scholarly journals Naphthalene diimide–amino acid conjugates as novel fluorimetric and CD probes for differentiation between ds-DNA and ds-RNA

2020 ◽  
Vol 16 ◽  
pp. 2032-2045
Author(s):  
Annike Weißenstein ◽  
Myroslav O Vysotsky ◽  
Ivo Piantanida ◽  
Frank Würthner
Keyword(s):  
Amino Acid ◽  
Unnatural Amino Acids ◽  
Rna Binding ◽  
Visible Range ◽  
Induced Circular Dichroism ◽  
Naphthalene Diimide ◽  
Threading Intercalation ◽  
The Difference ◽  
Stokes Shifts ◽  
Acid Unit

Two novel unnatural amino acids, prepared by linking a dicationic purple-coloured and fluorescent naphthalene diimide (NDI) at core position to amino acid side chains of variable length, strongly interacted with ds-DNA/RNA by threading intercalation. Different from a reference NDI dye with identical visible range absorbance (520–540 nm) and Stokes shifts in emission (+60 nm, quantum yield > 0.2), only these amino acid–NDI conjugates showed selective fluorimetric response for GC-DNA in respect to AT(U)-polynucleotides. The DNA/RNA binding-induced circular dichroism (ICD) response of NDI at 450–550 nm strongly depended on the length and rigidity of the linker to the amino acid unit, which controls the orientation of the NDI unit inside within the intercalative binding site. The ICD selectivity also depends on the type of polynucleotide, thus the studied NDI dyes act as dual fluorimetric/ICD probes for sensing the difference between here used GC-DNA, AT-DNA and AU-RNA.

scholarly journals Transferability of N-terminal mutations of pyrrolysyl-tRNA synthetase in one species to that in another species on unnatural amino acid incorporation efficiency

Amino Acids ◽  
2020 ◽  
Author(s):  
Thomas L. Williams ◽  
Debra J. Iskandar ◽  
Alexander R. Nödling ◽  
Yurong Tan ◽  
Louis Y. P. Luk ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Genetic Code ◽  
Unnatural Amino Acids ◽  
Trna Synthetase ◽  
Unnatural Amino Acid ◽  
Amino Acid Incorporation ◽  
Acid Incorporation ◽  
Genetic Code Expansion ◽  
Incorporation Efficiency

AbstractGenetic code expansion is a powerful technique for site-specific incorporation of an unnatural amino acid into a protein of interest. This technique relies on an orthogonal aminoacyl-tRNA synthetase/tRNA pair and has enabled incorporation of over 100 different unnatural amino acids into ribosomally synthesized proteins in cells. Pyrrolysyl-tRNA synthetase (PylRS) and its cognate tRNA from Methanosarcina species are arguably the most widely used orthogonal pair. Here, we investigated whether beneficial effect in unnatural amino acid incorporation caused by N-terminal mutations in PylRS of one species is transferable to PylRS of another species. It was shown that conserved mutations on the N-terminal domain of MmPylRS improved the unnatural amino acid incorporation efficiency up to five folds. As MbPylRS shares high sequence identity to MmPylRS, and the two homologs are often used interchangeably, we examined incorporation of five unnatural amino acids by four MbPylRS variants at two temperatures. Our results indicate that the beneficial N-terminal mutations in MmPylRS did not improve unnatural amino acid incorporation efficiency by MbPylRS. Knowledge from this work contributes to our understanding of PylRS homologs which are needed to improve the technique of genetic code expansion in the future.

scholarly journals Data mining of coronavirus: SARS-CoV-2, SARS-CoV and MERS-CoV

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Jung Eun Huh ◽  
Seunghee Han ◽  
Taeseon Yoon
Keyword(s):  
Machine Learning ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Decision Tree ◽  
Machine Learning Algorithms ◽  
High Similarity ◽  
Incubation Periods ◽  
Initial Question ◽  
The Difference ◽  
Blast Program

Abstract Objective In this study we compare the amino acid and codon sequence of SARS-CoV-2, SARS-CoV and MERS-CoV using different statistics programs to understand their characteristics. Specifically, we are interested in how differences in the amino acid and codon sequence can lead to different incubation periods and outbreak periods. Our initial question was to compare SARS-CoV-2 to different viruses in the coronavirus family using BLAST program of NCBI and machine learning algorithms. Results The result of experiments using BLAST, Apriori and Decision Tree has shown that SARS-CoV-2 had high similarity with SARS-CoV while having comparably low similarity with MERS-CoV. We decided to compare the codons of SARS-CoV-2 and MERS-CoV to see the difference. Though the viruses are very alike according to BLAST and Apriori experiments, SVM proved that they can be effectively classified using non-linear kernels. Decision Tree experiment proved several remarkable properties of SARS-CoV-2 amino acid sequence that cannot be found in MERS-CoV amino acid sequence. The consequential purpose of this paper is to minimize the damage on humanity from SARS-CoV-2. Hence, further studies can be focused on the comparison of SARS-CoV-2 virus with other viruses that also can be transmitted during latent periods.

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.

scholarly journals Redox-sensitive reversible self-assembly of amino acid–naphthalene diimide conjugates

2017 ◽  
Vol 7 (6) ◽  
pp. 20160099 ◽  
Author(s):  
Wathsala Liyanage ◽  
Paul W. Rubeo ◽  
Bradley L. Nilsson
Keyword(s):  
Amino Acid ◽  
Self Assembly ◽  
Functional Materials ◽  
Supramolecular Materials ◽  
Responsive Materials ◽  
Naphthalene Diimide ◽  
Reducing Conditions ◽  
Aqueous Solvent ◽  
Stimulus Responsive ◽  
Fibril Aggregates

Peptide and low molecular weight amino acid-based materials that self-assemble in response to environmental triggers are highly desirable candidates in forming functional materials with tunable biophysical properties. In this paper, we explore redox-sensitive self-assembly of cationic phenylalanine derivatives conjugated to naphthalene diimide (NDI). Self-assembly of the cationic Phe-NDI conjugates into nanofibrils was induced in aqueous solvent at high ionic strength. Under reducing conditions, these self-assembled Phe-NDI conjugate fibrils underwent a morphological change to non-fibril aggregates. Upon reoxidation, the initially observed fibrils were reformed. The study herein provides an interesting strategy to effect reversible switching of the structure of supramolecular materials that can be applied to the development of sophisticated stimulus-responsive materials.

Single amino acid substitution of rat MRP2 results in acquired transport activity for taurocholate

2001 ◽  
Vol 281 (4) ◽  
pp. G1034-G1043 ◽  
Author(s):  
Kousei Ito ◽  
Hiroshi Suzuki ◽  
Yuichi Sugiyama
Keyword(s):  
Amino Acids ◽  
Multidrug Resistance ◽  
Amino Acid ◽  
Membrane Vesicles ◽  
Single Amino Acid ◽  
Sf9 Cells ◽  
Transport Activity ◽  
Wild Type ◽  
Cationic Amino Acids ◽  
The Difference

Multidrug resistance-associated protein 3 (MRP3), unlike other MRPs, transports taurocholate (TC). The difference in TC transport activity between rat MRP2 and MRP3 was studied, focusing on the cationic amino acids in the transmembrane domains. For analysis, transport into membrane vesicles from Sf9 cells expressing wild-type and mutated MRP2 was examined. Substitution of Arg at position 586 with Leu and Ile and substitution of Arg at position 1096 with Lys, Leu, and Met resulted in the acquisition of TC transport activity, while retaining transport activity for glutathione and glucuronide conjugates. Substitution of Leu at position 1084 of rat MRP3 (which corresponds to Arg-1096 in rat MRP2) with Lys, but not with Val or Met, resulted in the loss of transport activity for TC and glucuronide conjugates. These results suggest that the presence of the cationic charge at Arg-586 and Arg-1096 in rat MRP2 prevents the transport of TC, whereas the presence of neutral amino acids at the corresponding position of rat MRP3 is required for the transport of substrates.

Influence of Blood Group and Secretor Status on Carbohydrate Structures in Human Gastric Mucins: Implications for Peptic Ulcer

1995 ◽  
Vol 89 (4) ◽  
pp. 405-415 ◽  
Author(s):  
R. L. Sidebotham ◽  
J. H. Baron ◽  
J. Schrager ◽  
J. Spencer ◽  
J. R. Clamp ◽  
...  
Keyword(s):  
Peptic Ulcer ◽  
Amino Acid ◽  
Blood Group ◽  
Average Length ◽  
Amino Acid Residues ◽  
Secretor Status ◽  
Increased Risk ◽  
The Mean ◽  
The Difference ◽  
Carbohydrate Chains

1. The content and distribution of carbohydrate was examined in mucus glycopolypeptides from human antral mucosae. 2. The mean amount of carbohydrate per 1000 amino acid residues was found to be similar in glycopolypeptides with A, B or H activity. It was slightly, though significantly, less in glycopolypeptides lacking these determinants, because carbohydrate chains were of a shorter average length than in the A-, B- or H-active preparations. This difference was reflected in the sizes of oligosaccharide—alcohols released from representative glycopolypeptides with alkaline borohydride. 3. Differences between A-, B- or H-active and non-secretor glycopolypeptides in terms of the mean number of carbohydrate chains per 1000 amino acid residues were found to be small, and without significance. 4. The average number of peripheral monosaccharide units per 1000 amino acid residues was greater in A-active than in H-active, and least in non-secretor, glycopolypeptides. This order was reversed for monosaccharide units incorporated into skeletal (core plus backbone) structures. The difference in each case was statistically significant. 5. These findings suggest that the increased risk of peptic ulcer associated with blood group O and non-secretor status is unlikely to be attributable to an inherent deficiency in the protective mucus layer, linked to differences between mucins that are associated with A, B or H activity. Other hypotheses linked to infection with Helicobacter pylori are examined.

scholarly journals Phenylalanine requirement in children with classical PKU determined by indicator amino acid oxidation

2002 ◽  
Vol 283 (6) ◽  
pp. E1249-E1256 ◽  
Author(s):  
Glenda Courtney-Martin ◽  
Rachelle Bross ◽  
Mahroukh Raffi ◽  
Joe T. R. Clarke ◽  
Ronald O. Ball ◽  
...  
Keyword(s):  
Amino Acid ◽  
Acid Oxidation ◽  
Phenylalanine Concentration ◽  
Two Phase ◽  
Amino Acid Oxidation ◽  
Blood Phenylalanine ◽  
Plasma Phenylalanine ◽  
Crossover Analysis ◽  
The Mean ◽  
The Difference

Dietary restriction of phenylalanine is the main treatment for phenylketonuria (PKU), and current estimates of requirements are based on plasma phenylalanine concentration and growth. The present study aimed to determine more precisely the phenylalanine requirements in patients with the disease by use of indicator amino acid oxidation, withl-[1-13C]lysine as the indicator. Breath13CO2 production (F13 co 2) was used as the end point. Finger-prick blood samples were also collected for measurement of phenylalanine to relate phenylalanine intake to blood phenylalanine levels. The mean phenylalanine requirement, estimated using a two-phase linear regression crossover analysis, was 14 mg · kg−1 · day−1, and the safe population intake (upper 95% confidence interval of the mean) was found to be 19.5 mg · kg−1 · day−1. A balance between phenylalanine intake and the difference between fed and fasted blood phenylalanine concentration was observed at an intake of 20 mg · kg−1 · day−1. The similarity between these two values (19.5 and 20 mg · kg−1 · day−1) suggests that the maximal phenylalanine intake for children with PKU should be no higher than 20 mg · kg−1 · day−1.

scholarly journals DIGITAL IMAGE ANALYSIS OF THE VISIBLE REGION THROUGH SIMULATION OF ROCK ART PAINTINGS

2016 ◽  
Author(s):  
Berta Carrión-Ruiz ◽  
Silvia Blanco-Pons ◽  
Jose Luis Lerma
Keyword(s):  
Rock Art ◽  
Visible Region ◽  
Visible Spectrum ◽  
Principal Component ◽  
Optical Filters ◽  
Visible Range ◽  
Redundant Data ◽  
The Difference ◽  
Entire Visible Spectrum ◽  
New Research

Non-destructive rock art recording techniques are getting special attention in the last years, opening new research lines in order to improve the level of documentation and understanding of our rich legacy. This paper applies the principal component analysis (PCA) technique in images that include wavelengths between 400-700 nm (visible  range). Our approach is focused on determining the difference provided by the image processing of the visible region through four spectral images versus an image that encompasses the entire visible spectrum. The images were taken by means of optical filters that take specific wavelengths and exclude parts of the spectrum. Simulation of rock art is prepared in laboratory. For this purpose, three different pigments were made simulating the material composition of rock art paintings. The advantages of studying the visible spectrum in separate images are analysed. In addition, PCA is applied to each of the images to reduce redundant data. Finally, PCA is applied to the image that contains the entire visible spectrum and is compared with previous results. Through the results of the four visible spectral images one can begin to draw conclusions about constituent painting materials without using decorrelation techniques.

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