P. Sulc

Single-Molecule Force Spectroscopy of Toehold-Mediated Strand Displacement

This study uses single-molecule force spectroscopy to analyze the kinetics of toehold-mediated strand displacement, revealing sequence-dependent dynamics and load effects in DNA and RNA interactions.

IgG-inspired, multivalent protein-DNA nanostructures for high-affinity, tunable, and reversible binding to biomolecular targets

This paper designs and tests a DNA-based synthetic antibody (nano-synbody) that binds SARS-CoV-2 spike proteins with high affinity and reversibility through multivalency.

High-speed 3D DNA PAINT and unsupervised clustering for unlocking 3D DNA origami cryptography

This paper develops a DNA origami cryptography protocol using high-speed 3D DNA-PAINT and unsupervised clustering to enhance encryption key size and information retrieval accuracy.

DNA Nanostructure-Guided Assembly of Proteins into Programmable Shapes

This paper describes a method using DNA origami to guide the assembly of protein-DNA conjugates into programmable nanostructures with controlled stoichiometry and geometry.

RNA-induced allosteric coupling drives viral capsid assembly in bacteriophage MS2

This study shows RNA-induced allostery drives capsid assembly in bacteriophage MS2 by altering protein flexibility and dynamic coupling.

Generative and interpretable machine learning for aptamer design and analysis of in vitro sequence selection

This study uses Restricted Boltzmann Machines to analyze SELEX data for thrombin aptamers, enabling sequence fitness estimation, classification, and novel molecule generation, which is validated experimentally.

A rhythmically pulsing leaf-spring nanoengine that drives a passive follower

This paper describes a DNA-nanomachine that performs rhythmic pulsing motion driven by chemical energy and couples it to a passive follower unit.

Kinetics of RNA and RNA:DNA hybrid strand displacement

This study experimentally examines how toehold length, location, and mismatches affect strand displacement kinetics in RNA and RNA-DNA hybrid systems.

Phenotype bias determines how RNA structures occupy the morphospace of all possible shapes

The paper shows that RNA secondary structure morphospace is dominated by phenotype bias, not natural selection, as frequent structures are more likely to appear from random mutations.

Understanding DNA interactions in crowded environments with a coarse-grained model

This study uses a coarse-grained model to investigate how crowding affects DNA duplex and hairpin formation, finding that crowders increase melting temperature and enhance hybridization kinetics.

Design, optimization, and analysis of large DNA and RNA nanostructures through interactive visualization, editing, and molecular simulation

The paper introduces oxView and open-source tools for visualizing and analyzing large DNA/RNA nanostructures simulated with oxDNA, enabling design, optimization, and structural analysis.

Y-RNAs Lead an Endogenous Program of RIG-I Agonism Mobilized upon RNA Virus Infection and Targeted by HIV

This study identifies Y-RNAs as endogenous RIG-I ligands that are targeted by HIV through DUSP11 downregulation, enhancing their immunogenicity and triggering antiviral responses.