Shiekh, S. A. | Search bioRxiv

bioRxiv2025

Impact of Molecular Crowding on Accessibility of Telomeric Overhangs Forming Multiple G-quadruplexes

Telomeric overhangs, composed of repeating GGGTTA sequences, can fold into multiple G-quadruplex (GQ) structures that are essential for maintaining genomic stability and regulating telomere length. Molecular crowding--a defining feature of the cellular environment--affects folding kinetics, conformation, and stability of individual GQs. However, its influence on the overall architecture and accessibility of telomeric overhangs containing multiple GQs remains largely unexplored. In this study, we employed single-molecule Forster Resonance Energy Transfer (smFRET) and FRET-Point Accumulation for Imaging in Nanoscale Topography (FRET-PAINT) to address this question. We examined the accessibility of telomeric overhangs capable of forming one to six GQs to a short complementary peptide nucleic acid (PNA) imager probe under molecular crowding conditions. These conditions were simulated by polyethylene glycol (PEG) molecules of two different molecular weights: 200 Da (PEG-200) and 6000 Da (PEG-6000). Our results reveal a systematic reduction in the overhang accessibility with increasing PEG concentration--showing approximately a 3-fold reduction at 30% (v/v) PEG-200 and an 8-fold reduction at 30% PEG-6000. We also observed a progressive compaction of the overhang as PEG concentration increased, suggesting molecular crowding promotes architectural condensation, thereby reducing probe accessibility. These findings offer new insights into how the crowded cellular environment may compact telomeric overhangs and modulate their structural and functional properties.

biophysics↗

bioRxiv2024

Combining the CRISPR Activation and Interference Capabilities Using dCas9 and G-Quadruplex Structures

We demonstrate that both CRISPR interference and CRISPR activation can be achieved at RNA and protein levels by targeting the vicinity of a putative G-quadruplex forming sequence (PQS) in the c-Myc promoter with nuclease-dead Cas9 (dCas9). The achieved suppression and activation in Burkitts Lymphoma cell line and in in vitro studies are at or beyond those reported with alternative approaches. When the template strand (contains the PQS) was targeted with CRISPR-dCas9, the G-quadruplex was destabilized and c-Myc mRNA and protein levels increased by 2.1-fold and 1.6-fold, respectively, compared to controls in the absence of CRISPR-dCas9. Targeting individual sites in the non-template strand with CRISPR-dCas9 reduced both the c-Myc mRNA and protein levels (by 1.8-fold and 2.5-fold, respectively), while targeting two sites simultaneously further suppressed both the mRNA (by 3.6-fold) and protein (by 9.8-fold) levels. These were consistent with cell viability assays when single or dual sites in the non-template strand were targeted (1.7-fold and 4.7-fold reduction in viability, respectively). We also report extensive in vitro biophysical studies which are in quantitative agreement with these cellular studies and provide important mechanistic details about how the transcription is modulated via the interactions of RNA polymerase, CRISPR-dCas9, and the G-quadruplex.

molecular biology↗