ABSTRACT
Peptide nucleic acid (PNA) modified with unnatural nucleobases enables the formation of a highly stable triplex with a double-stranded RNA at physiological pH. In this communication, we evaluated kinetics and thermodynamics of PNA/RNA triplex formation as a function of both pH and temperature. Protonation entropy was found to be the major factor responsible for the destabilization of the triplex and for the progressive decrease in the association rate at more basic pHs.
Subject(s)
Nucleic Acid Conformation , Peptide Nucleic Acids/chemistry , RNA, Double-Stranded/chemistry , Entropy , Hydrogen-Ion Concentration , Kinetics , ThermodynamicsABSTRACT
Correction for 'Triplex-forming peptide nucleic acid modified with 2-aminopyridine as a new tool for detection of A-to-I editing' by Chiara Annoni et al., Chem. Commun., 2016, 52, 7935-7938.
ABSTRACT
RNA editing from adenosine to inosine (A-to-I editing) is one of the mechanisms that regulate and diversify the transcriptome. Here, a triplex-forming peptide nucleic acid (PNA) modified with a 2-aminopyridine nucleobase was applied for the recognition of the A-to-I editing event in double-stranded RNAs. The triplex-forming PNA enabled sequence-specific detection of single nucleobase editing at sub-nanomolar concentration.
Subject(s)
Adenosine/analysis , Aminopyridines/chemistry , Inosine/analysis , Peptide Nucleic Acids/chemistry , Fluorescence , Hydrogen-Ion Concentration , Peptide Nucleic Acids/chemical synthesisABSTRACT
Hyperphosphorylation of the microtubule-associated protein tau is believed to play a crucial role in the neurofibrillary tangles formation in Alzheimer's disease brain. In this study, fibril formation of peptides containing the critical sequences for tau aggregation VQIINK and a plausible serine phosphorylation site of tau at its C-terminal was investigated. All the peptides formed fibrils with the typical cross-b structural core. However, stability of the fibrils was highly sensitive to the pH conditions for the phosphorylated VQIINK peptide, suggesting a regulatory role of phosphorylation for the amyloid-formation of tau.
Subject(s)
Microtubules/metabolism , Oligopeptides/metabolism , Peptides/metabolism , tau Proteins/metabolism , Amino Acid Sequence , Carrier Proteins/chemistry , Carrier Proteins/metabolism , Circular Dichroism , Humans , Hydrogen-Ion Concentration , Microscopy, Atomic Force , Microscopy, Electron, Transmission , Microtubules/chemistry , Neurofibrillary Tangles , Oligopeptides/chemistry , Peptides/chemical synthesis , Peptides/chemistry , Phosphorylation , Protein Binding , Protein Stability , Spectroscopy, Fourier Transform Infrared , Static Electricity , tau Proteins/chemistryABSTRACT
The Maf protein family belongs to the activator protein 1 (AP-1) superfamily of transcription factors that bind specific DNA target sequences through a basic region and exploit a leucine zipper (LZ) motif for protein-protein interactions leading to homo- or hetero-dimerization. Mafs unique DNA-binding domain contains a highly conserved extended homology region (EHR) that allows to recognize longer DNA sequences than other basic leucine zipper (bZIP) transcription factors. Inspired by the fact that overexpression of Mafs is observed in about 50% of cases of multiple myeloma, a hematological malignant disorder, we undertook a peptide inhibitor approach. The LZ domain of c-Maf, one of large Mafs, was produced by solid phase peptide synthesis. We characterized its secondary structure and dimerization properties, and found that dimerization and folding events are strictly coupled. Moreover, potential peptidic c-Maf dimerization inhibitors were computationally designed and synthesized. These compounds were demonstrated by circular dichroism (CD) spectroscopy and MALDI-TOF mass spectrometry to bind to c-Maf LZ monomers, to drive folding of their partially disordered structure and to efficiently compete with dimerization, suggesting a way for interfering with the function of c-Maf and, more generally, of intrinsically disordered proteins, till now considered undruggable targets.
ABSTRACT
Ratiometric fluorescent sensors were constructed from RNA aptamers by generating modular ribonucleopeptide complexes. Fluorescent ribonucleopeptides containing fluorophore seminaphthorhodafluor tethered to their peptide subunit revealed a dual emission property, which permitted a ratiometric fluorescent measurement of a substrate-binding event. The strategy successfully afforded ratiometric fluorescent sensors for biologically active small ligands, tetracycline, dopamine and streptomycin.
Subject(s)
Aptamers, Nucleotide/chemistry , Biosensing Techniques , Fluorescent Dyes/chemistry , Peptides/chemistry , Amino Acid Sequence , Benzopyrans/chemistry , Biosensing Techniques/methods , Dopamine/analysis , Molecular Sequence Data , Naphthols/chemistry , Rhodamines/chemistry , Spectrometry, Fluorescence/methods , Streptomycin/analysis , Tetracycline/analysisABSTRACT
An expedient chemical synthesis of a 75mer peptide corresponding to the DNA binding domain (DBD, 227-301) of the human MafA leucine zipper transcription factor is reported. The application of microwave-assisted solid phase peptide synthesis (MW-SPPS) with a protocol modified respect to the standard one allowed obtaining the desired 75mer peptide in a short time with high quantity and optimal purity. MW-SPPS methodology was thus demonstrated as a valuable alternative to recombinant methods to obtain protein domains. Considering that recent findings suggest an involvement of MafA in the pathogenesis of diabetes mellitus, we also performed circular dichroism studies both on DBD folding and its interaction with MafA recognition element (MARE) on insulin enhancer. From our results, it was evicted that a disorder to order transition occurs after DBD interaction with insulin MARE which is mediated by specific structural elements on the N-terminus of the DBD.
