Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2025.10.16.682820

Locked Nucleic Acid Stabilized Liquid Crystalline Phases

Kodikara, S. G.·Sprunt, S.·Balci, H.
View original source ↗Export metadata ↓

Abstract

Liquid crystalline (LC) phases formed by gapped DNA (GDNA) constructs, where two rigid duplexes are connected with a flexible single stranded linker, offer a versatile platform to investigate interactions between DNA molecules. Base pairs containing a locked nucleic acid (LNA-DNA or LNA-LNA pairs) are generally more stable compared to DNA-DNA pairs due to enhanced hydrogen bonding and/or attractive base stacking interactions. In concentrated solutions of GDNA constructs, the stability of terminal base pairs and the base stacking interactions between neighboring duplexes are critical for the formation of a bilayer smectic phase. By using temperature-resolved synchrotron small-angle X-ray scattering (SAXS) measurements, we quantified the impact of single LNA modification of terminal base pairs on the thermal stability of smectic LC phases. We observe that LNA-DNA terminal AT base pairing (A+T) increases the stability of the bilayer smectic phase by [~]9-18 {degrees}C relative to DNA-DNA pairing at the same duplex concentrations. While relatively large, this increase is still significantly less than the up to [~]30 {degrees}C increase observed when AT DNA-DNA pairs are replaced by GC pairs, suggesting the stacking interactions between A+T LNA-DNA base pairs are significantly weaker than those between unmodified GC base pairs. Our study illustrates the sensitivity of LC ordering in dense DNA solutions to a single nucleotide modification and demonstrates that LNA modifications can provide a new mechanism for tuning the stability of nucleic acid-based materials.

Source connections

Explore related subjects

biophysicsPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Kodikara, S. G., Sprunt, S., Balci, H.. 2025-10-16. Locked Nucleic Acid Stabilized Liquid Crystalline Phases. https://doi.org/10.1101/2025.10.16.682820

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Design of colipids with controlled lateral distance of head group moieties for targeting strategies in the field of lipid-based nanoparticles

Lipid nanoparticles and liposomes are nanoparticle drug formulations which are firmly established in clinics. In order to expand their application and improve efficacy, surface modifications can be a key strategy, especially for cell specific targeting. Targeting can be achieved by integrating ligand functionalized lipids or lipidoids on the nanoparticle surface. In this case, not solely the targeting ligand itself, but also the structure of the whole targeting lipid/lipidoid can affect the interaction of the targeting ligand with the binding motive on cells. Especially, distal spacer structures between lipid anchor and ligand unit, often composed of polyethylene glycol chains, provide a certain distance of the ligand from the nanoparticle surface. A concept which is currently neglected is the control of the lateral distance between ligand structures on the nanoparticle. Herein we investigated the possibility to design lipidoids with a lateral spacer composed of polyethylene glycol units. We synthesized and characterized different lipidoids which provide a primary amine in the head group for possible ligand coupling. In our model lipidoids the head groups were functionalized with a paramagnetic probe to apply electron paramagnetic resonance (EPR) methods for the characterization of the lipidoid interaction with model nanoparticles, in our case liposomes. Continuous wave EPR was used to study the efficiency of the novel lipidoids to integrate into lipid bilayers of model liposomes, which was shown to depend on lipidoid structure and liposome composition. Furthermore, using double electron-electron resonance (DEER), we observed lipidoid conformational changes occurring upon integration into liposomes.

biophysics↗
bioRxiv2026

Binding mechanisms of therapeutic antibodies to human claudin-18.2

Claudin-18.2 (CLDN18.2) is a tight junction component with highly restricted expression in the paracellular space of nonmalignant gastric epithelial cells. It becomes accessible on tumor cell surface during malignant transformation, making CLDN18.2 an attractive target for targeted therapies against gastric cancer. Recently, zolbetuximab has become the first FDA-approved monoclonal antibody that targets CLDN18.2 in advanced gastric cancer, and others like osemitamab have entered phase 3 clinical trials. However, the high-resolution structure of CLDN18.2 is lacking, and how CLDN18.2 is recognized by therapeutic antibodies remains undefined. Here, we report cryo-EM structures of human claudin-18.2 (hCLDN18.2) in complex with the Fab fragments of zolbetuximab and osemitamab, revealing the structure of hCLDN18.2 and its binding mechanism to the therapeutic antibodies. Further analyses reveal that three residues in the first extracellular loop of hCLDN18.2 that are different from human claudin-18.1 (hCLDN18.1) play a critical role in antibody binding. Our data elucidate the structural basis for selective binding of therapeutic antibodies to hCLDN18.2, which should aid rational design of next-generation immunotherapies targeting hCLDN18.2.

biophysics↗
bioRxiv2026

Structural relationships between the SLC12 cotransporter C-terminal domain, universal stress proteins and adenylating enzymes

Several SLC12 cotransporters bind ATP in a cytoplasmic C-terminal domain (CTD). We analysed 16,192 CTD-containing SLC12 sequences and compared 42,845 representative structures to examine the relationship between this nucleotide site, universal stress proteins (USPs) and adenylating enzymes. In phosphorylated NKCC1, D891 and D927 lie near the ATP phosphate chain, while R801 and K889 form a basic phosphate-binding clamp. NKCC1 retains this arrangement, whereas KCC paralogs replace or lose several corresponding groups. In structural comparisons with USP and adenylating-enzyme references, both CTD lobes score between universal stress proteins and EC-annotated domains, and the two lobes form separate lineages that include bacterial transporters. Lobe-specific and nucleotide-frame comparisons place ATP in the corresponding structural region used for -phosphate chemistry by catalytic members of this fold. Published work on UspG provides a precedent for protein-bound AMP in a natural USP. In the examined SLC12 structures and USP models, candidate protein hydroxyls lack an in-line geometry for attack at ATP P. Protein adenylation would require a change in protein or nucleotide geometry, or a different acceptor. These results define a structural basis for testing conditional protein adenylation at SLC12 nucleotide sites. The required evidence is a covalent protein-AMP adduct, identification of its acceptor and measurement of the expected pyrophosphate coproduct, with soluble nucleotide analysis to distinguish accompanying ATP reactions.

biophysics↗