Nucleic Acids and Their Complexes

1999 ◽  
Author(s):  
A.-C. Dock-Bregeon ◽  
D. Moras
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Chemical Properties ◽  
Preparation Methods ◽  
Synthetic Dna ◽  
Dna And Rna ◽  
Physico Chemical ◽  
Structure Determinations ◽  
Rna Crystallography ◽  
Rna Domains

At first glance crystallizing nucleic acids poses the same problems as crystallizing proteins since most of the variables to investigate are alike. It is thus astonishing that crystallization data banks (1) that describe so many successful protein crystallizations are so poor in information on nucleic acids. This relies on the physico-chemical and biochemical characteristics of nucleic acids distinguishing them from proteins. The aim of this chapter is to underline features explaining the difficulties often encountered in nucleic acid crystallization and to discuss strategies that could help to crystallize them more readily, either as free molecules or as complexes with proteins. Other general principles, in particular for RNA crystallization, are discussed in ref. 2. Among natural nucleic acids only the smaller ones provide good candidates for successful crystallizations. Large DNAs or RNAs can a priori be excluded because of their flexibility that generates conformational heterogeneity not compatible with crystallization. Thus the smaller RNAs with more compact structures (with 75-120 nt), especially transfer RNAs (tRNAs), but also 5S RNA, were the first natural nucleic acids to be crystallized (3, 4). At present attempts are being made with other RNA systems, such as ribozymes and introns, fragments of mRNA, viroids, viral and other tRNA-like RNAs, SELEX-evolved RNAs, and crystallization successes leading to X-ray structure determinations were reported for RNA domains of up to 160 nt long, with the resolution of the P4-P6 domain of the self-splicing Tetrahymena intron (5). The recent excitement in nucleic acid crystallography, and particularly in RNA crystallography, have partly been due to technological improvements in the preparation methods of the molecules. Advances in oligonucleotide chemical synthesis provide opportunity for making large amounts of pure desoxyribo- and more recently of ribo-oligomers of any desired sequence. This led to the crystallization of a number of DNA and RNA fragments and was followed by the co-crystallization of complexes between proteins and such synthetic fragments. Transcription methods of RNAs from synthetic DNA templates were also essential for rejuvenating the structural biology of RNAs. In the case of complexes of proteins with RNAs, the main difficulty was to purify large quantities of homogeneous biological material with well defined physico-chemical properties.

An Investigation of the Anomalous Staining of Chromatin by the Acid Dyes, Methyl Blue and Aniline Blue

1962 ◽  
Vol s3-103 (64) ◽  
pp. 519-530
Author(s):  
R. B. McKAY
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Methyl Blue ◽  
Aniline Blue ◽  
Acid Dyes ◽  
Dna And Rna ◽  
Basic Dyes ◽  
Blue Stain ◽  
High Degree ◽  
Mechanism Of The Reaction

Methyl blue and aniline blue, though acid dyes, stain the chromatin of the spermatogenetic cells of the mouse (especially of the primary spermatocytes) strongly. Extraction of the basiphil nucleic acid constituents from the chromatin causes loss of this property, while destruction of acidophilia in the protein constituents does not. It has been concluded that the dyes interact with the nucleic acids. Further, they appear to react with both DNA and RNA in the chromatin, although they show no affinity for the cytoplasm of the exocrine cells in sections of pancreas, which is rich in RNA. The mechanism of the reaction has not been fully elucidated, although apparently the dyes do not behave as basic dyes towards the nucleic acids, and the interaction is non-ionic. Methyl blue and aniline blue stain strongly other ‘acidic’ substrates, such as cellulose and nitrocellulose, and attempts have been made to relate the staining of nucleic acids to the staining of these substrates, particularly cellulose; for the staining properties of this substrate have been intensively investigated elsewhere. No satisfactory correlation, however, has been obtained, for nitrocellulose has been found to be less strongly stained at pH 3.0 than at pH 7.1, while the reverse is true for cellulose. Further, only one of 3 direct cotton dyes used appears to have any affinity for the chromatin of the spermatogenetic cells. Direct cotton dyes have large flat molecules with a high degree of conjugation. It is suggested that these characteristics are essential for interaction with nucleic acids, and also that the molecule must be reasonably compact. Finally, it has been shown that methyl blue, aniline blue, and 3 direct cotton dyes of the azo type have no ability to stain the glycogen in liver cells, yet glycogen is very closely related to cellulose.

scholarly journals De Novo Nucleic Acids: A Review of Synthetic Alternatives to DNA and RNA That Could Act as Bio-Information Storage Molecules

Life ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 346
Author(s):  
Kevin G Devine ◽  
Sohan Jheeta
Keyword(s):  
Nucleic Acids ◽  
Genetic Information ◽  
De Novo ◽  
Chemical Properties ◽  
Amino Acid Sequences ◽  
Information Storage ◽  
Heterocyclic Base ◽  
Dna And Rna ◽  
Phosphate Backbone ◽  
Physical And Chemical

Modern terran life uses several essential biopolymers like nucleic acids, proteins and polysaccharides. The nucleic acids, DNA and RNA are arguably life’s most important, acting as the stores and translators of genetic information contained in their base sequences, which ultimately manifest themselves in the amino acid sequences of proteins. But just what is it about their structures; an aromatic heterocyclic base appended to a (five-atom ring) sugar-phosphate backbone that enables them to carry out these functions with such high fidelity? In the past three decades, leading chemists have created in their laboratories synthetic analogues of nucleic acids which differ from their natural counterparts in three key areas as follows: (a) replacement of the phosphate moiety with an uncharged analogue, (b) replacement of the pentose sugars ribose and deoxyribose with alternative acyclic, pentose and hexose derivatives and, finally, (c) replacement of the two heterocyclic base pairs adenine/thymine and guanine/cytosine with non-standard analogues that obey the Watson–Crick pairing rules. This manuscript will examine in detail the physical and chemical properties of these synthetic nucleic acid analogues, in particular on their abilities to serve as conveyors of genetic information. If life exists elsewhere in the universe, will it also use DNA and RNA?

scholarly journals Physico-Chemical Properties of Nucleic Acids

Nature ◽  
1950 ◽  
Vol 166 (4213) ◽  
pp. 170-172
Author(s):  
D. O. JORDAN
Keyword(s):  
Nucleic Acids ◽  
Chemical Properties ◽  
Physico Chemical

scholarly journals Oligonucleotide-based systems: DNA, microRNAs, DNA/RNA aptamers

2016 ◽  
Vol 60 (1) ◽  
pp. 27-35 ◽  
Author(s):  
Pawan Jolly ◽  
Pedro Estrela ◽  
Michael Ladomery
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Rna Aptamers ◽  
Locked Nucleic Acid ◽  
Synthetic Analogue ◽  
Dna And Rna ◽  
Naturally Occurring ◽  
Wide Range ◽  
Synthetic Oligonucleotides ◽  
Shed Light

There are an increasing number of applications that have been developed for oligonucleotide-based biosensing systems in genetics and biomedicine. Oligonucleotide-based biosensors are those where the probe to capture the analyte is a strand of deoxyribonucleic acid (DNA), ribonucleic acid (RNA) or a synthetic analogue of naturally occurring nucleic acids. This review will shed light on various types of nucleic acids such as DNA and RNA (particularly microRNAs), their role and their application in biosensing. It will also cover DNA/RNA aptamers, which can be used as bioreceptors for a wide range of targets such as proteins, small molecules, bacteria and even cells. It will also highlight how the invention of synthetic oligonucleotides such as peptide nucleic acid (PNA) or locked nucleic acid (LNA) has pushed the limits of molecular biology and biosensor development to new perspectives. These technologies are very promising albeit still in need of development in order to bridge the gap between the laboratory-based status and the reality of biomedical applications.

Highly stable triple helix formation by homopyrimidine (l)-acyclic threoninol nucleic acids with single stranded DNA and RNA

2015 ◽  
Vol 13 (8) ◽  
pp. 2366-2374 ◽  
Author(s):  
Vipin Kumar ◽  
Venkitasamy Kesavan ◽  
Kurt V. Gothelf
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Triple Helix ◽  
Helical Structures ◽  
Single Stranded Dna ◽  
Dna And Rna ◽  
Helix Formation ◽  
Triple Helix Formation

Homopyrimidine acyclic (l)-threoninol nucleic acid (aTNA) was synthesized and found to form highly stable (l)-aTNA–DNA–(l)-aTNA and (l)-aTNA–RNA–(l)-aTNA triple helical structures.

scholarly journals Dissecting and predicting different types of binding sites in nucleic acids based on structural information

2021 ◽  
Author(s):  
Zheng Jiang ◽  
Si-Rui Xiao ◽  
Rong Liu
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Binding Sites ◽  
Structural Information ◽  
Machine Learning Algorithms ◽  
Nucleic Acid Binding ◽  
Integrative Framework ◽  
Dna And Rna ◽  
Feature Spaces ◽  
Critical Binding

Abstract The biological functions of DNA and RNA generally depend on their interactions with other molecules, such as small ligands, proteins and nucleic acids. However, our knowledge of the nucleic acid binding sites for different interaction partners is very limited, and identification of these critical binding regions is not a trivial work. Herein, we performed a comprehensive comparison between binding and nonbinding sites and among different categories of binding sites in these two nucleic acid classes. From the structural perspective, RNA may interact with ligands through forming binding pockets and contact proteins and nucleic acids using protruding surfaces, while DNA may adopt regions closer to the middle of the chain to make contacts with other molecules. Based on structural information, we established a feature-based ensemble learning classifier to identify the binding sites by fully using the interplay among different machine learning algorithms, feature spaces and sample spaces. Meanwhile, we designed a template-based classifier by exploiting structural conservation. The complementarity between the two classifiers motivated us to build an integrative framework for improving prediction performance. Moreover, we utilized a post-processing procedure based on the random walk algorithm to further correct the integrative predictions. Our unified prediction framework yielded promising results for different binding sites and outperformed existing methods.

Introduction to DNA

2018 ◽  
pp. 1-10
Author(s):  
David Bensimon ◽  
Vincent Croquette ◽  
Jean-François Allemand ◽  
Xavier Michalet ◽  
Terence Strick
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Structural Properties ◽  
Helical Structure ◽  
3D Structures ◽  
Double Helical Structure ◽  
Dna And Rna

This chapter provides a quick introduction to the structural properties of nucleic acids (DNA and RNA). It describes the famed double-helical structure of DNA, the more complex 3D structures adopted by RNA, and the random (possibly) twisted coil that nucleic acid can display at large scales.

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