26 papers · ranked by Valyu relevance
Mohamed A. E. Soliman Mahdy
Genetic information is stored within the DNA molecule in the form of a triplet code, which is a sequence of three nucleotide bases which will translate through the mRNA to amino acid. Each triplet of nucleotide bases, which codes for a single amino acid is called a codon, it is the basic unit of genetic code. Gene…
Shubham Tripathi, Michael W. Deem
The standard genetic code is well known to be optimized for minimizing the phenotypic effects of single nucleotide substitutions, a property that was likely selected for during the emergence of a universal code. Given the fitness advantage afforded by high standing genetic diversity in a population in a dynamic…
Бранко Драгович
The genetic code is connection between 64 codons, which are building blocks of the genes, and 20 amino acids, which are building blocks of the proteins. In addition to coding amino acids, a few codons code stop signal, which is at the end of genes, i.e. it terminates process of protein synthesis. This article is a…
Shubham Tripathi, Michael W. Deem
The standard genetic code is well known to be optimized for minimizing the phenotypic effects of single nucleotide substitutions, a property that was likely selected for during the emergence of a universal code. Given the fitness advantage afforded by high standing genetic diversity in a population in a dynamic…
Balaji Kumar, Supreet Saini
Many theories have been proposed attempting to explain the origin of the genetic code. While strong reasons remain to believe that the genetic code evolved as a frozen accident, at least for the first few amino acids, other theories remain viable. In this work, we test the optimality of the standard genetic code…
Gabriel S. Zamudio, Marco V. José, Koji Tamura
In this work, we determine the biological and mathematical properties that are sufficient and necessary to uniquely determine both the primeval RNY (purine-any base-pyrimidine) code and the standard genetic code (SGC). These properties are: the evolution of the SGC from the RNY code; the degeneracy of both codes, and…
Tidjani Négadi
The mathematical concept of q-deformations, in particular the one of qnumbers, is used to study the genetic code(s). After considering two kinds of q-numbers, for comparison, a phenomenological classification scheme of the genetic code together with its numerous minor variants is, first, established. Next, numbers…
Maahil Arshad, Matthew Uchmanowicz, Vanshika Rana, Brett Trost + 2 more
The redundancy of the genetic code permits multiple codons to specify a single amino acid, but codon selection is far from random and reflects underlying functional significance. Most lifeforms exhibit codon bias, where the usage of certain codons is favored over others that code for the same amino acid and hence used…
Бранко Драгович, Andrei Yu. Khrennikov, N.Ž. Mišić
Ultrametric approach to the genetic code and the genome is considered and developed. p-Adic degeneracy of the genetic code is pointed out. Ultrametric tree of the codon space is presented. It is shown that codons and amino acids can be treated as p-adic ultrametric networks. Ultrametric modification of the Hamming…
Brian P. H. Metzger
The relationship between genetic code robustness and protein evolvability is unknown. A new study in PLOS Biology using in silico rewiring of genetic codes and functional protein data identified a positive correlation between code robustness and protein evolvability that is protein-specific.
V.I. Shcherbak, Maxim A. Makukov
Recent biotech achievements make it possible to employ genomic DNA as data storage more durable than any media currently used (Bancroft et al., 2001; Yachie et al., 2008; Ailenberg & Rotstein, 2009). Perhaps the most direct application for that was proposed even before the advent of synthetic biology. Considering…
Konrad Pawlak, Paweł Błażej, Dorota Mackiewicz, Paweł Mackiewicz + 1 more
'Nunzio D’Agostino'] The standard genetic code (SGC) plays a fundamental role in encoding biological information, but its evolutionary origins remain unresolved and widely debated. Thus, we used a methodology based on the evolutionary algorithm to investigate the emergence of stable coding systems. The simulation began…
C. Manuel Carlevaro, Ramiro M. Irastorza, Fernando Vericat
A heuristic diagram of the evolution of the standard genetic code is presented. It incorporates, in a way that resembles the energy levels of an atom, the physical notion of broken symmetry and it is consistent with original ideas by Crick on the origin and evolution of the code as well as with the chronological order…
Kwok-Fong Chan, Stelios Koukouravas, Joshua Yi Yeo, Darius Wen-Shuo Koh + 1 more
Mutations underpin the processes in life, be it beneficial or detrimental. While mutations are assumed to be random in the bereft of selection pressures, the genetic code has underlying computable probabilities in amino acid phenotypic changes. With a wide range of implications including drug resistance, understanding…
Danielle Venton
It doesn't take much for an organism to accept something radically new into its life. That is the conclusion of a recent inquiry into the mutability of life's fundamental genetic code by Ting-Fung Chan, a computational biologist at the Chinese University of Hong Kong and his colleagues. “There are not actually that…
Paweł Błażej, Małgorzata Wnetrzak, Dorota Mackiewicz, Paweł Mackiewicz
Compounds including non-canonical amino acids or other artificially designed molecules can find a lot of applications in medicine, industry and biotechnology. They can be produced thanks to the modification or extension of the standard genetic code (SGC). Such peptides or proteins including the non-canonical amino…
Robersy Sanchez, Jesús Barreto
Experimental studies reveal that genome architecture splits into natural domains suggesting a well-structured genomic architecture, where, for each species, genome populations are integrated by individual mutational variants. Herein, we show that the architecture of population genomes from the same or closed related…
Miloje Rakočević
In some previous works (2018a,b; 2019, 2021a,b, 2022) we presented a new type of mirror symmetry, expressed in the set of protein amino acids; such a symmetry, that it simultaneously represents the semiotic essence of the genetic code. In this paper we provide new evidences that the genetic code represents the unity of…
Authors not listed
Genetics is the study of genes-the heritable information that contains the codes for proteins and other molecules which form and maintain an organism’s structure and function. In most organisms, these genes are found in strands of deoxyribonucleic acid (DNA) molecules. The specific structure of the DNA (described…
Kevin J. Mitchell, Nick Cheney
How does the genome encode the form of the organism? What is the nature of this genomic code? Common metaphors, such as a "blueprint" or "program", fail to capture the complex, indirect, and evolutionarily dynamic relationship between the genome and organismal form, or the constructive, interactive processes that…
Dixita Limbachiya, Manish K. Gupta
Digital data explosion drives a demand for robust and reliable data storage medium. Development of better digital storage device to accumulate Zetta bytes (1 ZB = 1021 bytes ) of data that will be generated in near future is a big challenge. Looking at limitations of present day digital storage devices, it will soon be…
Authors not listed
RNA droplets assembled from co-transcriptionally folded nanostructures have recently emerged as a promising platform for constructing protocells and minimal synthetic cell models. In these systems, a custom-designed DNA template encodes an RNA nanostar, which is produced by transcription and self-assembles into…
Benjamin King, Max Winokan, Paul Stevenson, Jim Al-Khalili + 2 more
The adenine-thymine tautomer (A-T) has previously been discounted as a spontaneous mutagenesis mechanism due to the energetic instability of the tautomeric configuration. We study the stability of A-T while the nucleobases undergo DNA strand separation. Our calculations indicate an increase in the stability of A-T as…
Authors not listed
Molecular mechanisms governing initiation steps of the assembly of thousands of endogenous multi-protein complexes (EMCs) remain incompletely understood. Here, multiple lines of observations are reported reflecting the biological functions-aligned initiation sequence of hybrid assembly pathways (HAPs) of EMCs. HAPs…
HANIYEH ABDOLLAHZADEH, Tonya Peeples, Mohammad Shahcheraghi
DNA-based nanomaterials have shown great potential in numerous applications, thanks to their unique properties including DNA's various molecular interactions, programmability, and versatility with biological modules. Meanwhile, the DNA origami platforms have shown promise in the creation of drug carriers. This…
Emilie S. Henault, Maria Harris Rasmussen, Jan H. Jensen
We attempt to explain why search algorithms can find molecules with particular properties in an enormous chemical space (ca 10 60 molecules) by considering only a tiny subset (typically 10 3−6 molecules). Using a very simple example, we show that the number of potential paths that the search algorithms can follow to…