Year-end Sale % OFF 
Abstract
Radiotherapy, the most common therapy for the treatment of solid tumors, exerts its effects by inducing DNA damage. To fully understand the extent and nature of this damage, DNA models that mimic the in vivo situation should be utilized. In a cellular context, genomic DNA constantly interacts with proteins and these interactions could influence both the primary radical processes (triggered by ionizing radiation) and secondary reactions, ultimately leading to DNA damage. However, this is seldom addressed in the literature. In this work, we propose a general approach to tackle these shortcomings. We synthesized a protein-DNA complex that more closely represents DNA in the physiological environment than oligonucleotides solution itself, while being sufficiently simple to permit further chemical analyses. Using click chemistry, we obtained an oligonucleotide-peptide conjugate, which, if annealed with the complementary oligonucleotide strand, forms a complex that mimics the specific interactions between the GCN4 protein and DNA. The covalent bond connecting the oligonucleotide and peptide constitutes a part of substituted triazole, which forms due to the click reaction between the short peptide corresponding to the specific amino acid sequence of GCN4 protein (yeast transcription factor) and a DNA fragment that is recognized by the protein. DNAse footprinting demonstrated that the part of the DNA fragment that specifically interacts with the peptide in the complex is protected from DNAse activity. Moreover, the thermodynamic characteristics obtained using differential scanning calorimetry (DSC) are consistent with the interaction energies calculated at the level of metadynamics. Thus, we present an efficient approach to generate a well-defined DNA-peptide conjugate that mimics a real DNA-peptide complex. These complexes can be used to investigate DNA damage under conditions very similar to those present in the cell.
Highlights
The radio- and photodegradation of DNA is typically studied using simple molecular models such as nucleobases, nucleotides or short fragments of single- or double-stranded DNA [1]
Most of the specific interactions are mediated by α-helix domains [24]
Three major protein domains interact with DNA: α-helices, β-sheets or a mixture of the well-known proteins belonging to this family is GCN4, a eukaryotic transcriptional activator that both structures (α/β)
Summary
The radio- and photodegradation of DNA is typically studied using simple molecular models such as nucleobases, nucleotides or short fragments of single- or double-stranded DNA (ssDNA or dsDNA) [1]. In vivo, genomic DNA interacts with a large number of proteins that are responsible for various processes in living organisms [2,3]. Contacts between amino acids and nucleobases represent a minority (in respect to interaction with backbone) of the total number of DNA-protein interactions but are critical factors for DNA sequence recognition. The most abundant of these interactions are between guanine bases and arginine/lysine residues, which are present almost in all classes of proteins that interact with DNA [5,6,7]. The presence of proton-donating or proton-accepting groups in the vicinity of native or modified DNA bases changes their electron affinity and spectral properties
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
