Biology subjects

Dettmer, S. J.

Publications and source records attributed to Dettmer, S. J..

3 recordsLinked to original sources

bioRxiv2025

A Flexible Quadruple-Stranded Helicate Demonstrates a Strong Binding Preference for DNA Three-Way Junctions by Induced-Fit

Nucleic acid junctions are key to many biological functions from recombination and repair to viral NA insertion, and are an attractive, functional biomolecular target. We describe a quadruple-stranded di-platinum helicate that binds both three-way (3WJ) and four-way DNA junctions (4WJ). This allows us to probe the relative importance of size and shape in junction-binder design. Despite the helicates tetragonal symmetry/shape being compatible with the 4WJ, microscale thermophoresis (MST), isothermal calorimetry (ITC) and gel electrophoresis competition experiments demonstrate that this metallo-supramolecule displays a stronger affinity for 3WJs (Kd = 12 nM) than for 4WJs (Kd > 4 {micro}M) and other DNA structures. The experimental findings are supported by molecular dynamics simulations which reveal the critical role of size. Whilst the open form of the 4WJ is promoted when the helicate is in the cavity, the helicates small size means it is unable to maintain {pi} contacts with all four junction base-pairs simultaneously. Although the helicate is slightly too large for the smaller 3WJ cavity, simulations and experiments show that it can open up the cavity (increasing the junctions hydrodynamic radius) by disrupting a base-pair. The flexible helicate also responds to the cavity upon binding by favouring one enantiomer and allowing the helicate to adopt a stable final structure inside the 3WJ that is an induced-fit of the two dynamic structures (supramolecule and DNA). This contrasts with previous lock-and-key examples of junction recognition and opens up new possibilities for how to design DNA and RNA junction-binding compounds. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=72 SRC="FIGDIR/small/671622v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@175cabborg.highwire.dtl.DTLVardef@50f114org.highwire.dtl.DTLVardef@372e1org.highwire.dtl.DTLVardef@6b2960_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2025

Interactions of Elongated Dinuclear Metallo-Cylinders with DNA Three-Way and Four-Way Junctions

Non-canonical DNA structures play important roles in processing of the genetic code. Three-way (3WJ) and four-way (4WJ) junctions are dynamic, multi-stranded structures containing an open cavity at the centre. We have previously demonstrated that supramolecular dinuclear metallo-cylinders bind well inside 3WJ cavities, having an optimally complementary size and shape match, cationic charge to bind the anion, as well as the ability to {pi}-stack with the branchpoint nucleobases. Herein we show that a longer metallo-cylinder with a similar but extended central {pi}-surface, binds to both 3WJ and 4WJ structures with good selectivity over double-stranded DNA. Experimental investigations, informed by molecular dynamics (MD) simulations, reveal that while this longer cylinder can bind 3WJs as the previously studied cylinders, the extended {pi}-surface of the cylinder now also facilitates 4WJ binding. The simulations capture two metastable 4WJ conformations - one resembling a 3WJ, and another where the extended length enables the cylinder to angle into and stabilise a rhombus-shaped 4WJ cavity. The ability to tune the structure of supramolecular assemblies is important for targeting different DNA structures with varying specificity and in this work we demonstrate the usefulness of overall length as a parameter for modulating DNA binding.

biophysics↗

bioRxiv2023

Organometallic Pillarplexes that bind DNA 4-way Holliday Junctions and Forks.

Holliday 4-way junctions are key to important biological DNA processes (insertion, recombination and repair) and are dynamic structures which adopt either open or closed conformations, with the open conformation being the biologically active form. Tetracationic metallo-supramolecular pillarplexes display aryl faces about a cylindrical core giving them an ideal structure to interact with the central cavities of open DNA junctions. Combining experimental studies and MD simulations we show that an Au pillarplex can bind DNA 4-way junctions (Holliday junctions) in their open form, a binding mode not accessed by synthetic agents before. The Au pillarplexes can bind designed 3-way junctions too but their large size leads them to open up and expand that junction, disrupting the base pairing which manifests in an increase in hydrodynamic size and a lower junction thermal stability. At high loading they re-arrange both 4-way and 3-way junctions into Y-shaped DNA forks to increase the available junction-like binding sites. The structurally related Ag pillarplexes show similar DNA junction binding behaviour, but a lower solution stability. This pillarplex binding contrasts with (but complements) that of the metallo-supramolecular cylinders, which prefer 3-way junctions and we show can rearrange 4-way junctions into 3-way junction structures. The pillarplexes ability to bind open 4-way junctions creates exciting possibilities to modulate and switch such structures in biology, as well as in synthetic nucleic acid nanostructures where they are key interconnecting components. Studies in human cells, confirm that the pillarplexes do reach the nucleus, with antiproliferative activity at levels similar to those of cisplatin. The findings provide a new roadmap for targeting higher order junction structures using a metallo-supramolecular approach, as well as expanding the toolbox available to design bioactive junction-binders into organometallic chemistry. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=188 SRC="FIGDIR/small/522759v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@10fac36org.highwire.dtl.DTLVardef@1f32f9forg.highwire.dtl.DTLVardef@bb8d72org.highwire.dtl.DTLVardef@1433de5_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗