Interactions of molecules with nucleic acids. I. An algorithm to generate nucleic acid structures with an application to the B-DNA structure and a counterclockwise helix

Biopolymers ◽  
1979 ◽  
Vol 18 (4) ◽  
pp. 959-980 ◽  
Author(s):  
Kenneth J. Miller
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Dna Structure ◽  
Nucleic Acid Structures

Mercury Electrodes in Nucleic Acid Electrochemistry: Sensitive Analytical Tools and Probes of DNA Structure. A Review

2004 ◽  
Vol 69 (4) ◽  
pp. 715-747 ◽  
Author(s):  
Miroslav Fojta
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Double Helix ◽  
Dna Structure ◽  
Electrochemical Analysis ◽  
Label Free ◽  
Helix Formation ◽  
Mercury Electrodes ◽  
Dna Strand ◽  
Dna Double Helix

This review is devoted to applications of mercury electrodes in the electrochemical analysis of nucleic acids and in studies of DNA structure and interactions. At the mercury electrodes, nucleic acids yield faradaic signals due to redox processes involving adenine, cytosine and guanine residues, and tensammetric signals due to adsorption/desorption of polynucleotide chains at the electrode surface. Some of these signals are highly sensitive to DNA structure, providing information about conformation changes of the DNA double helix, formation of DNA strand breaks as well as covalent or non-covalent DNA interactions with small molecules (including genotoxic agents, drugs, etc.). Measurements at mercury electrodes allow for determination of small quantities of unmodified or electrochemically labeled nucleic acids. DNA-modified mercury electrodes have been used as biodetectors for DNA damaging agents or as detection electrodes in DNA hybridization assays. Mercury film and solid amalgam electrodes possess similar features in the nucleic acid analysis to mercury drop electrodes. On the contrary, intrinsic (label-free) DNA electrochemical responses at other (non-mercury) solid electrodes cannot provide information about small changes of the DNA structure. A review with 188 references.

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.

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.

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 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.

scholarly journals Solving nucleic acid structures by molecular replacement: examples from group II intron studies

2013 ◽  
Vol 69 (11) ◽  
pp. 2174-2185 ◽  
Author(s):  
Marco Marcia ◽  
Elisabeth Humphris-Narayanan ◽  
Kevin S. Keating ◽  
Srinivas Somarowthu ◽  
Kanagalaghatta Rajashankar ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Molecular Replacement ◽  
Cellular Viability ◽  
Rna Molecules ◽  
Search Models ◽  
Key Players ◽  
Group Ii ◽  
Nucleic Acid Structures ◽  
Near Future

Structured RNA molecules are key players in ensuring cellular viability. It is now emerging that, like proteins, the functions of many nucleic acids are dictated by their tertiary folds. At the same time, the number of known crystal structures of nucleic acids is also increasing rapidly. In this context, molecular replacement will become an increasingly useful technique for phasing nucleic acid crystallographic data in the near future. Here, strategies to select, create and refine molecular-replacement search models for nucleic acids are discussed. Using examples taken primarily from research on group II introns, it is shown that nucleic acids are amenable to different and potentially more flexible and sophisticated molecular-replacement searches than proteins. These observations specifically aim to encourage future crystallographic studies on the newly discovered repertoire of noncoding transcripts.

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