Small molecule-based proximity labeling for nuclear lamins

Abstract

<p>Proximity labeling is indispensable for studying organelle transcriptomes and proteomes with spatial specificity¹. Nuclear lamins belong to the type V intermediate filament proteins, which assemble into a complex network for maintaining nuclear shape and regulating chromatin structure². Here we seek to develop a novel chemical method for the study of proximal RNAs or proteins of lamins to decipher unique biomolecule characteristics and molecular interactions. By our design, LBL1-DBF consists of lamins-targeting moiety lamin-binding ligand 1 (LBL1)³, photosensitizers with dibromofluorescein (DBF) motif as labeling group⁴, and a suitable linker. With the LBL1-DBF, proximal biomolecules are oxidized by singlet oxygen generated by DBF upon green light irradiation. The oxidation state of biomolecules can then react with propargylamine (PA) or other primary amines in solutions for transcriptomic or proteomic analysis⁵. Here, two final products (LBL1-EG3-DBF and LBL1-C3-DBF) were obtained, and their photophysical properties were characterized. With the probes in hand, imaging experiments were conducted in different cell lines with photo-oxidation labeling procedures. Once the feasibility of small molecule-based proximity labeling for nuclear lamins is verified, RNAs or proteins will be isolated after in cellulo labeling for following RNA sequencing or proteomic analysis.</p><p>All in all, my current work started from a reported anticancer agent LBL1³, and the following research found that it targets lamin A. Following the design idea of proximity labeling: combining the organelle-targeting moiety and labeling group, we seek to design a novel proximity labeling method for lamins-associated proteins and RNAs study. Final products (Ac-DBF-EG3-LBL1 and Ac-DBF-C3-LBL1) were obtained and characterized for photophysical properties. Although the initial imaging results are not very satisfactory, it still will be a breakthrough once the feasibility of small molecule-based proximity labeling for nuclear lamins is verified.</p>