Use of 6‐Methylisoxanthopterin, a Fluorescent Guanine Analog, to Probe Fob1‐Mediated Dynamics at the Stalling Fork Barrier DNA Sequences

Site-Specific Investigation of DNA Holliday Junction Dynamics and Structure with 6-Methylisoxanthopterin, a Fluorescent Guanine Analog

DNA Holliday Junction (HJ) formation and resolution is requisite for maintaining genomic stability in processes such as replication fork reversal and double-strand break repair. If HJs are not resolved, chromosome disjunction and aneuploidy result, hallmarks of tumor cells. To understand the structural features that lead to processing of these four-stranded joint molecule structures, we seek to identify structural and dynamic features unique to the central junction core. We incorporate the fluorescent guanine analog 6-methylisoxanthopterin (6-MI) at ten different locations throughout a model HJ structure to obtain site-specific information regarding the structure and dynamics of bases relative to those in a comparable sequence context in duplex DNA. These comparisons were accomplished through measuring fluorescence lifetime, relative brightness, fluorescence anisotropy, and thermodynamic stability, along with fluorescence quenching assays. These time-resolved and steady-state fluorescence measurements demonstrate that the structural distortions imposed by strand crossing result in increased solvent exposure, less stacking of bases and greater extrahelical nature of bases within the junction core. The 6-MI base analogs in the junction reflect these structural changes through an increase in intensity relative to those in the duplex. Molecular dynamics simulations performed using a model HJ indicate the primary sources of deformation are in the shift and twist parameters of the bases at the central junction step. These results suggest that junction-binding proteins may use the unique structure and dynamics of the bases at the core for recognition.

Morphological Evolution of Strongly Fluorescent Water Soluble AIEEgen-Triblock Copolymer Mixed Aggregates with Shape-Dependent Cell Permeability

Dimethyl-2,5-bis(4-methoxyphenylamino)terephthalate (DBMPT) is a water-insoluble fluorogenic molecule, which has been rendered water-soluble in physiological conditions, by the addition of triblock copolymers (TBPs), P123 (PEO₁₉PPO₆₉PEO₁₉), and F127 (PEO₁₀₀PPO₆₅PEO₁₀₀). DBMPT-TBP mixed aggregates, formed in the process, exhibit significant aggregation-induced enhancement of emission, with nanosecond fluorescence lifetimes. Dynamics involved in suppression of nonradiative pathways and consequent enhancement of fluorescence are followed by femtosecond transient absorption and time-resolved fluorescence spectroscopic techniques. Interestingly, shapes of the aggregates formed with the two TBPs are found to be very different, even though they differ only in the length of hydrophilic blocks. DBMPT-P123 aggregates are micrometer-sized and spherical, while DBMPT-F127 aggregates form nanorods. Evolution of their morphologies, as a function of TBP concentration, is monitored using cryo-TEM, FESEM, and fluorescence lifetime imaging microscopy. Fluorescence lifetime distribution provides useful insight into microheterogeneity in these mixed aggregates. Excellent cell permeability is observed for DBMPT-F127 nanorods, in contrast to DBMPT-P123 microspheres. These fluorescent nanorods exhibit the ability to mark lipid droplets within the cell and hence bear the promise for application in intracellular imaging.