Thymine cocrystals based on DNA-inspired binding motifs

CrystEngComm ◽  
2017 ◽  
Vol 19 (37) ◽  
pp. 5679-5685 ◽  
Author(s):  
Elizabeth S. Koch ◽  
Kelly A. McKenna ◽  
Hyo Jung Kim ◽  
Victor G. Young ◽  
Jennifer A. Swift
Keyword(s):  
Nucleic Acid ◽  
Base Pairing ◽  
Binding Motifs

Cocrystal design through DNA-type base pairing between a nucleic acid and complementary heterocycles.

scholarly journals Synthesis of phosphoramidites of isoGNA, an isomer of glycerol nucleic acid

2014 ◽  
Vol 10 ◽  
pp. 2131-2138 ◽  
Author(s):  
Keunsoo Kim ◽  
Venkateshwarlu Punna ◽  
Phaneendrasai Karri ◽  
Ramanarayanan Krishnamurthy
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Structural Unit ◽  
Easy Access ◽  
Alternative Route ◽  
Base Pairing ◽  
Limited Base ◽  
Glycerol Nucleic Acid ◽  
Adenine Derivative

IsoGNA, an isomer of glycerol nucleic acid GNA, is a flexible (acyclic) nucleic acid with bases directly attached to its linear backbone. IsoGNA exhibits (limited) base-pairing properties which are unique compared to other known flexible nucleic acids. Herein, we report on the details of the preparation of isoGNA phosphoramidites and an alternative route for the synthesis of the adenine derivative. The synthetic improvements described here enable an easy access to isoGNA and allows for the further exploration of this structural unit in oligonucleotide chemistry thereby spurring investigations of its usefulness and applicability.

scholarly journals Direct Measurement of Specific Interactions between Nucleic Acid Base Pairing.

2002 ◽  
Vol 59 (12) ◽  
pp. 792-799
Author(s):  
Takahiro HARADA ◽  
Takashi MIYAHARA ◽  
Naotoshi NAKASHIMA ◽  
Kazue KURIHARA
Keyword(s):  
Nucleic Acid ◽  
Direct Measurement ◽  
Specific Interactions ◽  
Base Pairing ◽  
Acid Base ◽  
Nucleic Acid Base

scholarly journals Characterization of Rous Sarcoma Virus Gag Particles Assembled In Vitro

2001 ◽  
Vol 75 (6) ◽  
pp. 2753-2764 ◽  
Author(s):  
Fang Yu ◽  
Swati M. Joshi ◽  
Yu May Ma ◽  
Richard L. Kingston ◽  
Martha N. Simon ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Rous Sarcoma Virus ◽  
Radial Distance ◽  
Binding Motif ◽  
Gag Protein ◽  
Binding Motifs ◽  
Rous Sarcoma ◽  
Sarcoma Virus ◽  
The Mean

ABSTRACT Purified retrovirus Gag proteins or Gag protein fragments are able to assemble into virus-like particles (VLPs) in vitro in the presence of RNA. We have examined the role of nucleic acid and of the NC domain in assembly of VLPs from a Rous sarcoma virus (RSV) Gag protein and have characterized these VLPs using transmission electron microscopy (TEM), scanning TEM (STEM), and cryoelectron microscopy (cryo-EM). RNAs of diverse sizes, single-stranded DNA oligonucleotides as small as 22 nucleotides, double-stranded DNA, and heparin all promoted efficient assembly. The percentages of nucleic acid by mass, in the VLPs varied from 5 to 8%. The mean mass of VLPs, as determined by STEM, was 6.5 × 107 Da for both RNA-containing and DNA oligonucleotide-containing particles, corresponding to a stoichiometry of about 1,200 protein molecules per VLP, slightly lower than the 1,500 Gag molecules estimated previously for infectious RSV. By cryo-EM, the VLPs showed the characteristic morphology of immature retroviruses, with discernible regions of high density corresponding to the two domains of the CA protein. In spherically averaged density distributions, the mean radial distance to the density corresponding to the C-terminal domain of CA was 33 nm, considerably smaller than that of equivalent human immunodeficiency virus type 1 particles. Deletions of the distal portion of NC, including the second Zn-binding motif, had little effect on assembly, but deletions including the charged residues between the two Zn-binding motifs abrogated assembly. Mutation of the cysteine and histidine residues in the first Zn-binding motif to alanine did not affect assembly, but mutation of the basic residues between the two Zn-binding motifs, or of the basic residues in the N-terminal portion of NC, abrogated assembly. Together, these findings establish VLPs as a good model for immature virions and establish a foundation for dissection of the interactions that lead to assembly.

Photon antennae assembled by nucleic acid base pairing

1991 ◽  
Vol 95 (4) ◽  
pp. 1530-1532 ◽  
Author(s):  
Anthony Harriman ◽  
Darren J. Magda ◽  
Jonathan L. Sessler
Keyword(s):  
Nucleic Acid ◽  
Base Pairing ◽  
Acid Base ◽  
Nucleic Acid Base

scholarly journals A comprehensive classification of nucleic acid structural families based on strand direction and base pairing

1992 ◽  
Vol 20 (19) ◽  
pp. 5011-5016 ◽  
Author(s):  
Richard Lavery ◽  
Krystyna Zakrzewska ◽  
Jian-Sheng Sun ◽  
Stephen C. Harvey
Keyword(s):  
Nucleic Acid ◽  
Base Pairing ◽  
Comprehensive Classification

scholarly journals In-depth Bioinformatic Analyses of Human SARS-CoV-2, SARS-CoV, MERS-CoV, and Other Nidovirales Suggest Important Roles of Noncanonical Nucleic Acid Structures in Their Lifecycles

2020 ◽  
Author(s):  
Martin Bartas ◽  
Václav Brázda ◽  
Natália Bohálová ◽  
Alessio Cantara ◽  
Adriana Volná ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Genomic Sequence ◽  
Inverted Repeats ◽  
Genomic Rna ◽  
Molecular Processes ◽  
Rna Packaging ◽  
Binding Motifs ◽  
G Quadruplex ◽  
Human Proteins ◽  
Nucleic Acid Structures

AbstractNoncanonical nucleic acid structures play important roles in the regulation of molecular processes. Considering the importance of the ongoing coronavirus crisis, we decided to evaluate genomes of all coronaviruses sequenced to date (stated more broadly, the order Nidovirales) to determine if they contain noncanonical nucleic acid structures. We discovered much evidence of putative G-quadruplex sites and even much more of inverted repeats (IRs) loci, which in fact are ubiquitous along the whole genomic sequence and indicate a possible mechanism for genomic RNA packaging. The most notable enrichment of IRs was found inside 5′UTR for IRs of size 12+ nucleotides, and the most notable enrichment of putative quadruplex sites (PQSs) was located before 3′UTR, inside 5′UTR, and before mRNA. This indicates crucial regulatory roles for both IRs and PQSs. Moreover, we found multiple G-quadruplex binding motifs in human proteins having potential for binding of SARS-CoV-2 RNA. Noncanonical nucleic acids structures in Nidovirales and in novel SARS-CoV-2 are therefore promising druggable structures that can be targeted and utilized in the future.

scholarly journals Utilizing the bioorthogonal base-pairing system ofl-DNA to design ideal DNA nanocarriers for enhanced delivery of nucleic acid cargos

2014 ◽  
Vol 5 (4) ◽  
pp. 1533-1537 ◽  
Author(s):  
Kyoung-Ran Kim ◽  
Taemin Lee ◽  
Byeong-Su Kim ◽  
Dae-Ro Ahn
Keyword(s):  
Nucleic Acid ◽  
Base Pairing

Parallel nucleic acid helices with hoogsteen base pairing: Symmetry and structure

Biopolymers ◽  
1994 ◽  
Vol 34 (12) ◽  
pp. 1573-1581 ◽  
Author(s):  
G. Raghunathan ◽  
H. Todd Miles ◽  
V. Sasisekharan
Keyword(s):  
Nucleic Acid ◽  
Pairing Symmetry ◽  
Base Pairing ◽  
Hoogsteen Base Pairing
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