Special Issue "Nucleic Acid Crystallography"

A special issue of Crystals (ISSN 2073-4352). This special issue belongs to the section "Biomolecular Crystals".

Deadline for manuscript submissions: closed (31 July 2017)

Special Issue Editor

Guest Editor
Dr. Jinwei Zhang

Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 50 South Drive, Bethesda, MD 20892, USA
E-Mail
Interests: noncoding RNA; riboswitch; RNA structure; RNA-protein interaction; nucleic acid crystallography

Special Issue Information

Dear Colleagues,

In the past decade, significant strides have been made in the field of nucleic acids crystallography. To name just one statistic, the number of riboswitch entries in the PDB has grown from 1 in 2004 to 190 in late 2015. This flourish is in part propelled by an accelerated pace in the discovery and functional characterization of emerging noncoding RNA structures, such as ribozymes and riboswitches. It is also enabled by a number of technical innovations, such as artificial and modified nucleic acids, novel phasing methods of nucleic acid crystals, post-crystallization treatment strategies, Raman crystallography, and serial femtosecond crystallography, etc. Sufficient numbers of unique nucleic acid structures are now available to begin to reveal general principles that govern nucleic acid folding, assembly, architecture, and interaction with metabolites, proteins, and other nucleic acids.

This Special Issue is dedicated to providing a snapshot of the state of the art in the methods, applications, and trends of nucleic acids crystallography. We welcome research and review articles that cover any aspect of nucleic acid crystallography.

Dr. Jinwei Zhang
Guest Editor

Manuscript Submission Information

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Keywords

  • Nucleic acids
  • Noncoding RNA
  • Phasing
  • Riboswitch
  • Interaction

Published Papers (3 papers)

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Research

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Open AccessFeature PaperArticle Phosphorus SAD Phasing for Nucleic Acid Structures: Limitations and Potential
Crystals 2016, 6(10), 125; doi:10.3390/cryst6100125
Received: 14 August 2016 / Revised: 12 September 2016 / Accepted: 13 September 2016 / Published: 1 October 2016
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Abstract
Phasing of nucleic acid crystal diffraction data using the anomalous signal of phosphorus, P-SAD, at Cukα wavelength has been previously demonstrated using Z-DNA. Since the original work on P-SAD with Z-DNA there has been, with a notable exception, a conspicuous absence of
[...] Read more.
Phasing of nucleic acid crystal diffraction data using the anomalous signal of phosphorus, P-SAD, at Cukα wavelength has been previously demonstrated using Z-DNA. Since the original work on P-SAD with Z-DNA there has been, with a notable exception, a conspicuous absence of applications of the technique to additional nucleic acid crystal structures. We have reproduced the P-SAD phasing of Z-DNA using a rotating-anode source and have attempted to phase a variety of nucleic acid crystals using P-SAD without success. A comparison of P-SAD using Z-DNA and a representative nucleic acid, the Dickerson-Drew dodecamer, is presented along with a S-SAD using only two sulfurs to phase a 2’-thio modified DNA decamer. A theoretical explanation for the limitation of P-SAD applied to nucleic acids is presented to show that the relatively high atomic displacement parameter of phosphorus in the nucleic acid backbone is responsible for the lack of success in applying P-SAD to nucleic acid diffraction data. Full article
(This article belongs to the Special Issue Nucleic Acid Crystallography)
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Review

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Open AccessReview Structural Basis of DEAH/RHA Helicase Activity
Crystals 2017, 7(8), 253; doi:10.3390/cryst7080253
Received: 6 July 2017 / Revised: 12 August 2017 / Accepted: 13 August 2017 / Published: 15 August 2017
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Abstract
DEAH/RHA helicases are members of a large group of proteins collectively termed DExH-box, which also include Ski2-like and NS3/NPH-II helicases. By binding and remodeling DNA and RNA, DEAH/RHA helicases play critical roles in many cellular processes ranging from transcription and splicing to ribosome
[...] Read more.
DEAH/RHA helicases are members of a large group of proteins collectively termed DExH-box, which also include Ski2-like and NS3/NPH-II helicases. By binding and remodeling DNA and RNA, DEAH/RHA helicases play critical roles in many cellular processes ranging from transcription and splicing to ribosome biogenesis, innate immunity and stress granule formation. While numerous crystal structures of other DExH-box proteins helicases have been reported, no structures of DEAH/RHA helicases bound to nucleic acid substrates have been available until the recent co-crystal structures of the maleless (MLE) and Prp43p bound to RNA. This review examines how these new structures provide a starting point to understand how DEAH/RHA helicases bind to, translocate on, and unwind nucleic acid substrates. Full article
(This article belongs to the Special Issue Nucleic Acid Crystallography)
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Figure 1

Open AccessFeature PaperReview 3D DNA Crystals and Nanotechnology
Crystals 2016, 6(8), 97; doi:10.3390/cryst6080097
Received: 28 July 2016 / Revised: 11 August 2016 / Accepted: 12 August 2016 / Published: 18 August 2016
Cited by 2 | PDF Full-text (5867 KB) | HTML Full-text | XML Full-text
Abstract
DNA’s molecular recognition properties have made it one of the most widely used biomacromolecular construction materials. The programmed assembly of DNA oligonucleotides has been used to create complex 2D and 3D self-assembled architectures and to guide the assembly of other molecules. The origins
[...] Read more.
DNA’s molecular recognition properties have made it one of the most widely used biomacromolecular construction materials. The programmed assembly of DNA oligonucleotides has been used to create complex 2D and 3D self-assembled architectures and to guide the assembly of other molecules. The origins of DNA nanotechnology are rooted in the goal of assembling DNA molecules into designed periodic arrays, i.e., crystals. Here, we highlight several DNA crystal structures, the progress made in designing DNA crystals, and look at the current prospects and future directions of DNA crystals in nanotechnology. Full article
(This article belongs to the Special Issue Nucleic Acid Crystallography)
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