Biology subjects

Bricker, R.

Publications and source records attributed to Bricker, R..

3 recordsLinked to original sources

bioRxiv2026

DNA-Lipid Nanodiscs with a Polyethylene Glycol Interface

Nanoscale bilayer mimetics such as protein or polymer-based nanodiscs are versatile tools to study the physical chemistry of lipid bilayers or the structures and functions of membrane proteins. Here, we introduce DNA-Lipid Nanodiscs (DLNs) in which the interface between hydrophobic lipids and the charged DNA is mediated through amphiphilic poly(ethylene)glycol (PEG). For this, we modified oligonucleotides with PEG and hybridized them to a single-stranded ring to form functionalized minicircles with a well-defined diameter. The center of these minicircles can be filled with a lipid bilayer through addition of detergent-solubilized lipids followed by detergent removal. Simulations reveal that the methylene groups in PEG form dynamic interactions with the acyl chains of lipids, effectively shielding the hydrophobic mismatch. As proof of concept towards incorporation of complex membrane proteins, we inserted the biotinylated transmembrane domain of synaptobrevin into these nanodiscs and bound them to streptavidin-modified quantum dots as a marker for successful incorporation. We envision these atomically precise, modular DNA scaffolds to be widely applicable in future studies of membrane proteins and nanoscale lipid membranes. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=117 SRC="FIGDIR/small/705827v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@17cfcb5org.highwire.dtl.DTLVardef@b2dd2corg.highwire.dtl.DTLVardef@d6899aorg.highwire.dtl.DTLVardef@e400c4_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

S-Alkyl-Phosphorothioate Modifications Reduce Thermal and Structural Stability of DNA Duplexes

While phosphorothioate (PS) oligonucleotides are usually used in therapeutic applications, they also offer the cheapest and synthetically most straightforward route to introduce hydrophobic modifications for applications in structural DNA nanotechnology and biophysics. For this, the sulfur atom is S-alkylated with alkyl iodides, enabling a hydrophobically tunable interface of DNA nanostructures with lipid bilayers. While longer and more alkyls per helical turn should lead to stronger interactions with lipid membranes, we found that excessive S-alkylations strongly inhibit hybridization of oligonucleotides to their complementary strands and decrease their melting temperature, despite a reduction in electrostatic repulsion between the two strands. Moreover, both the type and placement of alkyl modifications influence the melting temperature. Atomistic molecular dynamics simulations reveal two complementary mechanisms that explain the experimental findings. First, S-alkylated oligonucleotides are more compact and less dynamic than unmodified ones, likely inhibiting their ability to hybridize to their complementary strands. Second, S-alkyls in double-stranded DNA promote defect formation due to alkyl modifications having hydrophobic interactions with other alkyl groups and nucleobases, therefore reducing the thermal and structural stability of alkylated DNA duplexes. This study serves as a practical guide for tuning hydrophobicity while maintaining structural stability in membrane-interfacing DNA nanostructures.

biochemistry↗

bioRxiv2024

Bending Unwinds DNA

DNA is under high bending and torsional strain in many biological contexts 1,2, but elastic limits of tightly bent DNA under simultaneous torsional strain are not fully understood 3-22. We synthesized DNA circles with all possible radii of curvature between r {approx} 2.7 - 5.7 nm in increments of{Delta} r = 0.05 nm and defined helical repeats ranging from h {approx} 10 - 13 base pairs per helical turn. Nuclease digest reveals that DNA can be bent to r {approx} 3.0 nm without kinking, but only when h < ~10.9 bp/turn, while underwound DNA kinks irrespective of curvature. Histone proteins overwind DNA and thereby mechanically stabilize it. The natural helical repeat h0 increases from 10.45 to >11 bp/turn due to twist-bend coupling, which is not caused by kinking before ligation. These findings require reassessing our models and the energetics of molecular mechanisms involving DNA under mechanical stress.

biophysics↗