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 Synthetic Life with Alternative Nucleic Acids as Genetic Materials

Molecules ◽  
2020 ◽  
Vol 25 (15) ◽  
pp. 3483
Author(s):  
Peng Nie ◽  
Yanfen Bai ◽  
Hui Mei
Keyword(s):  
Nucleic Acids ◽  
Genetic Information ◽  
Structural Parameters ◽  
Living Cells ◽  
Information Storage ◽  
Chemically Modified ◽  
Synthetic Life ◽  
Living Organisms

DNA, the fundamental genetic polymer of all living organisms on Earth, can be chemically modified to embrace novel functions that do not exist in nature. The key chemical and structural parameters for genetic information storage, heredity, and evolution have been elucidated, and many xenobiotic nucleic acids (XNAs) with non-canonical structures are developed as alternative genetic materials in vitro. However, it is still particularly challenging to replace DNAs with XNAs in living cells. This review outlines some recent studies in which the storage and propagation of genetic information are achieved in vivo by expanding genetic systems with XNAs.

Separation of Nucleic Acids Using Single- and Multimodal Chromatography

2018 ◽  
Vol 20 (1) ◽  
pp. 49-55 ◽  
Author(s):  
Tiago Matos ◽  
Leif Bülow
Keyword(s):  
Nucleic Acids ◽  
Chemical Properties ◽  
Single Mode ◽  
Major Groove ◽  
Base Pairs ◽  
Chromatographic Separations ◽  
Multimodal Chromatography ◽  
Phosphate Backbone ◽  
Target Molecules ◽  
Polymerase Chain

The needs for purified nucleic acids for preparative and analytical applications have increased constantly, demanding for the development of new and more efficient methods for their recovery and isolation. DNA molecules harbour some intrinsic chemical properties that render them suitable for chromatographic separations. These include a negatively charged phosphate backbone as well as a hydrophobic character originating mainly from the major groove of DNA which exposes the base pairs on the surface of the molecule. In addition, single stranded DNA often allows for a free exposure of the hydrophobic aromatic bases. In this review, multimodal chromatography (MMC) has been evaluated as an alternative tool for complex separations of nucleic acids. MMC embraces more than one kind of interaction between the chromatographic ligand and the target molecules. These resins have often proved superior to conventional single-mode chromatographic materials for DNA isolation, including, e.g., the purification of plasmid DNA from crude cell lysates and for the preparation of DNA fragments before or after a polymerase chain reaction (PCR).

scholarly journals A world beyond double-helical nucleic acids: the structural diversity of tetra-stranded G-quadruplexes

ChemTexts ◽  
2021 ◽  
Vol 7 (4) ◽  
Author(s):  
Klaus Weisz
Keyword(s):  
Hydrogen Bond ◽  
Nucleic Acids ◽  
Genetic Information ◽  
Structural Diversity ◽  
Base Pairing ◽  
Rna Sequences ◽  
Dna And Rna ◽  
Regulatory Functions ◽  
Insight Into

AbstractNucleic acids can adopt various secondary structures including double-, triple-, and tetra-stranded helices that differ by the specific hydrogen bond mediated pairing pattern between their nucleobase constituents. Whereas double-helical DNA relies on Watson–Crick base pairing to play a prominent role in storing genetic information, G-quadruplexes are tetra-stranded structures that are formed by the association of guanine bases from G-rich DNA and RNA sequences. During the last few decades, G-quadruplexes have attracted considerable interest after the realization that they form and exert regulatory functions in vivo. In addition, quadruplex architectures have also been recognized as versatile and powerful tools in a growing number of technological applications. To appreciate the astonishing structural diversity of these tetra-stranded structures and to give some insight into basic interactions that govern their folding, this article gives an overview of quadruplex structures and rules associated with the formation of different topologies. A brief discussion will also focus on nonconventional quadruplexes as well as on general principles when targeting quadruplexes with ligands. Graphic abstract

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.

scholarly journals Machines on Genes: Enzymes that Make, Break and Move DNA and RNA

2010 ◽  
Vol 38 (2) ◽  
pp. 381-383 ◽  
Author(s):  
W. Marshall Stark ◽  
Ben F. Luisi ◽  
Richard P. Bowater
Keyword(s):  
Gene Expression ◽  
Molecular Biology ◽  
Nucleic Acids ◽  
Present Article ◽  
Genetic Information ◽  
Clear View ◽  
Dna And Rna ◽  
Repair Enzymes ◽  
University Of Cambridge ◽  
Enzyme Substrates

As the vital information repositories of the cell, the nucleic acids DNA and RNA pose many challenges as enzyme substrates. To produce, maintain and repair DNA and RNA, and to extract the genetic information that they encode, a battery of remarkable enzymes has evolved, which includes translocases, polymerases/replicases, helicases, nucleases, topoisomerases, transposases, recombinases, repair enzymes and ribosomes. An understanding of how these enzymes function is essential if we are to have a clear view of the molecular biology of the cell and aspire to manipulate genomes and gene expression to our advantage. To bring together scientists working in this fast-developing field, the Biochemical Society held a Focused Meeting, ‘Machines on Genes: Enzymes that Make, Break and Move DNA and RNA’, at Robinson College, University of Cambridge, U.K., in August 2009. The present article summarizes the research presented at this meeting and the reviews associated with the talks which are published in this issue of Biochemical Society Transactions.

scholarly journals Heterochiral nucleic acid circuits

2019 ◽  
Vol 3 (5) ◽  
pp. 501-506 ◽  
Author(s):  
Adam M. Kabza ◽  
Brian E. Young ◽  
Nandini Kundu ◽  
Jonathan T. Sczepanski
Keyword(s):  
Synthetic Biology ◽  
Nucleic Acids ◽  
Chemical Properties ◽  
Sequence Information ◽  
Physical And Chemical Properties ◽  
Strand Displacement ◽  
Potential Applications ◽  
The Stability ◽  
Physical And Chemical ◽  
And Chemical Properties

The programmability of DNA/RNA-based molecular circuits provides numerous opportunities in the field of synthetic biology. However, the stability of nucleic acids remains a major concern when performing complex computations in biological environments. Our solution to this problem is l-(deoxy)ribose nucleic acids (l-DNA/RNA), which are mirror images (i.e. enantiomers) of natural d-nucleotides. l-oligonucleotides have the same physical and chemical properties as their natural counterparts, yet they are completely invisible to the stereospecific environment of biology. We recently reported a novel strand-displacement methodology for transferring sequence information between oligonucleotide enantiomers (which are incapable of base pairing with each other), enabling bio-orthogonal l-DNA/RNA circuits to be easily interfaced with living systems. In this perspective, we summarize these so-called ‘heterochiral’ circuits, provide a viewpoint on their potential applications in synthetic biology, and discuss key problems that must be solved before achieving the ultimate goal of the engineering complex and reliable functionality.

scholarly journals Theoretical methods for measuring chemo-physical properties of nucleic acids during the radicalization of dna and the incidence of cancer

2019 ◽  
Vol 32 (01) ◽  
pp. 01-12
Author(s):  
Mehdi Imanzadeh ◽  
Karim Zare ◽  
Majid Monajjemi ◽  
Ali Shamel
Keyword(s):  
Nucleic Acids ◽  
Genetic Material ◽  
Chemical Properties ◽  
Relevant Information ◽  
Dna Damages ◽  
Theoretical Methods ◽  
Chemical Agents ◽  
Incidence Of Cancer ◽  
Comprehensive Survey ◽  
Physical And Chemical

One of cases considered for diagnosing DNA damages is diagnosing DNA probable damages against oxidizing agents, including oxidizing chemicals and various incident rays which cause the bases in the DNA to be oxidized and especially bases G in the DNA sequence which is more easily oxidized than the other bases. Therefore, the main objective of this comprehensive survey is to provide relevant information on measure physical chemical properties of nucleic acids during DNA radicalization and incidence of cancer using theoretical methods. The aim of the present study is to examine the single-stranded NBO with sequences of GG, CG, AA AG AC: AT CT GT TT followed by the levels of energy and form of orbital LUMO and HOMO obtained from Gaussian computations for above double-stranded sequences. Our results showed that form B genetic material is the most stable structure against physical and chemical agents. Only the number of molecular population and the levels of molecular dynamic vibration and molecular thermochemistry such as enthalpie and entropie are temperature independent. In addition to this, the gap between the layers and the potential and energy needed to oxidize the components in the two strands of DNA and its optimum structure will not change with temperature. Optimum conditions on DNA and its bonds are the temperature of 37 ° C and pH is 7 to 8.7. DNA has form B and the rate of physical protection is the highest.

Statistical criteria of stellar population types

1966 ◽  
Vol 24 ◽  
pp. 101-110
Author(s):  
W. Iwanowska
Keyword(s):  
Stellar Population ◽  
Chemical Properties ◽  
Spectrophotometric Study ◽  
Physical And Chemical Properties ◽  
Population Type ◽  
The Galaxy ◽  
Distribution Parameters ◽  
Physical And Chemical ◽  
Statistical Criteria ◽  
And Chemical Properties

In connection with the spectrophotometric study of population-type characteristics of various kinds of stars, a statistical analysis of kinematical and distribution parameters of the same stars is performed at the Toruń Observatory. This has a twofold purpose: first, to provide a practical guide in selecting stars for observing programmes, second, to contribute to the understanding of relations existing between the physical and chemical properties of stars and their kinematics and distribution in the Galaxy.

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