrane Ruffling ◽  
Silica Bead ◽  
Mechanistic Insight ◽  
Silica Beads ◽  
Lps Activation ◽  
Kinetics Of ◽  
Insight Into

As professional phagocytes, macrophages are susceptible to endolysosomal membrane damage inflicted by the pathogens and noxious particles they ingest. Whether macrophages have mechanisms for limiting such damage is not well understood. Previously, we reported a phenomenon, termed “inducible renitence,” in which lipopolysaccharide (LPS) activation of macrophages protected their endolysosomes against damage initiated by the phagocytosis of silica beads. To gain mechanistic insight into the process, we analyzed the kinetics of renitence and morphological features of LPS-activated versus resting macrophages following silica bead–mediated injury. We discovered novel vacuolar structures that form in LPS-activated but not resting macrophages following silica bead phagocytosis. Because of their correlation with renitence and damage-resistant nature, we termed these structures “renitence vacuoles” (RVs). RVs formed coincident with silica bead uptake in a process associated with membrane ruffling and macropinocytosis. However, unlike normal macropinosomes (MPs), which shrink within 20 min of formation, RVs persisted around bead-containing phagosomes. RVs fused with lysosomes, whereas associated phagosomes typically did not. These findings are consistent with a model in which RVs, as persistent MPs, prevent fusion between damaged phagosomes and intact lysosomes and thereby preserve endolysosomal integrity.

scholarly journals Spectroscopy and Kinetics of Wild-Type and Mutant Tyrosine Hydroxylase: Mechanistic Insight into O2Activation

2009 ◽  
Vol 131 (22) ◽  
pp. 7685-7698 ◽  
Author(s):  
Marina S. Chow ◽  
Bekir E. Eser ◽  
Samuel A. Wilson ◽  
Keith O. Hodgson ◽  
Britt Hedman ◽  
...  
Keyword(s):  
Tyrosine Hydroxylase ◽  
Wild Type ◽  
Mechanistic Insight ◽  
Kinetics Of ◽  
Insight Into

scholarly journals Covert sleep-related biological processes are revealed by probabilistic analysis in Drosophila

2020 ◽  
Vol 117 (18) ◽  
pp. 10024-10034 ◽  
Author(s):  
Timothy D. Wiggin ◽  
Patricia R. Goodwin ◽  
Nathan C. Donelson ◽  
Chang Liu ◽  
Kien Trinh ◽  
...  
Keyword(s):  
Biological Processes ◽  
Movement Data ◽  
Mechanistic Insight ◽  
Sleep Depth ◽  
Report Analysis ◽  
Hidden States ◽  
Computational Analyses ◽  
And Control ◽  
Insight Into

Sleep pressure and sleep depth are key regulators of wake and sleep. Current methods of measuring these parameters in Drosophila melanogaster have low temporal resolution and/or require disrupting sleep. Here we report analysis tools for high-resolution, noninvasive measurement of sleep pressure and depth from movement data. Probability of initiating activity, P(Wake), measures sleep depth while probability of ceasing activity, P(Doze), measures sleep pressure. In vivo and computational analyses show that P(Wake) and P(Doze) are largely independent and control the amount of total sleep. We also develop a Hidden Markov Model that allows visualization of distinct sleep/wake substates. These hidden states have a predictable relationship with P(Doze) and P(Wake), suggesting that the methods capture the same behaviors. Importantly, we demonstrate that both the Doze/Wake probabilities and the sleep/wake substates are tied to specific biological processes. These metrics provide greater mechanistic insight into behavior than measuring the amount of sleep alone.

Current-Signature-Based Analysis of Complex Test Fails

1999 ◽  
Author(s):  
Anne E. Gattiker ◽  
Phil Nigh ◽  
Wojciech Maly
Keyword(s):  
Failure Analysis ◽  
Physical Nature ◽  
Channel Length ◽  
Test Methods ◽  
Multiple Test ◽  
Physical Mechanisms ◽  
Test Behavior ◽  
Complex Test ◽  
Current Signature ◽  
Insight Into

Abstract This article provides an analysis of a class of failures observed during the SEMATECH-sponsored Test Methods Experiment. The analysis focuses on use of test-based failure analysis and IDDQ signature analysis to gain insight into the physical mechanisms underlying such subtle failures. In doing so, the analysis highlights techniques for understanding failure mechanisms using only tester data. In the experiment, multiple test methods were applied to a 0.45 micrometer effective channel length ASIC. Specifically, ICs that change test behavior from before to after burn-in are studied to understand the physical nature of the mechanism underlying their failure. Examples of the insights provided by the test-based analysis include identifying cases where there are multiple or complex defects and distinguishing cases where the defect type is likely to be a short versus an open and determining if the defect is marginal. These insights can be helpful for successful failure analysis.

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