HELIX: a new modular nucleic acid crystallization screen

2014 ◽  
Vol 47 (3) ◽  
pp. 948-955 ◽  
Author(s):  
Julia Viladoms ◽  
Gary N. Parkinson
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Data Bank ◽  
Diverse Range ◽  
X Ray Crystallography ◽  
Molecular Weights ◽  
Anomalous Data ◽  
Crystallization Conditions ◽  
Nucleic Acid Structures ◽  
Screen Layout

Crystallization of nucleic acids remains a bottleneck to their structural characterization by X-ray crystallography. A new 96-well-format initial screen for nucleic acids, called HELIX, has been developed at UCL School of Pharmacy, London, on the basis of a detailed analysis of the crystallization conditions from 1450 nucleic acid structures deposited in the Protein Data Bank (PDB), combined with observations and experience acquired in the authors' nucleic acids crystallography laboratory during the crystallization of DNA/RNA quadruplexes and ligand complexes. Despite using traditional buffers, precipitants and salts, the resulting modular screen is designed to offer a variety of approaches to enhance successful crystallization of oligonucleotides with a diverse range of topologies, sequences and molecular weights. HELIX includes a set of 24 conditions divided into four sets that can be mixed (inter- and intra-set) to provide a customizable orthogonal screening tool for experienced users, termed VariX. Additionally, mindful of synchrotron anomalous data collection, cacodylate buffers are avoided in the formulations and an optimized cryocrystallization module is included. This article reviews the crystallization trends and data derived from the PDB and discusses the HELIX screen layout, formulation and results from in-house crystallization trials.

Nucleic Acid Molecules Prepared by Monolayer Techniques

1972 ◽  
Vol 30 ◽  
pp. 178-179
Author(s):  
Dimitrij Lang
Keyword(s):  
Electron Microscopy ◽  
Standard Deviation ◽  
Nucleic Acid ◽  
Cytochrome C ◽  
Nucleic Acids ◽  
Contour Length ◽  
Sample Standard Deviation ◽  
Molecular Weights ◽  
Length Measurements ◽  
Protein Monolayer

The success of the protein monolayer technique for electron microscopy of individual DNA molecules is based on the prevention of aggregation and orientation of the molecules during drying on specimen grids. DNA adsorbs first to a surface-denatured, insoluble cytochrome c monolayer which is then transferred to grids, without major distortion, by touching. Fig. 1 shows three basic procedures which, modified or not, permit the study of various important properties of nucleic acids, either in concert with other methods or exclusively:1) Molecular weights relative to DNA standards as well as number distributions of molecular weights can be obtained from contour length measurements with a sample standard deviation between 1 and 4%.

scholarly journals Topology-based classification of tetrads and quadruplex structures

2019 ◽  
Vol 36 (4) ◽  
pp. 1129-1134 ◽  
Author(s):  
Mariusz Popenda ◽  
Joanna Miskiewicz ◽  
Joanna Sarzynska ◽  
Tomasz Zok ◽  
Marta Szachniuk
Keyword(s):  
Nucleic Acid ◽  
3D Structure ◽  
Data Bank ◽  
Supplementary Information ◽  
The Novel ◽  
Disease Treatment ◽  
Structure Topology ◽  
Secondary Structure Topology ◽  
Nucleic Acid Structures

Abstract Motivation Quadruplexes attract the attention of researchers from many fields of bio-science. Due to a specific structure, these tertiary motifs are involved in various biological processes. They are also promising therapeutic targets in many strategies of drug development, including anticancer and neurological disease treatment. The uniqueness and diversity of their forms cause that quadruplexes show great potential in novel biological applications. The existing approaches for quadruplex analysis are based on sequence or 3D structure features and address canonical motifs only. Results In our study, we analyzed tetrads and quadruplexes contained in nucleic acid molecules deposited in Protein Data Bank. Focusing on their secondary structure topology, we adjusted its graphical diagram and proposed new dot-bracket and arc representations. We defined the novel classification of these motifs. It can handle both canonical and non-canonical cases. Based on this new taxonomy, we implemented a method that automatically recognizes the types of tetrads and quadruplexes occurring as unimolecular structures. Finally, we conducted a statistical analysis of these motifs found in experimentally determined nucleic acid structures in relation to the new classification. Availability and implementation https://github.com/tzok/eltetrado/ Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals High-yield fabrication of DNA and RNA constructs for single molecule force and torque spectroscopy experiments

2019 ◽  
Vol 47 (22) ◽  
pp. e144-e144 ◽  
Author(s):  
Flávia S Papini ◽  
Mona Seifert ◽  
David Dulin
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Single Molecule ◽  
Magnetic Tweezers ◽  
High Yield ◽  
High Quality ◽  
Single Molecule Biophysics ◽  
Dna And Rna ◽  
Rna Hairpins ◽  
Nucleic Acid Structures

Abstract Single molecule biophysics experiments have enabled the observation of biomolecules with a great deal of precision in space and time, e.g. nucleic acids mechanical properties and protein–nucleic acids interactions using force and torque spectroscopy techniques. The success of these experiments strongly depends on the capacity of the researcher to design and fabricate complex nucleic acid structures, as the outcome and the yield of the experiment also strongly depend on the high quality and purity of the final construct. Though the molecular biology techniques involved are well known, the fabrication of nucleic acid constructs for single molecule experiments still remains a difficult task. Here, we present new protocols to generate high quality coilable double-stranded DNA and RNA, as well as DNA and RNA hairpins with ∼500–1000 bp long stems. Importantly, we present a new approach based on single-stranded DNA (ssDNA) annealing and we use magnetic tweezers to show that this approach simplifies the fabrication of complex DNA constructs, such as hairpins, and converts more efficiently the input DNA into construct than the standard PCR-digestion-ligation approach. The protocols we describe here enable the design of a large range of nucleic acid construct for single molecule biophysics experiments.

scholarly journals Cyclic Automated Model Building (CAB) Applied to Nucleic Acids

Crystals ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 280
Author(s):  
Maria Cristina Burla ◽  
Benedetta Carrozzini ◽  
Giovanni Luca Cascarano ◽  
Carmelo Giacovazzo ◽  
Giampiero Polidori
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Model Building ◽  
State Of The Art ◽  
Molecular Replacement ◽  
Dna And Rna ◽  
Protein Model ◽  
Rna Fragments ◽  
Nucleic Acid Structures ◽  
Automated Model Building

Obtaining high-quality models for nucleic acid structures by automated model building programs (AMB) is still a challenge. The main reasons are the rather low resolution of the diffraction data and the large number of rotatable bonds in the main chains. The application of the most popular and documented AMB programs (e.g., PHENIX.AUTOBUILD, NAUTILUS and ARP/wARP) may provide a good assessment of the state of the art. Quite recently, a cyclic automated model building (CAB) package was described; it is a new AMB approach that makes the use of BUCCANEER for protein model building cyclic without modifying its basic algorithms. The applications showed that CAB improves the efficiency of BUCCANEER. The success suggested an extension of CAB to nucleic acids—in particular, to check if cyclically including NAUTILUS in CAB may improve its effectiveness. To accomplish this task, CAB algorithms designed for protein model building were modified to adapt them to the nucleic acid crystallochemistry. CAB was tested using 29 nucleic acids (DNA and RNA fragments). The phase estimates obtained via molecular replacement (MR) techniques were automatically submitted to phase refinement and then used as input for CAB. The experimental results from CAB were compared with those obtained by NAUTILUS, ARP/wARP and PHENIX.AUTOBUILD.

scholarly journals Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures

2019 ◽  
Vol 47 (W1) ◽  
pp. W26-W34 ◽  
Author(s):  
Shuxiang Li ◽  
Wilma K Olson ◽  
Xiang-Jun Lu
Keyword(s):  
Nucleic Acid ◽  
Structural Parameters ◽  
Rigid Base ◽  
Helical Structures ◽  
X Ray Crystallography ◽  
Building Models ◽  
Web Standards ◽  
Initial Release ◽  
Nucleic Acid Structures ◽  
Intuitive Interface

Abstract Web 3DNA (w3DNA) 2.0 is a significantly enhanced version of the widely used w3DNA server for the analysis, visualization, and modeling of 3D nucleic-acid-containing structures. Since its initial release in 2009, the w3DNA server has continuously served the community by making commonly-used features of the 3DNA suite of command-line programs readily accessible. However, due to the lack of updates, w3DNA has clearly shown its age in terms of modern web technologies and it has long lagged behind further developments of 3DNA per se. The w3DNA 2.0 server presented here overcomes all known shortcomings of w3DNA while maintaining its battle-tested characteristics. Technically, w3DNA 2.0 implements a simple and intuitive interface (with sensible defaults) for increased usability, and it complies with HTML5 web standards for broad accessibility. Featurewise, w3DNA 2.0 employs the most recent version of 3DNA, enhanced with many new functionalities, including: the automatic handling of modified nucleotides; a set of ‘simple’ base-pair and step parameters for qualitative characterization of non-Watson–Crick double-helical structures; new structural parameters that integrate the rigid base plane and the backbone phosphate group, the two nucleic acid components most reliably determined with X-ray crystallography; in silico base mutations that preserve the backbone geometry; and a notably improved module for building models of single-stranded RNA, double-helical DNA, Pauling triplex, G-quadruplex, or DNA structures ‘decorated’ with proteins. The w3DNA 2.0 server is freely available, without registration, at http://web.x3dna.org.

scholarly journals High-order structures from nucleic acids for biomedical applications

2020 ◽  
Vol 4 (4) ◽  
pp. 1074-1088 ◽  
Author(s):  
Alyssa C. Hill ◽  
Jonathan Hall
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Biomedical Applications ◽  
Dna Nanotechnology ◽  
High Order ◽  
Rna Nanotechnology ◽  
Nucleic Acid Structures ◽  
Order Structures

This article reviews important developments in DNA nanotechnology and RNA nanotechnology and highlights supramolecular nucleic acid structures with biomedical applications.

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