scholarly journals Isonitrile-Derivatized Indole as an Infrared Probe for Hydrogen-Bonding Environments

Molecules ◽  
2019 ◽  
Vol 24 (7) ◽  
pp. 1379 ◽  
Author(s):  
Min You ◽  
Liang Zhou ◽  
Xinyue Huang ◽  
Yang Wang ◽  
Wenkai Zhang
Keyword(s):  
Hydrogen Bond ◽  
Indole Ring ◽  
Hydrogen Bond Donor ◽  
Model Compounds ◽  
Pump Probe ◽  
Site Specific ◽  
Structure And Dynamics ◽  
Protic Solvents ◽  
Local Environments ◽  
A Site

The isonitrile (NC) group has been shown to be a promising infrared probe for studying the structure and dynamics of biomolecules. However, there have been no systematic studies performed on the NC group as an infrared probe, when it is bonded to an indole ring. Here, we systematically study the NC stretching mode of two model compounds, 5-isocyano-1H-indole (5ICI) and 5-isocyano-1-methyl-1H-indole (NM5ICI), using Fourier transform infrared (FTIR) spectroscopy. The NC stretching frequency is shown to be strongly dependent on the polarizability of protic solvents and the density of hydrogen-bond donor groups in the solvent when NC is bonded to an indole ring. Infrared pump–probe studies of 5ICI in DMSO and in EtOH further support that the NC stretching mode could be used as a site-specific infrared probe for local environments when NC is bonded to an indole ring.

scholarly journals 4-Cyanoindole-2′-deoxyribonucleoside as a Dual Fluorescence and Infrared Probe of DNA Structure and Dynamics

Molecules ◽  
2019 ◽  
Vol 24 (3) ◽  
pp. 602 ◽  
Author(s):  
Ismail A. Ahmed ◽  
Arusha Acharyya ◽  
Christina M. Eng ◽  
Jeffrey M. Rodgers ◽  
William F. DeGrado ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Rna Structure ◽  
High Throughput Screening ◽  
Local Environment ◽  
Spectroscopic Properties ◽  
Site Specific ◽  
Structure And Dynamics ◽  
High Fluorescence ◽  
Fluorescence Quencher ◽  
A Site

Unnatural nucleosides possessing unique spectroscopic properties that mimic natural nucleobases in both size and chemical structure are ideally suited for spectroscopic measurements of DNA/RNA structure and dynamics in a site-specific manner. However, such unnatural nucleosides are scarce, which prompts us to explore the utility of a recently found unnatural nucleoside, 4-cyanoindole-2′-deoxyribonucleoside (4CNI-NS), as a site-specific spectroscopic probe of DNA. A recent study revealed that 4CNI-NS is a universal nucleobase that maintains the high fluorescence quantum yield of 4-cyanoindole and that among the four natural nucleobases, only guanine can significantly quench its fluorescence. Herein, we further show that the C≡N stretching frequency of 4CNI-NS is sensitive to the local environment, making it a useful site-specific infrared probe of oligonucleotides. In addition, we demonstrate that the fluorescence-quencher pair formed by 4CNI-NS and guanine can be used to quantitatively assess the binding affinity of a single-stranded DNA to the protein system of interest via fluorescence spectroscopy, among other applications. We believe that this fluorescence binding assay is especially useful as its potentiality allows high-throughput screening of DNA–protein interactions.

scholarly journals Investigating the role of a backbone to substrate hydrogen bond in OMP decarboxylase using a site-specific amide to ester substitution

2014 ◽  
Vol 111 (42) ◽  
pp. 15066-15071 ◽  
Author(s):  
Bijoy J. Desai ◽  
Yuki Goto ◽  
Alessandro Cembran ◽  
Alexander A. Fedorov ◽  
Steven C. Almo ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Site Specific ◽  
A Site

Anion effect on alkali ion-crown complex formation in a moderately concentrated solutions: A sensitive probe of hidden interionic interactions operating in dissociating protic solvents

1990 ◽  
Vol 55 (5) ◽  
pp. 1149-1161
Author(s):  
Jiří Závada ◽  
Václav Pechanec ◽  
Oldřich Kocián
Keyword(s):  
Hydrogen Bond ◽  
Complex Formation ◽  
Charge Density ◽  
Macrocyclic Ligand ◽  
Simple Explanation ◽  
Anion Effect ◽  
Protic Solvents ◽  
The Individual ◽  
Alkali Salts ◽  
Alkali Ion

A powerful anion effect destabilizing alkali ion-crown complex formation has been found to operate in moderately concentrated protic (H2O, CH3OH, C2H5OH) solution, following the order HO- > AcO- > Cl- > Br- > NO3- > I- > NCS-. Evidence is provided that the observed effect does not originate from ion-pairing. A simple explanation is provided in terms of concordant hydrogen bond bridges of exalted stability between the gegenions, M+···OR-H···(OR-H)n···OR-H···A-. It is proposed that encapsulation of alkali ion by the macrocyclic ligand leads to a dissipation of the cation charge density destroying its ability to participate in the hydrogen bond bridge. An opposition against the alkali ion-crown complex formation arises accordingly in the solution in dependence on strength of the hydrogen bridge; for a given cation, the hydrogen bond strength increases with increasing anion charge density from NCS- to HO-(RO-). It is pointed out, at the same time, that the observed anion effect does not correlate with the known values of activity coefficients of the individual alkali salts which are almost insensitive to anion variation under the investigated conditions. As a resolution of the apparent paradoxon it is proposed that, in absence of the macrocyclic ligand, the stabilizing (concordant) bonding between the gegenions is nearly balanced by a destabilizing (discordant) hydrogen bonding between the ions of same charge (co-ions). Intrinsic differences among the individual salts are thus submerged in protic solvents and become apparent only when the concordant bonding is suppressed in the alkali ion-crown complex formation.

scholarly journals Functional expression of a yeast mitochondrial intron-encoded protein requires RNA processing at a conserved dodecamer sequence at the 3' end of the gene.

1989 ◽  
Vol 9 (4) ◽  
pp. 1507-1512 ◽  
Author(s):  
H Zhu ◽  
H Conrad-Webb ◽  
X S Liao ◽  
P S Perlman ◽  
R A Butow
Keyword(s):  
Genetic Analysis ◽  
Rna Processing ◽  
Fold Increase ◽  
Functional Expression ◽  
Rrna Gene ◽  
Yeast Mitochondria ◽  
Wild Type ◽  
Site Specific ◽  
Var1 Gene ◽  
A Site

All mRNAs of yeast mitochondria are processed at their 3' ends within a conserved dodecamer sequence, 5'-AAUAAUAUUCUU-3'. A dominant nuclear suppressor, SUV3-I, was previously isolated because it suppresses a dodecamer deletion at the 3' end of the var1 gene. We have tested the effects of SUV3-1 on a mutant containing two adjacent transversions within a dodecamer at the 3' end of fit1, a gene located within the 1,143-base-pair intron of the 21S rRNA gene, whose product is a site-specific endonuclease required in crosses for the quantitative transmission of that intron to 21S alleles that lack it. The fit1 dodecamer mutations blocked both intron transmission and dodecamer cleavage, neither of which was suppressed by SUV3-1 when present in heterozygous or homozygous configurations. Unexpectedly, we found that SUV3-1 completely blocked cleavage of the wild-type fit1 dodecamer and, in SUV3-1 homozygous crosses, intron conversion. In addition, SUV3-1 resulted in at least a 40-fold increase in the amount of excised intron accumulated. Genetic analysis showed that these phenotypes resulted from the same mutation. We conclude that cleavage of a wild-type dodecamer sequence at the 3' end of the fit1 gene is essential for fit1 expression.

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