Spherical Nucleic Acid Nanoparticle Conjugates Enhance G-Quadruplex Formation and Increase Serum Protein Interactions

2014 ◽  
Vol 127 (2) ◽  
pp. 537-541 ◽  
Author(s):  
Alyssa B. Chinen ◽  
Chenxia M. Guan ◽  
Chad A. Mirkin
Keyword(s):  
Nucleic Acid ◽  
Serum Protein ◽  
Protein Interactions ◽  
Spherical Nucleic Acid ◽  
G Quadruplex ◽  
Quadruplex Formation

scholarly journals Energy Transfer as A Driving Force in Nucleic Acid–Protein Interactions

Molecules ◽  
2019 ◽  
Vol 24 (7) ◽  
pp. 1443
Author(s):  
Zavyalova ◽  
Kopylov
Keyword(s):  
Energy Transfer ◽  
Nucleic Acid ◽  
Protein Interactions ◽  
Protein Complexes ◽  
Protein Structures ◽  
Quantitative Structure Activity Relationship ◽  
Efficient Energy Transfer ◽  
Acid Protein ◽  
G Quadruplex ◽  
Interface Organization

Many nucleic acid–protein structures have been resolved, though quantitative structure-activity relationship remains unclear in many cases. Thrombin complexes with G-quadruplex aptamers are striking examples of a lack of any correlation between affinity, interface organization, and other common parameters. Here, we tested the hypothesis that affinity of the aptamer–protein complex is determined with the capacity of the interface to dissipate energy of binding. Description and detailed analysis of 63 nucleic acid–protein structures discriminated peculiarities of high-affinity nucleic acid–protein complexes. The size of the amino acid sidechain in the interface was demonstrated to be the most significant parameter that correlates with affinity of aptamers. This observation could be explained in terms of need of efficient energy transfer from interacting residues. Application of energy dissipation theory provided an illustrative tool for estimation of efficiency of aptamer–protein complexes. These results are of great importance for a design of efficient aptamers.

Partial Purification of a Specific Plasminogen Activator from Porcine Parotid Glands

1974 ◽  
Vol 31 (03) ◽  
pp. 403-414 ◽  
Author(s):  
Terence Cartwright
Keyword(s):  
Nucleic Acid ◽  
Salivary Glands ◽  
Plasminogen Activator ◽  
Protein Interactions ◽  
Partial Purification ◽  
Protein Protein Interactions ◽  
Parotid Glands ◽  
Two Stage ◽  
Preliminary Characterization ◽  
Specific Inhibitors

SummaryA method is described for the extraction with buffers of near physiological pH of a plasminogen activator from porcine salivary glands. Substantial purification of the activator was achieved although this was to some extent complicated by concomitant extraction of nucleic acid from the glands. Preliminary characterization experiments using specific inhibitors suggested that the activator functioned by a similar mechanism to that proposed for urokinase, but with some important kinetic differences in two-stage assay systems. The lack of reactivity of the pig gland enzyme in these systems might be related to the tendency to protein-protein interactions observed with this material.

scholarly journals DNA polymerase δ stalls on telomeric lagging strand templates independently from G-quadruplex formation

2013 ◽  
Vol 41 (22) ◽  
pp. 10323-10333 ◽  
Author(s):  
Justin D. Lormand ◽  
Noah Buncher ◽  
Connor T. Murphy ◽  
Parminder Kaur ◽  
Marietta Y. Lee ◽  
...  
Keyword(s):  
Dna Polymerase ◽  
Dna Polymerase Δ ◽  
G Quadruplex ◽  
Quadruplex Formation ◽  
Lagging Strand

scholarly journals Overlapping but distinct: a new model for G-quadruplex biochemical specificity

2021 ◽  
Author(s):  
Martin Volek ◽  
Sofia Kolesnikova ◽  
Katerina Svehlova ◽  
Pavel Srb ◽  
Ráchel Sgallová ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Drug Design ◽  
Solution Structure ◽  
Biochemical Data ◽  
Biological Regulation ◽  
New Model ◽  
G Quadruplex ◽  
Range Of Functions ◽  
Nucleic Acid Structures ◽  
Sequence Requirements

Abstract G-quadruplexes are noncanonical nucleic acid structures formed by stacked guanine tetrads. They are capable of a range of functions and thought to play widespread biological roles. This diversity raises an important question: what determines the biochemical specificity of G-quadruplex structures? The answer is particularly important from the perspective of biological regulation because genomes can contain hundreds of thousands of G-quadruplexes with a range of functions. Here we analyze the specificity of each sequence in a 496-member library of variants of a reference G-quadruplex with respect to five functions. Our analysis shows that the sequence requirements of G-quadruplexes with these functions are different from one another, with some mutations altering biochemical specificity by orders of magnitude. Mutations in tetrads have larger effects than mutations in loops, and changes in specificity are correlated with changes in multimeric state. To complement our biochemical data we determined the solution structure of a monomeric G-quadruplex from the library. The stacked and accessible tetrads rationalize why monomers tend to promote a model peroxidase reaction and generate fluorescence. Our experiments support a model in which the sequence requirements of G-quadruplexes with different functions are overlapping but distinct. This has implications for biological regulation, bioinformatics, and drug design.

scholarly journals TGF‐β‐induced fibrotic stress increases G‐quadruplex formation in human fibroblasts

FEBS Letters ◽  
2019 ◽  
Vol 593 (22) ◽  
pp. 3149-3161 ◽  
Author(s):  
Priyanka Toshniwal ◽  
Michelle Nguyen ◽  
Aurore Guédin ◽  
Helena Viola ◽  
Diwei Ho ◽  
...  
Keyword(s):  
Human Fibroblasts ◽  
G Quadruplex ◽  
Quadruplex Formation

TT Dimerization and Its Effect on Human Telomere G-Quadruplex Formation

2015 ◽  
Vol 36 (6) ◽  
pp. 1729-1732
Author(s):  
In Sun Kim ◽  
Young Jun Seo
Keyword(s):  
G Quadruplex ◽  
Quadruplex Formation ◽  
Human Telomere
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