scholarly journals Structure approaches to study of DNA aptamers in solution

2021 ◽  
pp. 76-78
Author(s):  
R.V. Moryachkov ◽  
◽  
P.A. Nikolaeva ◽  
V.A. Spiridonova ◽  
◽  
...  
Keyword(s):  
Spatial Structure ◽  
Nucleic Acids ◽  
Conformational Changes ◽  
High Potential ◽  
Target Protein ◽  
Complete Picture ◽  
Dna Aptamers ◽  
Complementary Methods ◽  
Effi Ciency ◽  
Approaches To Study

The high potential of aptamers – specifi c molecular agents based on short single-stranded nucleic acids – makes high demands on the molecules under development for the effi ciency of interaction with target biomolecules. In this work, approaches are considered for studying the spatial structure of DNA aptamers in solution using various complementary methods, which make it possible to obtain a more complete picture of the formation of the structure and conformational changes, to track the interaction with the target protein, the tendency to oligomerization, and to characterize the spatial structure of both individual molecules and complexes.

Advances in functional nucleic acid based paper sensors

2020 ◽  
Vol 8 (16) ◽  
pp. 3213-3230
Author(s):  
Rudi Liu ◽  
Erin M. McConnell ◽  
Jiuxing Li ◽  
Yingfu Li
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Dna Aptamers ◽  
Extensive Review ◽  
Recognition Elements ◽  
Functional Nucleic Acids

This article provides an extensive review of paper-based sensors that utilize functional nucleic acids, particularly DNA aptamers and DNAzymes, as recognition elements.

scholarly journals Cu2+-based distance measurements by pulsed EPR provide distance constraints for DNA backbone conformations in solution

2020 ◽  
Vol 48 (9) ◽  
pp. e49-e49 ◽  
Author(s):  
Shreya Ghosh ◽  
Matthew J Lawless ◽  
Hanna J Brubaker ◽  
Kevin Singewald ◽  
Michael R Kurpiewski ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Conformational Changes ◽  
Continuous Wave ◽  
Md Simulations ◽  
Distance Measurements ◽  
Paramagnetic Resonance ◽  
Pulsed Epr ◽  
Distance Distributions ◽  
Dna Backbone ◽  
Double Electron Electron Resonance

Abstract Electron paramagnetic resonance (EPR) has become an important tool to probe conformational changes in nucleic acids. An array of EPR labels for nucleic acids are available, but they often come at the cost of long tethers, are dependent on the presence of a particular nucleotide or can be placed only at the termini. Site directed incorporation of Cu2+-chelated to a ligand, 2,2′dipicolylamine (DPA) is potentially an attractive strategy for site-specific, nucleotide independent Cu2+-labelling in DNA. To fully understand the potential of this label, we undertook a systematic and detailed analysis of the Cu2+-DPA motif using EPR and molecular dynamics (MD) simulations. We used continuous wave EPR experiments to characterize Cu2+ binding to DPA as well as optimize Cu2+ loading conditions. We performed double electron-electron resonance (DEER) experiments at two frequencies to elucidate orientational selectivity effects. Furthermore, comparison of DEER and MD simulated distance distributions reveal a remarkable agreement in the most probable distances. The results illustrate the efficacy of the Cu2+-DPA in reporting on DNA backbone conformations for sufficiently long base pair separations. This labelling strategy can serve as an important tool for probing conformational changes in DNA upon interaction with other macromolecules.

Hydroxyproline-Based DNA Mimics: A Review on Synthesis and Properties

2006 ◽  
Vol 71 (7) ◽  
pp. 929-955 ◽  
Author(s):  
Vladimir A. Efimov ◽  
Oksana G. Chakhmakhcheva
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Phosphonic Acid ◽  
Peptide Nucleic Acids ◽  
Biological Properties ◽  
High Potential ◽  
Physicochemical And Biological Properties

With the aim to improve physicochemical and biological properties of natural oligonucleotides, many types of DNA analogues and mimics are designed on the basis of hydroxyproline and its derivatives, and their properties are evaluated. Among them, two types of DNA mimics representing hetero-oligomers constructed from alternating monomers of phosphono peptide nucleic acids and monomers on the base of trans-1-acetyl-4-hydroxy-L-proline (HypNA-pPNAs) and oligomers constructed from monomers containing (2S,4R)-1-acetyl-4-hydroxypyrrolidine-2-phosphonic acid backbone (pHypNAs) are of particular interest. In a set of in vitro and in vivo assays, it was shown that HypNA-pPNAs and pHypNAs demonstrated a high potential for the use in nucleic acid based diagnostics, isolation of nucleic acids and antisense experiments. A review with 53 references.

The role of water structure in conformational changes of nucleic acids in ambient and high-pressure conditions

2001 ◽  
Vol 260 (2) ◽  
pp. 293-307 ◽  
Author(s):  
Jan Barciszewski ◽  
Janusz Jurczak ◽  
Sylwester Porowski ◽  
Thomas Specht ◽  
Volker A. Erdmann
Keyword(s):  
High Pressure ◽  
Nucleic Acids ◽  
Conformational Changes ◽  
Water Structure

Nucleic acids-protein interactions. Conformational changes induced by the binding of aromatic amines to polyadenylic acid

Biochimie ◽  
1976 ◽  
Vol 58 (4) ◽  
pp. 395-402 ◽  
Author(s):  
Maurice Durand ◽  
Hanna N. Borazan ◽  
Jean-Claude Maurizot ◽  
Jean-Luc Dimicoli ◽  
Claude Hélène
Keyword(s):  
Nucleic Acids ◽  
Conformational Changes ◽  
Protein Interactions ◽  
Aromatic Amines ◽  
Polyadenylic Acid

scholarly journals Drying and temperature induced conformational changes of nucleic acids and stallion sperm chromatin in trehalose preservation formulations

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Raffaele Brogna ◽  
Juezhu Fan ◽  
Harald Sieme ◽  
Willem F. Wolkers ◽  
Harriëtte Oldenhof
Keyword(s):  
Reactive Oxygen Species ◽  
Dna Damage ◽  
Nucleic Acids ◽  
Conformational Changes ◽  
Chromatin Structure ◽  
Reactive Oxygen ◽  
Sperm Chromatin ◽  
Oxygen Species ◽  
Spectral Changes ◽  
And Storage

AbstractEven though dried sperm is not viable, it can be used for fertilization as long as its chromatin remains intact. In this study, we investigated drying- and temperature-induced conformational changes of nucleic acids and stallion sperm chromatin. Sperm was diluted in preservation formulations with and without sugar/albumin and subjected to convective drying at elevated temperatures on glass substrates. Accumulation of reactive oxygen species was studied during storage at different temperatures, and the sperm chromatin structure assay was used to assess DNA damage. Fourier transform infrared spectroscopy was used to identify dehydration and storage induced conformational changes in isolated DNA and sperm chromatin. Furthermore, hydrogen bonding in the preservation solutions associated with storage stability were investigated. Reactive oxygen species and DNA damage in dried sperm samples were found to accumulate with increasing storage temperature and storage duration. Non-reducing disaccharides (i.e., trehalose, sucrose) and albumin counteracted oxidative stress and preserved sperm chromatin during dried storage, whereas glucose increased DNA damage during storage. When sperm was dried in the presence of trehalose and albumin, no spectral changes were detected during storage at refrigeration temperatures, whereas under accelerated aging conditions, i.e., storage at 37 °C, spectral changes were detected indicating alterations in sperm chromatin structure.

scholarly journals Small-angle neutron scattering studies suggest the mechanism of BinAB protein internalization

IUCrJ ◽  
2020 ◽  
Vol 7 (2) ◽  
pp. 166-172
Author(s):  
Mahima Sharma ◽  
Vinod K. Aswal ◽  
Vinay Kumar ◽  
R. Chidambaram
Keyword(s):  
Neutron Scattering ◽  
Conformational Changes ◽  
Small Angle ◽  
Small Angle Neutron Scattering ◽  
Solution Structure ◽  
Expression System ◽  
Radius Of Gyration ◽  
Macromolecular Systems ◽  
Approaches To Study ◽  
Protein Components

Small-angle neutron scattering (SANS) is one of the most widely used neutron-based approaches to study the solution structure of biological macromolecular systems. The selective deuterium labelling of different protein components of a complex provides a means to probe conformational changes in multiprotein complexes. The Lysinibacillus sphaericus mosquito-larvicidal BinAB proteins exert toxicity through interaction with the receptor Cqm1 protein; however, the nature of the complex is not known. Rationally engineered deuterated BinB (dBinB) protein from the L. sphaericus ISPC-8 species was synthesized using an Escherichia coli-based protein-expression system in M9 medium in D2O for `contrast-matched' SANS experiments. SANS data were independently analysed by ab initio indirect Fourier transform-based modelling and using crystal structures. These studies confirm the dimeric status of Cqm1 in 100% D2O with a longest intramolecular vector (D max) of ∼94 Å and a radius of gyration (R g) of ∼31 Å. Notably, BinB binds to Cqm1, forming a heterodimeric complex (D max of ∼129 Å and R g of ∼40 Å) and alters its oligomeric status from a dimer to a monomer, as confirmed by matched-out Cqm1–dBinB (D max of ∼70 Å and R g of ∼22 Å). The present study thus provides the first insight into the events involved in the internalization of larvicidal proteins, likely by raft-dependent endocytosis.

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