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.

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.

The reduction of doxorubicin at a mercury electrode and monitoring its interaction with DNA using constant current chronopotentiometry

2009 ◽  
Vol 74 (11-12) ◽  
pp. 1727-1738 ◽  
Author(s):  
Jan Vacek ◽  
Luděk Havran ◽  
Miroslav Fojta
Keyword(s):  
Double Helix ◽  
Mercury Electrode ◽  
Electrode Reaction ◽  
Ex Situ ◽  
Constant Current ◽  
Adsorbed State ◽  
Electrode Processes ◽  
Dna Double Helix ◽  
First Time

In this report, voltammetry with linear scan and chronopotentiometric stripping (CPS) with constant current were used for the analysis of doxorubicin (DOX) at a hanging mercury drop electrode (HMDE). CPS was used for the study of DOX in situ electrochemical reduction in adsorbed state and for ex situ (adsorptive transfer) analysis of the drug. For the first time, CPS was used to study the reversible reduction of the DOX quinine moiety at –0.45 V (vs Ag|AgCl|3 M KCl) as well as electrode processes giving rise to an irreversible signal around –1.45 V at the HMDE in 0.2 M acetate or Britton–Robinson buffers at different pH values. The dependence of the latter signal on pH revealed involvement of protonation equilibria; however, neither CV nor CPS data confirmed the catalytic character of the electrode reaction previously suggested by other authors. The CPS method was also applied to monitor the DOX interaction with double- (ds) and single-stranded (ss) DNA. In the presence of dsDNA, more pronounced changes in DOX signal intensity were observed, in agreement with a strong intercalation of the DOX redox centre into the DNA double helix.

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

Comparison of the Global Genomic and Transcription-Coupled Repair Rates of Different Lesions in Human Cells

2004 ◽  
Vol 59 (5-6) ◽  
pp. 445-453 ◽  
Author(s):  
Boyko Atanassov ◽  
Aneliya Velkova ◽  
Emil Mladenov ◽  
Boyka Anachkova ◽  
George Russev
Keyword(s):  
Dna Sequences ◽  
Chemical Nature ◽  
Excision Repair ◽  
Uv Light ◽  
Double Helix ◽  
Human Cells ◽  
The Other ◽  
Specific Sequence ◽  
Dna Double Helix ◽  
Transcription Coupled Repair

There are two subclasses of nucleotide excision repair (NER). One is the global genomic repair (GGR) which removes lesions throughout the genome regardless of whether any specific sequence is transcribed or not. The other is the transcription-coupled repair (TCR), which removes lesions only from the transcribed DNA sequences. There are data that GGR rates depend on the chemical nature of the lesions in a manner that the lesions inflicting larger distortion on the DNA double helix are repaired at higher rate. It is not known whether the TCR repair rates depend on the type of lesions and in what way. To address this question human cells were transfected with pEGFP and pEYFP plasmids treated with UV light, cis-diamminedichloroplatinum(II) (cisplatin) and angelicin and 24 h later the restored fluorescence was measured and used to calculate the respective NER rates. In a parallel series of experiments the same plasmids were incubated in repair-competent protein extracts to determine GGR rates in the absence of transcription. From the two sets of data, the TCR rates were calculated. We found out that cisplatin, UV light and angelicin lesions were repaired by GGR with different efficiency, which corresponded to the degree of DNA helix distortion induced by these agents. On the other hand the three lesions were repaired by TCR at very similar rates which showed that TCR efficiency was not directly connected with the chemical nature of the lesions.

scholarly journals Ionic strength modulates HU protein-induced DNA supercoiling

2021 ◽  
Author(s):  
Alexander Zhang ◽  
Yan Yan ◽  
Fenfei Leng ◽  
David Dunlap ◽  
Laura Finzi
Keyword(s):  
Single Molecule ◽  
Structural Changes ◽  
Magnetic Measurements ◽  
Double Helix ◽  
Bacterial Genome ◽  
Dna Supercoiling ◽  
Coli Strain ◽  
Dna Unwinding ◽  
Dna Compaction ◽  
Dna Double Helix

The histone-like protein from E. coli strain U93 (HU) is an abundant nucleoid-associated protein that contributes to the compaction of the bacterial genome as well as to the regulation of many of its transactions. Despite many years of investigations, the way and extent to which HU binding alters the DNA double helix and/or generates hierarchical structures using DNA as a scaffold is not completely understood. Here we combined single-molecule magnetic measurements with circular dichroism studies to monitor structural changes in the DNA-HU fiber as HU concentration was increased from 0 to 1000 nM under low and physiological monovalent salt conditions. We confirmed that DNA compaction correlated with HU concentration in a biphasic manner but DNA unwinding varied monotonically with HU concentration in 100 mM KCl. Instead, in more physiological 200 mM salt conditions, DNA compaction was monotonic while HU-induced DNA unwinding was negligible. Differential compaction and unwinding of DNA may be part of the response of bacteria to large variations in salt concentrations.

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.

Single Amino Acid Based Self-Assemblies of Cysteine and Methionine

2018 ◽  
Author(s):  
Nidhi Gour ◽  
Bharti Koshti ◽  
Chandra Kanth P. ◽  
Dhruvi Shah ◽  
Vivek Shinh Kshatriya ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Self Assembly ◽  
Aromatic Amino Acids ◽  
Neutral Condition ◽  
Single Amino Acid ◽  
Binding Assays ◽  
Human Neuroblastoma ◽  
Cytotoxicity Assays ◽  
First Time

We report for the very first time self-assembly of Cysteine and Methionine to discrenible strucutres under neutral condition. To get insights into the structure formation, thioflavin T and Congo red binding assays were done which revealed that aggregates may not have amyloid like characteristics. The nature of interactions which lead to such self-assemblies was purported by coincubating assemblies in urea and mercaptoethanol. Further interaction of aggregates with short amyloidogenic dipeptide diphenylalanine (FF) was assessed. While cysteine aggregates completely disrupted FF fibres, methionine albeit triggered fibrillation. The cytotoxicity assays of cysteine and methionine structures were performed on Human Neuroblastoma IMR-32 cells which suggested that aggregates are not cytotoxic in nature and thus, may not have amyloid like etiology. The results presented in the manuscript are striking, since to the best of our knowledge,this is the first report which demonstrates that even non-aromatic amino acids (cysteine and methionine) can undergo spontaneous self-assembly to form ordered aggregates.

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