News | Fernando Moreno Herrero Lab

3^rd Workshop on Advanced Nanobioscience

Fernando Moreno-Herrero, together with Ana G. del Arco, organized “The 3rd Workshop on Advanced Nanobioscience”, which took place in Madrid, at the National Center of Biotechnology (CNB-CSIC) on 26th May 2023.

Every year, the Macromolecular Structures Department hosts a one-day workshop focusing on current topics of relevance. For this occasion, several exciting topics were planned for discussion: mass photometry, nanopore biophysics, Optical and Magnetic Tweezers, Atomic Force Microscopy, and other fluorescence-based methods.

SBE “Manuel Rico” – Bruker Prize awarded to Fernando Moreno-Herrero

Fernando Moreno-Herrero has been awarded with the “Manuel Rico” – Bruker Prize of The Spanish Biophysical Society 2023 in recognition of his pioneering work in the development of molecular biophysics using Atomic Force Microscopy and Magnetic Tweezers in Spain. The jury highlights his pioneering biophysical studies on the molecular machinery involved in DNA repair, organization, and replication. This year’s award has been jointly granted to Fernando Moreno-Herrero and Teresa Giráldez Fernández, professor at the University of La Laguna.

APLF and long non-coding RNA NIHCOLE promote stable DNA synapsis in non-homologous end joining

Here, we show that Ku70-Ku80 and APLF establish a minimal complex sufficient to support DNA synapsis. APLF and long non-coding RNA NIHCOLE promote stable DNA synapsis in non-homologous end joining. Additionally, we show how APLF promotes synapsis of DNA ends for several minutes under pN forces and lncRNA NIHCOLE stabilises these synapsis via a small and structured domain relevant in DNA repair by NHEJ.

Human HELB is a processive motor protein which catalyses RPA clearance from single-stranded DNA

Here, we characterize the biochemical activities of the human DNA helicase B (HELB) using bulk and single-molecule methods.
We found that HELB is a monomeric protein that binds to ssDNA with a site size of 20nt, unexpectedly large for SF1 helicases, suggesting an additional binding site.
HELB binds specifically to human RPA, which enhances its ATPase and ssDNA translocase activities.
Translocating HELB concomitantly clears RPA from ssDNA.

A molecular view of DNA flexibility

Here, we review recent single-molecule experiments and molecular dynamics simulations that are providing novel insights into DNA mechanics from such a molecular perspective.

Purified Smc5/6 Complex Exhibits DNA Substrate Recognition and Compaction

Eukaryotic SMC complexes, cohesin, condensin, and Smc5/6, use ATP hydrolysis to power a plethora of functions requiring organization and restructuring of eukaryotic chromosomes in interphase and during mitosis. The Smc5/6 mechanism of action and its activity on DNA are largely unknown. Here we purified the budding yeast Smc5/6 holocomplex and characterized its core biochemical and biophysical activities.

Double-stranded RNA bending by AU-tract sequences

Sequence-dependent structural deformations of the DNA double helix (dsDNA) have been extensively studied, where adenine tracts (A-tracts) provide a striking example for global bending in the molecule. However, in contrast to dsDNA, sequence-dependent structural features of dsRNA have received little attention. In this work, we demonstrate that the nucleotide sequence can induce a bend in a canonical Watson-Crick base-paired dsRNA helix.

Characterizing microfluidic approaches for a fast and efficient reagent exchange in single-molecule studies

Single-molecule experiments usually take place in flow cells. This experimental approach is essential for experiments requiring a liquid environment, but is also useful to allow the exchange of reagents before or during measurements. This is crucial in experiments that need to be triggered by ligands or require a sequential addition of proteins.

Bulk and single-molecule analysis of a bacterial DNA2-like helicase nuclease reveals a single-stranded DNA looping motor

DNA2 is an essential enzyme involved in DNA replication and repair in eukaryotes. In a search for homologues of this protein, we identified and characterised Geobacillus stearothermophilus Bad, a bacterial DNA helicase–nuclease with similarity to human DNA2.

Understanding the paradoxical mechanical response of in-phase A-tracts at different force regimes

A-tracts are A:T rich DNA sequences that exhibit unique structural and mechanical properties associated with several functions in vivo. The crystallographic structure of A-tracts has been well characterized. However, the mechanical properties of these sequences is controversial and their response to force remains unexplored