scholarly journals Structure and Function of Multimeric G-Quadruplexes

Molecules ◽  
2019 ◽  
Vol 24 (17) ◽  
pp. 3074 ◽  
Author(s):  
Sofia Kolesnikova ◽  
Edward A. Curtis
Keyword(s):  
Nucleic Acid ◽  
Building Blocks ◽  
Structure And Function ◽  
Limited Information ◽  
Functional Elements ◽  
Future Studies ◽  
And Function ◽  
Nucleic Acid Structures ◽  
Sequence Requirements ◽  
Order Structures

G-quadruplexes are noncanonical nucleic acid structures formed from stacked guanine tetrads. They are frequently used as building blocks and functional elements in fields such as synthetic biology and also thought to play widespread biological roles. G-quadruplexes are often studied as monomers, but can also form a variety of higher-order structures. This increases the structural and functional diversity of G-quadruplexes, and recent evidence suggests that it could also be biologically important. In this review, we describe the types of multimeric topologies adopted by G-quadruplexes and highlight what is known about their sequence requirements. We also summarize the limited information available about potential biological roles of multimeric G-quadruplexes and suggest new approaches that could facilitate future studies of these structures.

scholarly journals Structure and Function of Multimeric G-quadruplexes

2019 ◽  
Author(s):  
Sofia Kolesnikova ◽  
Edward A. Curtis
Keyword(s):  
Nucleic Acid ◽  
Building Blocks ◽  
Structure And Function ◽  
Limited Information ◽  
Functional Elements ◽  
Future Studies ◽  
And Function ◽  
Nucleic Acid Structures ◽  
Sequence Requirements ◽  
Order Structures

G-quadruplexes are noncanonical nucleic acid structures formed from stacked guanine tetrads. They are frequently used as building blocks and functional elements in fields such as synthetic biology and also thought to play widespread biological roles. G-quadruplexes are often studied as monomers but can also form a variety of higher-order structures. This increases the structural and functional diversity of G-quadruplexes, and recent evidence suggests that it could also be biologically important. In this review we describe the types of multimeric topologies adopted by G-quadruplexes and highlight what is known about their sequence requirements. We also summarize the limited information available about potential biological roles of multimeric G-quadruplexes and suggest new approaches that could facilitate future studies of these structures.

Building ZOOB Models to Help Students Learn about Nucleic Acid Structure and Function

2017 ◽  
Vol 79 (4) ◽  
pp. 294-300
Author(s):  
Elizabeth A. Mulligan
Keyword(s):  
Nucleic Acid ◽  
Deductive Reasoning ◽  
Building Blocks ◽  
Structure And Function ◽  
Nucleic Acid Structure ◽  
Simplified Models ◽  
Collaborative Activity ◽  
Dna And Rna ◽  
And Function ◽  
Acid Structure

This paper describes a collaborative activity for students, which allows them to build simplified models of individual nucleotides, DNA, and RNA using ZOOB building blocks. These models help students learn about nucleic acid structure and the process of transcription. In addition, students learn how to work in groups as well as practice critical thinking and deductive reasoning while building these models.

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.

ChemInform Abstract: Applications of Psoralens as Probes of Nucleic Acid Structure and Function

ChemInform ◽  
2010 ◽  
Vol 22 (16) ◽  
pp. no-no
Author(s):  
Y. B. SHI ◽  
S. E. LIPSON ◽  
D. Y. CHI ◽  
H. P. SPIELMANN ◽  
J. A. MONFORTE ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Structure And Function ◽  
Nucleic Acid Structure ◽  
And Function ◽  
Acid Structure

scholarly journals Synthetic Biology Open Language Visual (SBOL Visual) Version 2.1

2019 ◽  
Vol 16 (2) ◽  
Author(s):  
Curtis Madsen ◽  
Angel Goni Moreno ◽  
Zachary Palchick ◽  
Umesh P ◽  
Nicholas Roehner ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Synthetic Biology ◽  
Molecular Species ◽  
Chemical Process ◽  
Structure And Function ◽  
Genomic Context ◽  
Functional Relationships ◽  
Synthetic Biology Open Language ◽  
And Function ◽  
Biological Organisms

AbstractPeople who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and other molecular species . Some typical practices and conventions have begun to emerge for such diagrams. The Synthetic Biology Open Language Visual (SBOL Visual) has been developed as a standard for organizing and systematizing such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. This document details version 2.1 of SBOL Visual, which builds on the prior SBOL Visual 2.0 standard by expanding diagram syntax to include methods for showing modular structure and mappings between elements of a system, interactions arrows that can split or join (with the glyph at the split or join indicating either superposition or a chemical process), and adding new glyphs for indicating genomic context (e.g., integration into a plasmid or genome) and for stop codons.

scholarly journals Implementation of High-Throughput Sequencing (HTS) in Aptamer Selection Technology

2020 ◽  
Vol 21 (22) ◽  
pp. 8774
Author(s):  
Natalia Komarova ◽  
Daria Barkova ◽  
Alexander Kuznetsov
Keyword(s):  
Nucleic Acid ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Combinatorial Libraries ◽  
Structure And Function ◽  
Huge Number ◽  
Systematic Evolution ◽  
And Function ◽  
Exponential Enrichment

Aptamers are nucleic acid ligands that bind specifically to a target of interest. Aptamers have gained in popularity due to their high potential for different applications in analysis, diagnostics, and therapeutics. The procedure called systematic evolution of ligands by exponential enrichment (SELEX) is used for aptamer isolation from large nucleic acid combinatorial libraries. The huge number of unique sequences implemented in the in vitro evolution in the SELEX process imposes the necessity of performing extensive sequencing of the selected nucleic acid pools. High-throughput sequencing (HTS) meets this demand of SELEX. Analysis of the data obtained from sequencing of the libraries produced during and after aptamer isolation provides an informative basis for precise aptamer identification and for examining the structure and function of nucleic acid ligands. This review discusses the technical aspects and the potential of the integration of HTS with SELEX.

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