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Some mathematical refinements concerning error minimization in the genetic code [article]

Harry Buhrman, Peter T. S. van der Gulik, Steven M. Kelk, Wouter M. Koolen, Leen Stougie
2010 arXiv   pre-print
Using a modified error function, the genetic code is found to be more error robust compared to a background of randomly generated codes with increasing space size.  ...  We do this by leaving the fixed block model, and using the wobble rules to formulate the characteristics acceptable for a genetic code.  ...  In our first extension, the "stop block" consists of three stop codons, as in the standard genetic code. However, their location is free, under the condition that they do not end in U or C.  ... 
arXiv:0909.1442v2 fatcat:rgz7izhsh5fmtfrs27kixsosse

Some Mathematical Refinements Concerning Error Minimization in the Genetic Code

H. Buhrman, P. T. S. van der Gulik, S. M. Kelk, W. M. Koolen, L. Stougie
2011 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
The genetic code is known to have a high level of error robustness and has been shown to be very error robust compared to randomly selected codes, but to be significantly less error robust than a certain  ...  Using a modified error function, the genetic code is found to be more error robust compared to a background of randomly generated codes with increasing space size.  ...  Furthermore, they gratefully acknowledge the large improvements of the manuscript by comments from Paul G. Higgs and two anonymous referees.  ... 
doi:10.1109/tcbb.2011.40 pmid:21358008 fatcat:l76oqie6h5fiblrideony6vhni

Fail-safe genetic codes designed to intrinsically contain engineered organisms

2019 Nucleic Acids Research  
Here, we propose restructuring the genetic code itself such that point mutations in protein-coding sequences are selected against.  ...  We also designed quadruplet-codon codes that should ensure all single point mutations in protein-coding sequences are selected against while maintaining expression of 20 or more amino acids.  ...  ACKNOWLEDGEMENTS The authors thank Akshay Maheshwari and Sam Bray for discussions regarding principles and applications of genetic code engineering, Conary Meyer, Eric Wei, Rolando Perez and Keoni Gandall  ... 
doi:10.1093/nar/gkz745 pmid:31511890 pmcid:PMC6821295 fatcat:pmfsm6ol6zftfaljchbnjroru4

Overcoming Challenges in Engineering the Genetic Code

M.J. Lajoie, D. Söll, G.M. Church
2016 Journal of Molecular Biology  
Codon suppression, reassignment, and creation are all ways of changing a genetic code.  ...  2 3 4 5 6 7 8 Abstract: Withstanding 3.5 billion years of genetic drift, the canonical genetic code remains such a fundamental foundation for the complexity of life that it is highly conserved across all  ...  While only a subset of sense codons likely need to be reassigned in order to achieve robust genetic isolation, this review will consider the 5 fundamental limits to changing the genetic code based on biochemical  ... 
doi:10.1016/j.jmb.2015.09.003 pmid:26348789 pmcid:PMC4779434 fatcat:qub2gcorfbdszcls7bkpqvv55a

Evolution of the genetic code: partial optimization of a random code for robustness to translation error in a rugged fitness landscape

Artem S Novozhilov, Yuri I Wolf, Eugene V Koonin
2007 Biology Direct  
Thus, the standard genetic code appears to be a point on an evolutionary trajectory from a random point (code) about half the way to the summit of the local peak.  ...  However, it remains unclear how much evolution the standard code underwent, what is the level of optimization, and what is the likely starting point.  ...  This work was supported by the Intramural Research Program of the National Library of Medicine at National Institutes of Health/DHHS.  ... 
doi:10.1186/1745-6150-2-24 pmid:17956616 pmcid:PMC2211284 fatcat:puxdru7imjfzvil56qmvfqeiwy

Designing siRNA That Distinguish between Genes That Differ by a Single Nucleotide

Dianne S. Schwarz, Hongliu Ding, Lori Kennington, Jessica T. Moore, Janell Schelter, Julja Burchard, Peter S. Linsley, Neil Aronin, Zuoshang Xu, Phillip D. Zamore
2006 PLoS Genetics  
PLoS Genet 2(9): e140.  ...  Using cell-free RNAi reactions in Drosophila embryo lysate and reporter assays and microarray analysis of off-target effects in cultured human cells, we identified positions within an siRNA that are most  ...  Acknowledgments We thank members of the Zamore, Xu, and Aronin laboratories and Nelson Lau for encouragement, helpful discussions, and comments on the manuscript. Funding.  ... 
doi:10.1371/journal.pgen.0020140 pmid:16965178 pmcid:PMC1560399 fatcat:o34elfmpxzactpbrarblc6zdda

Designing siRNA that distinguish between genes that differ by a single nucleotide

Dianne S Schwarz, Hongliu D Ding, Lori Kennington, Jessica T Moore, Janell Schelter, Julja Burchard, Peter S Linsley, Neil Aronin, Zuoshang Xu, Phillip D. Zamore
2005 PLoS Genetics  
PLoS Genet 2(9): e140.  ...  Using cell-free RNAi reactions in Drosophila embryo lysate and reporter assays and microarray analysis of off-target effects in cultured human cells, we identified positions within an siRNA that are most  ...  Acknowledgments We thank members of the Zamore, Xu, and Aronin laboratories and Nelson Lau for encouragement, helpful discussions, and comments on the manuscript. Funding.  ... 
doi:10.1371/journal.pgen.0020140.eor fatcat:g4r5gp23pbeufisuyeqaxllbvu

How Mitochondria Redefine the Code

Robin D. Knight, Laura F. Landweber, Michael Yarus
2001 Journal of Molecular Evolution  
We suggest that coding ambiguity, the extension of a tRNA's decoding capacity beyond its original set of codons, is the second event.  ...  Therefore, low codon frequencies can be related to codon reassignment, but appear to be neither necessary nor sufficient for reassignment. (3) Changes in the genetic code are not more likely to accompany  ...  mitochondrial genetic codes.  ... 
doi:10.1007/s002390010220 pmid:11675590 fatcat:aojyfkxdhncvhfvgik7jsds3jy

The case for an error minimizing standard genetic code

Stephen J Freeland, Tao Wu, Nick Keulmann
2003 Origins of life and evolution of the biosphere  
acids near to one another in coding space so as to minimize the impact of mutations and/or mistranslations.  ...  These weaknesses are illustrated here by means of a simple simulation model for adaptive genetic code evolution.  ...  Acknowledgements We are grateful to the John Templeton Foundation for Research Grant 938-COS27 and to UMBC's DRIF funding for financial support of this research.  ... 
pmid:14604186 fatcat:4iucs2zklvhgtlzrs6uuek6v5i

Molecular chaperones and selection against mutations

Katarzyna Tomala, Ryszard Korona
2008 Biology Direct  
This effect could not be linked to chaperone-mediated stabilization of mutated proteins.  ...  There are some examples that chaperones can alleviate the deleterious effects of mutations through increased assistance of destabilized proteins.  ...  We accept the opinion that molecular chaperones have a generally stabilizing effect on genetic networks and that mutations are more likely buffered when the net works are robust.  ... 
doi:10.1186/1745-6150-3-5 pmid:18298866 pmcid:PMC2267774 fatcat:434swvwjjfcbfeomj7tqxzixgy

Factors That Shape Eukaryotic tRNAomes: Processing, Modification and Anticodon–Codon Use

Richard Maraia, Aneeshkumar Arimbasseri
2017 Biomolecules  
) component of the genetic code.  ...  The genetics of tRNA function is relevant to health directly and as disease modifiers.  ...  of the genetic code.  ... 
doi:10.3390/biom7010026 pmid:28282871 pmcid:PMC5372738 fatcat:cqlgsstsozeynh2l6m735aiy6e

Exceptional error minimization in putative primordial genetic codes

Artem S Novozhilov, Eugene V Koonin
2009 Biology Direct  
codes are likely to have been nearly optimal with respect to the minimization of translation errors.  ...  The standard genetic code is redundant and has a highly non-random structure.  ...  Acknowledgements The authors' research is supported by intramural funds of the DHHS (NIH, National Library of Medicine).  ... 
doi:10.1186/1745-6150-4-44 pmid:19925661 pmcid:PMC2785773 fatcat:dm4mfodcpnhejpof444dsdkwny

The Contribution of Purifying Selection, Linkage, and Mutation Bias to the Negative Correlation between Gene Expression and Polymorphism Density in Yeast Populations

Agnieszka Marek, Katarzyna Tomala
2018 Genome Biology and Evolution  
We analyzed the DNA sequence of protein coding genes of 24 Saccharomyces cerevisiae and 58 Schizosaccharomyces pombe strains.  ...  Finally, we found that the impact of mutational bias was rather negligible.  ...  Thus, we show that in populations of both yeast species the decline in the genetic variation within extensively expressed genes was most likely produced by the purifying selection operating on gene protein  ... 
doi:10.1093/gbe/evy225 pmid:30321329 pmcid:PMC6250307 fatcat:sdfaxuyo2jdp3mhzestipitxta

Making Sense of "Nonsense" and More: Challenges and Opportunities in the Genetic Code Expansion, in the World of tRNA Modifications

Olubodun Michael Lateef, Michael Olawale Akintubosun, Olamide Tosin Olaoba, Sunday Ocholi Samson, Malgorzata Adamczyk
2022 International Journal of Molecular Sciences  
Genetic code extension offers the contingency of introducing more than one ncAA into protein through frameshift suppression, multi-site-specific incorporation of ncAAs, thereby increasing the vast number  ...  Genetic code expansion (GCE) explores beyond the natural translational processes to further enhance the structural properties and augment the functionality of a wide range of proteins.  ...  From the synthetic biology point of view, the canonical usage of genetic codes specifies amino acids with a limited number of functional groups, such as thiol ether, amides, and amines and alkyl and aryl  ... 
doi:10.3390/ijms23020938 pmid:35055121 pmcid:PMC8779196 fatcat:6nsy56nm55bhhjkeyegglqppny

Strategems in vitro for gene therapies directed to dominant mutations

S Millington-Ward
1997 Human Molecular Genetics  
ACKNOWLEDGEMENTS We would like to thank Drs W.Baehr and G.Travis for providing rhodopsin and peripherin cDNA clones.  ...  Polymorphism has been used extensively over the past decade to create genetic maps of the human genome.  ...  Degeneracy of the genetic code Human rhodopsin.  ... 
doi:10.1093/hmg/6.9.1415 pmid:9285777 fatcat:gjv4gf6fjzbjjafmeaqnlpnlkq
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