scholarly journals Single-Frame, Multiple-Frame and Framing Motifs in Genes

Life ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 18 ◽  
Author(s):  
Christian J. Michel
Keyword(s):  
Amino Acids ◽  
Early Life ◽  
Double Helix ◽  
Research Field ◽  
Reading Frame ◽  
Single Frame ◽  
The Origin Of Life ◽  
Multiple Frame ◽  
Dna Double Helix ◽  
Circular Code

We study the distribution of new classes of motifs in genes, a research field that has not been investigated to date. A single-frame motif SF has no trinucleotide in reading frame (frame 0) that occurs in a shifted frame (frame 1 or 2), e.g., the dicodon AAACAA is SF as the trinucleotides AAA and CAA do not occur in a shifted frame. A motif which is not single-frame SF is multiple-frame MF. Several classes of MF motifs are defined and analysed. The distributions of single-frame SF motifs (associated with an unambiguous trinucleotide decoding in the two 5'–3' and 3'–5' directions) and 5′ unambiguous motifs 5'U (associated with an unambiguous trinucleotide decoding in the 5'–3' direction only) are analysed without and with constraints. The constraints studied are: initiation and stop codons, periodic codons AAA,CCC,GGG,TTT, antiparallel complementarity and parallel complementarity. Taken together, these results suggest that the complementarity property involved in the antiparallel (DNA double helix, RNA stem) and parallel sequences could also be fundamental for coding genes with an unambiguous trinucleotide decoding in the two 5'–3' and 3'–5' directions or the 5'–3' direction only. Furthermore, the single-frame motifs SF with a property of trinucleotide decoding and the framing motifs F (also called circular code motifs; first introduced by Michel (2012)) with a property of reading frame decoding may have been involved in the early life genes to build the modern genetic code and the extant genes. They could have been involved in the stage without anticodon-amino acid interactions or in the Implicated Site Nucleotides (ISN) of RNA interacting with the amino acids. Finally, the SF and MF dipeptides associated with the SF and MF dicodons, respectively, are studied and their importance for biology and the origin of life discussed.

scholarly journals Bases alternatives et organismes synthétiques

2018 ◽  
Vol 34 (2) ◽  
pp. 179-182 ◽  
Author(s):  
Bertrand Jordan
Keyword(s):  
Amino Acids ◽  
Unnatural Amino Acids ◽  
Double Helix ◽  
Dna Double Helix

Alternative bases that can fit into the DNA double helix have now been used in vivo to direct the synthesis of proteins incorporating unnatural amino acids. This bioengineering feat is significant at both the conceptual and the practical levels

Life as a Machine

2020 ◽  
pp. 209-233
Author(s):  
John Parrington
Keyword(s):  
Amino Acids ◽  
Hot Springs ◽  
Double Helix ◽  
Bacterial Genome ◽  
Letter Pair ◽  
Human Beings ◽  
Specific Sequence ◽  
Dna Double Helix ◽  
First Time ◽  
Yeast Genomes

Bacteria are a source of many of the tools used in biotechnology. A technique called the polymerase chain reaction, or PCR, made it possible for the first time to amplify tiny starting amounts of DNA and has revolutionised medical diagnosis, testing of IVF embryos for mutations, and forensic science. PCR involves the repeated generation of DNA from a starting sequence in a cycle, one stage of which occurs at boiling point. Because of this PCR uses a DNA polymerase enzyme purified from an ‘extremophile’ bacterium that lives in hot springs. More recently scientists have constructed artificial bacterial or yeast genomes from scratch. The next step will be to create reconfigured bacteria and yeast with enhanced characteristics for use in agriculture, energy production, or generation of new materials. Some scientists are now seeking to expand the genetic code itself. The DNA code that human beings share with all other species on the planet has four ‘letters’, A, C, G, and T, which pair as A:T and C:G to join the two strands of the DNA double helix. And each particular triplet of DNA letters, for instance CGA, or TGC, codes for a specific amino acid, the 20 different amino acids joining together in a specific sequence to make up a particular protein. Scientists have now developed a new DNA letter pair, X:Y. By introducing this into an artificial bacterial genome, it is becoming possible to create many more amino acids than the current 20 naturally occurring ones, and thereby allowing many new types of proteins.

Protamine-DNA interaction

1978 ◽  
Vol 36 (2) ◽  
pp. 200-201
Author(s):  
D.P. Bazett-Jones ◽  
F.P. Ottensmeyer
Keyword(s):  
Small Volume ◽  
Double Helix ◽  
Dna Interaction ◽  
Dark Field ◽  
Sperm Head ◽  
Nuclear Proteins ◽  
Field Electron Microscopy ◽  
Dark Field Electron ◽  
Dna Double Helix ◽  
Positively Charged

Dark field electron microscopy has been used for the study of the structure of individual macromolecules with a resolution to at least the 5Å level. The use of this technique has been extended to the investigation of structure of interacting molecules, particularly the interaction between DNA and fish protamine, a class of basic nuclear proteins of molecular weight 4,000 daltons.Protamine, which is synthesized during spermatogenesis, binds to chromatin, displaces the somatic histones and wraps up the DNA to fit into the small volume of the sperm head. It has been proposed that protamine, existing as an extended polypeptide, winds around the minor groove of the DNA double helix, with protamine's positively-charged arginines lining up with the negatively-charged phosphates of DNA. However, viewing protamine as an extended protein is inconsistent with the results obtained in our laboratory.

scholarly journals Formation of Thiophene under Simulated Volcanic Hydrothermal Conditions on Earth—Implications for Early Life on Extraterrestrial Planets?

Life ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 149
Author(s):  
Thomas Geisberger ◽  
Jessica Sobotta ◽  
Wolfgang Eisenreich ◽  
Claudia Huber
Keyword(s):  
Fatty Acids ◽  
Hydrogen Sulfide ◽  
Early Life ◽  
Organic Molecules ◽  
Metal Sulfides ◽  
Early Earth ◽  
Hydrothermal Conditions ◽  
Evolution Of Metabolism ◽  
Thiophene Derivatives ◽  
The Origin Of Life

Thiophene was detected on Mars during the Curiosity mission in 2018. The compound was even suggested as a biomarker due to its possible origin from diagenesis or pyrolysis of biological material. In the laboratory, thiophene can be synthesized at 400 °C by reacting acetylene and hydrogen sulfide on alumina. We here show that thiophene and thiophene derivatives are also formed abiotically from acetylene and transition metal sulfides such as NiS, CoS and FeS under simulated volcanic, hydrothermal conditions on Early Earth. Exactly the same conditions were reported earlier to have yielded a plethora of organic molecules including fatty acids and other components of extant metabolism. It is therefore tempting to suggest that thiophenes from abiotic formation could indicate sites and conditions well-suited for the evolution of metabolism and potentially for the origin-of-life on extraterrestrial planets.

scholarly journals Sequence and structure of mtr, an amino acid transport gene of Neurospora crassa

Genome ◽  
1991 ◽  
Vol 34 (4) ◽  
pp. 644-651 ◽  
Author(s):  
Kenneth Koo ◽  
W. Dorsey Stuart
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Neurospora Crassa ◽  
Rna Binding ◽  
Signal Sequence ◽  
Average Length ◽  
Open Reading Frame ◽  
Mrna Transcript ◽  
S1 Nuclease ◽  
Reading Frame

The gene product of the mtr locus of Neurospora crassa is required for the transport of neutral aliphatic and aromatic amino acids via the N system. We have previously cloned three cosmids containing Neurospora DNA that complement the mtr-6(r) mutant allele. The cloned DNAs were tightly linked to restriction fragment length polymorphisms that flank the mtr locus. A 2.9-kbp fragment from one cosmid was subcloned and found to complement the mtr-6(r) allele. Here we report the sequence of the fragment that hybridized to a poly(A)+ mRNA transcript of about 2300 nucleotides. We have identified an 845-bp open reading frame (ORF) having a 59-bp intron as the potential mtr ORF. S1 nuclease analysis of the transcript confirmed the transcript size and the presence of the intron. A second open reading frame was found upstream in the same reading frame as the mtr ORF and appears to be present in the mRNA transcript. The mtr ORF is predicted to encode a 261 amino acid polypeptide with a molecular mass of 28 613 Da. The proposed polypeptide exhibits six potential α-helical transmembrane domains with an average length of 23 amino acids, does not have a signal sequence, and contains amino acid sequence homologous to an RNA binding motif.Key words: sequence, membranes, ribonucleoprotein.

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