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Crystals
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Nucleic Acid Crystallography
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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

Dr. Jinwei Zhang

E-Mail Website
Guest Editor
Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 50 South Drive, Bethesda, MD 20892, USA
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

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Crystals is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

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

Published Papers (3 papers)

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Research

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3656 KiB  
Article
Phosphorus SAD Phasing for Nucleic Acid Structures: Limitations and Potential
by Joel M. Harp, Pradeep S. Pallan and Martin Egli
Crystals 2016, 6(10), 125; https://doi.org/10.3390/cryst6100125 - 01 Oct 2016
Cited by 3 | Viewed by 5230
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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21528 KiB  
Review
Structural Basis of DEAH/RHA Helicase Activity
by Michael C. Chen and Adrian R. Ferré-D’Amaré
Crystals 2017, 7(8), 253; https://doi.org/10.3390/cryst7080253 - 15 Aug 2017
Cited by 5 | Viewed by 6517
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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5867 KiB  
Review
3D DNA Crystals and Nanotechnology
by Paul J. Paukstelis and Nadrian C. Seeman
Crystals 2016, 6(8), 97; https://doi.org/10.3390/cryst6080097 - 18 Aug 2016
Cited by 20 | Viewed by 11764
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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