scholarly journals A unified dinucleotide alphabet describing both RNA and DNA structures

2020 ◽  
Vol 48 (11) ◽  
pp. 6367-6381
Author(s):  
Jiří Černý ◽  
Paulína Božíková ◽  
Jakub Svoboda ◽  
Bohdan Schneider
Keyword(s):  
Nucleic Acid ◽  
Structural Features ◽  
Automated Assignment ◽  
Graphical Display ◽  
Rna Structures ◽  
Structural Alphabet ◽  
Dna Structures ◽  
Nucleic Acid Structures ◽  
First Time ◽  
Rna And Dna

Abstract By analyzing almost 120 000 dinucleotides in over 2000 nonredundant nucleic acid crystal structures, we define 96+1 diNucleotide Conformers, NtCs, which describe the geometry of RNA and DNA dinucleotides. NtC classes are grouped into 15 codes of the structural alphabet CANA (Conformational Alphabet of Nucleic Acids) to simplify symbolic annotation of the prominent structural features of NAs and their intuitive graphical display. The search for nontrivial patterns of NtCs resulted in the identification of several types of RNA loops, some of them observed for the first time. Over 30% of the nearly six million dinucleotides in the PDB cannot be assigned to any NtC class but we demonstrate that up to a half of them can be re-refined with the help of proper refinement targets. A statistical analysis of the preferences of NtCs and CANA codes for the 16 dinucleotide sequences showed that neither the NtC class AA00, which forms the scaffold of RNA structures, nor BB00, the DNA most populated class, are sequence neutral but their distributions are significantly biased. The reported automated assignment of the NtC classes and CANA codes available at dnatco.org provides a powerful tool for unbiased analysis of nucleic acid structures by structural and molecular biologists.

Application of constrained real-space refinement of flexible molecular fragments to automatic model building of RNA structures

2012 ◽  
Vol 45 (2) ◽  
pp. 309-315 ◽  
Author(s):  
Frantisek Pavelcik
Keyword(s):  
Nucleic Acid ◽  
Model Building ◽  
Real Space ◽  
Rna Structures ◽  
Molecular Fragments ◽  
Source Codes ◽  
Translation Function ◽  
Base Method ◽  
Nucleic Acid Structures ◽  
Automatic Model Building

New methods have been developed for locating phosphate groups and nucleic acid bases in the electron density of RNA structures. These methods utilize a constrained real-space refinement of molecular fragments and a phased rotation–conformation–translation function. Real-space refinement has also contributed to the improvement of the bone/base method of RNA model building and to redesigning the method of building double helices in nucleic acid structures. This improvement is reflected in the increased accuracy of the model building and the ability to better distinguish between correct and false solutions. A program,RSR, was created, and the programsNUT,HELandDHLwere upgraded and organized into a program system, which is CCP4 oriented. Source codes will also be released.

scholarly journals Intrastrand backbone-nucleobase interactions stabilize unwound right-handed helical structures of heteroduplexes of L-aTNA/RNA and SNA/RNA

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Yukiko Kamiya ◽  
Tadashi Satoh ◽  
Atsuji Kodama ◽  
Tatsuya Suzuki ◽  
Keiji Murayama ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Crystal Structures ◽  
Prebiotic Chemistry ◽  
Basic Research ◽  
Structural Features ◽  
Helical Structures ◽  
Base Pairs ◽  
Triplex Structure ◽  
Rna And Dna

Abstract Xeno nucleic acids, which are synthetic analogues of natural nucleic acids, have potential for use in nucleic acid drugs and as orthogonal genetic biopolymers and prebiotic precursors. Although few acyclic nucleic acids can stably bind to RNA and DNA, serinol nucleic acid (SNA) and L-threoninol nucleic acid (L-aTNA) stably bind to them. Here we disclose crystal structures of RNA hybridizing with SNA and with L-aTNA. The heteroduplexes show unwound right-handed helical structures. Unlike canonical A-type duplexes, the base pairs in the heteroduplexes align perpendicularly to the helical axes, and consequently helical pitches are large. The unwound helical structures originate from interactions between nucleobases and neighbouring backbones of L-aTNA and SNA through CH–O bonds. In addition, SNA and L-aTNA form a triplex structure via C:G*G parallel Hoogsteen interactions with RNA. The unique structural features of the RNA-recognizing mode of L-aTNA and SNA should prove useful in nanotechnology, biotechnology, and basic research into prebiotic chemistry.

scholarly journals DNA acting like RNA

2011 ◽  
Vol 39 (2) ◽  
pp. 635-640 ◽  
Author(s):  
Robert V. Brown ◽  
Laurence H. Hurley
Keyword(s):  
Gene Expression ◽  
Short Review ◽  
Rna Structures ◽  
Tertiary Structures ◽  
Control Of Gene Expression ◽  
Dna Structures ◽  
Folded Structures ◽  
Rna And Dna

Over the last decade or so, secondary non-B-DNA structures such as G-quadruplexes and i-motifs have come into focus as biologically functioning moieties that are potentially involved in telomeric interactions and the control of gene expression. In the present short review, we first describe the structural and dynamic parallels with complex RNA structures, including the importance of sequence and ions in folding, and then we describe the biological consequences of the folded structures. We conclude that there are considerable parallels between secondary and tertiary structures in RNA and DNA from both the folding and the biological perspectives.

scholarly journals Structural motifs and intramolecular interactions in non-canonical G-quadruplexes

2021 ◽  
Author(s):  
Jagannath Jana ◽  
Swantje Mohr ◽  
Yoanes Maria Vianney ◽  
Klaus Weisz
Keyword(s):  
Nucleic Acid ◽  
Structural Features ◽  
Intramolecular Interactions ◽  
Structural Motifs ◽  
Nucleic Acid Sequences

G-rich nucleic acid sequences encompassing G-tracts of varying lengths can fold into different non-canonical G-quadruplexes with distinct structural features.

scholarly journals Novel nucleic acid origami structures and conventional molecular beacon–based platforms: a comparison in biosensing applications

2021 ◽  
Author(s):  
Noemi Bellassai ◽  
Roberta D’Agata ◽  
Giuseppe Spoto
Keyword(s):  
Nucleic Acid ◽  
Structural Properties ◽  
Molecular Beacon ◽  
Dna Origami ◽  
Molecular Beacons ◽  
Conformational Polymorphism ◽  
Functional Systems ◽  
Similarities And Differences ◽  
Nucleic Acid Structures ◽  
Nucleic Acid Sequences

AbstractNucleic acid nanotechnology designs and develops synthetic nucleic acid strands to fabricate nanosized functional systems. Structural properties and the conformational polymorphism of nucleic acid sequences are inherent characteristics that make nucleic acid nanostructures attractive systems in biosensing. This review critically discusses recent advances in biosensing derived from molecular beacon and DNA origami structures. Molecular beacons belong to a conventional class of nucleic acid structures used in biosensing, whereas DNA origami nanostructures are fabricated by fully exploiting possibilities offered by nucleic acid nanotechnology. We present nucleic acid scaffolds divided into conventional hairpin molecular beacons and DNA origami, and discuss some relevant examples by focusing on peculiar aspects exploited in biosensing applications. We also critically evaluate analytical uses of the synthetic nucleic acid structures in biosensing to point out similarities and differences between traditional hairpin nucleic acid sequences and DNA origami. Graphical abstract

scholarly journals Overlapping but distinct: a new model for G-quadruplex biochemical specificity

2021 ◽  
Author(s):  
Martin Volek ◽  
Sofia Kolesnikova ◽  
Katerina Svehlova ◽  
Pavel Srb ◽  
Ráchel Sgallová ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Drug Design ◽  
Solution Structure ◽  
Biochemical Data ◽  
Biological Regulation ◽  
New Model ◽  
G Quadruplex ◽  
Range Of Functions ◽  
Nucleic Acid Structures ◽  
Sequence Requirements

Abstract G-quadruplexes are noncanonical nucleic acid structures formed by stacked guanine tetrads. They are capable of a range of functions and thought to play widespread biological roles. This diversity raises an important question: what determines the biochemical specificity of G-quadruplex structures? The answer is particularly important from the perspective of biological regulation because genomes can contain hundreds of thousands of G-quadruplexes with a range of functions. Here we analyze the specificity of each sequence in a 496-member library of variants of a reference G-quadruplex with respect to five functions. Our analysis shows that the sequence requirements of G-quadruplexes with these functions are different from one another, with some mutations altering biochemical specificity by orders of magnitude. Mutations in tetrads have larger effects than mutations in loops, and changes in specificity are correlated with changes in multimeric state. To complement our biochemical data we determined the solution structure of a monomeric G-quadruplex from the library. The stacked and accessible tetrads rationalize why monomers tend to promote a model peroxidase reaction and generate fluorescence. Our experiments support a model in which the sequence requirements of G-quadruplexes with different functions are overlapping but distinct. This has implications for biological regulation, bioinformatics, and drug design.

ALKYLATION, INTERCALATION, AND CONFORMATIONAL PROPERTIES OF NUCLEIC ACID STRUCTURES

1981 ◽  
Vol 367 (1 Quantum Chemi) ◽  
pp. 295-325 ◽  
Author(s):  
D. Malhotra ◽  
R. Pearlstein ◽  
O. Kikuchi ◽  
S. N. Mohammad ◽  
Y. Nakata ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Conformational Properties ◽  
Nucleic Acid Structures

scholarly journals Composition of Pseudomonas aeruginosa slime

1969 ◽  
Vol 112 (4) ◽  
pp. 521-525 ◽  
Author(s):  
M. R. W. Brown ◽  
J. H. Scott Foster ◽  
J. R. Clamp
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Hyaluronic Acid ◽  
Nucleic Acid ◽  
Growth Medium ◽  
Extraction Procedure ◽  
The Other ◽  
Minor Components ◽  
Polysaccharide Fraction ◽  
Defined Media ◽  
Rna And Dna

1. The slime produced by eight strains of Pseudomonas aeruginosa on a number of different media was demonstrated to be qualitatively the same. Small quantitative differences may be occasioned by differences in the extraction procedure, the growth medium or the strain of organism used. 2. The slime was shown to be predominantly polysaccharide with some nucleic acid material and a small amount of protein. 3. The hydrolysed polysaccharide fraction consists mainly of glucose with smaller amounts of mannose. This accounts for some 50–60% of the total slime. In addition, there is some 5% of hyaluronic acid. The nucleic acid material represents approx. 20% of the total weight, and is composed of both RNA and DNA. 4. Minor components are protein, rhamnose and glucosamine, the protein being less than 5% of the total. 5. Hyaluronic acid is produced in greater quantities from nutrient broth than from chemically defined media, and is more firmly attached to the cells than the other components.

Tumor cell metabolism in vitro: a study of incubation media

1970 ◽  
Vol 48 (4) ◽  
pp. 517-519 ◽  
Author(s):  
I. C. Caldwell ◽  
Marianne F. Chan
Keyword(s):  
Nucleic Acid ◽  
Structural Integrity ◽  
Cell Metabolism ◽  
Ehrlich Ascites Carcinoma ◽  
Leukemic Cells ◽  
Prolonged Incubation ◽  
Ehrlich Ascites ◽  
Eac Cells ◽  
Rna And Dna

A number of incubation media which have been used in studies of the metabolism of Ehrlich ascites carcinoma (EAC) cells in vitro have been examined with respect to their abilities to support the incorporation of radioactive precursors into nucleotides and nucleic acids, and to maintain the structural integrity and tumor-inducing abilities of EAC cells. Cells incubated in the chemically-defined "Fischer's medium for leukemic cells of mice" were able to produce lethal tumors in mice after more than 16 h of incubation, maintained their structural integrity on prolonged incubation, and catalyzed high rates of incorporation of exogenously added substrates into nucleotides, RNA, and DNA. However, cells incubated in balanced salts solutions supplemented with glucose had these characteristics: (a) were unable to produce lethal tumors after 4 h of incubation, (b) released large amounts of nucleotide, nucleic acid, and protein material into the medium after less than 2 h of incubation, and (c) catalyzed the incorporation of radioactive precursors into nucleotides and RNA at much lower rates than did cells incubated in Fischer's medium, and were virtually unable to catalyze the incorporation of adenine-14C into DNA.

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