Biology subjects

Dejeu, J.

Publications and source records attributed to Dejeu, J..

3 recordsLinked to original sources

bioRxiv2025

Antibody targeting the anti-parallel topology of human telomeric G-quadruplex DNA

G-quadruplexes (G4s) are four-stranded nucleic acid structures that have gathered a significant attention due to their involvement in key biological processes, including gene regulation, genome stability, and telomeres maintenance. Some G4 antibodies have been developed to selectively recognize these structures over duplex DNA; however, most, even the widely studied BG4 and 1H6, bind G4s in a general manner and lack discrimination between distinct topologies, particularly between parallel and antiparallel conformations. In this study, we report on the development and characterization of a novel antibody selected via phage display method using a constrained antiparallel G4 structure mimicking one of the conformation adopted in vitro by the human telomeric sequence. Our findings demonstrate that this new antibody selectively recognizes the antiparallel topology of the telomeric G4 sequence, a property further validated in cellular models.

biochemistry↗

bioRxiv2023

iMab Antibody Binds Single-Stranded Cytosine-Rich Sequences and Unfolds DNA i-Motifs

i-Motifs (iMs) are non-canonical, four-stranded secondary structures formed by stacking of hemi-protonated CH+{middle dot}C base pairs in cytosine-rich DNA sequences, predominantly at pH < 7. The presence of iM structures in cells was a matter of debate until the recent development of iM-specific antibody, iMab, that was instrumental for several studies that suggested the existence of iMs in live cells and their putative biological roles. We assessed the interaction of iMab with cytosine-rich oligonucleotides by biolayer interferometry (BLI), pull-down assay and bulk-FRET experiments. Our results suggest that binding of iMab to DNA oligonucleotides is governed by the presence of runs of at least two consecutive cytosines and is generally increased in acidic conditions, irrespectively of the capacity of the sequence to adopt, or not, an iM structure. Moreover, the results of the bulk-FRET assay indicate that interaction with iMab results in unfolding of iM structures even in acidic conditions (pH 5.8 or 6.5), similarly to what has been observed with hnRNP K, well-studied single- stranded DNA binding protein. Taken together, our results suggest that iMab actually binds to blocks of 2-3 cytosines in single-stranded DNA, and call for more careful interpretation of results obtained with this antibody.

biophysics↗

bioRxiv2023

Cell-free expression and characterization of multivalent rhamnose-binding lectins using biolayer interferometry

Lectins are important biological tools for binding glycans, but recombinant protein expression poses challenges for some lectin classes, limiting the pace of discovery and characterization. To discover and engineer lectins with new functions, workflows amenable to rapid expression and subsequent characterization are needed. Here, we present bacterial cell-free protein synthesis as a means for efficient, small-scale expression of multivalent, disulfide bond-rich, rhamnose-binding lectins. Furthermore, we demonstrate that the cell-free expressed lectins can be directly coupled with BLI analysis, either in solution or immobilized on the sensor, to measure interaction with carbohydrate ligands without purification. This workflow enables determination of lectin substrate specificity and estimation of binding affinity. Overall, we believe that this method will enable high-throughput expression, screening, and characterization of new and engineered multivalent lectins for applications in synthetic glycobiology.

synthetic biology↗