Mechanical Properties of Nucleic Acids

Mechanical Properties

We have investigated the mechanical properties of dsDNA and dsRNA using AFM, Magnetic Tweezers, Optical Tweezers and more recently with Molecular Dynamics simulations.

GC-rich DNA shows in circular-dicroism experiments a signal compatible with A-form DNA. We investigated the mechanical properties and stability conditions of GC-rich DNA and compared these with a control DNA of equal GC/AT content under a variety of buffers and a wide range of forces. To do this study we used Magnetic Tweezers and AFM.

Hormeno et al. Biophysical Journal 100, 1996-2006 (2011). Mechanical Properties of High GoC-content DNA with A-type base-stacking. LINK

Hormeno et al. Biophysical Journal 100, 2006-2015 (2011). Condensation prevails over B-A transition in the structure of DNA at low humidity. LINK

E. Herrero-Galan et al. JACS 135(1), 122-131 (2013). Mechanical identities of RNA and DNA double helices unveiled at the single-molecule level. LINK

 

Stretching forces induce local changes in the structure of nucleic acids molecule. We apply all-atom, microsecond-long molecular dynamics to simulate the structure of dsDNA and dsRNA subjected to stretching forces up to 20 pN. The goal is to understand how a force induces changes in the structure of NAs at the atomic level, which can produce inhibition or promotion of protein binding, which ultimately affects their functionality.

Marín-González*, Vilhena* et al. Proceedings of the National Academy of Sciences USA 114(27), 7049-7054 (2017). doi: 10.1073/pnas.1705642114. Double stranded DNA and RNA under constant stretching forces: atomistic insights from microsecond-long molecular dynamics. LINK

Marín-González*, Vilhena* et al. bioRxiv  doi: https://doi.org/10.1101/283648. DNA crookedness regulates DNA mechanical properties at short length scales.

 

High-resolution imaging of nucleic acids with AFM

By applying different high-sensitive force-detection AFM methods we have we have visualized the double helix of dsRNA under near-physiological conditions and at sufficient resolution to resolve the A-form sub-helical pitch periodicity. We have shown that the limiting factors for high-resolution AFM imaging of soft materials in liquid medium are, rather than the imaging mode, the force between the tip and the sample and the sharpness of the tip apex.

Ares et al. Nanoscale 8,11818-11826 (2016). High resolution atomic force microscopy of double-stranded RNA. LINK 

 

 

 

ANTIGUO – SE PODRÍA QUITAR A PARTIR DE AQUÍ

Mechanical Properties and high resolution imaging of Nucleic Acids

 

We have investigated the mechanical properties of dsDNA and dsRNA using AFM, Magnetic Tweezers, and Optical Tweezers. GC-rich DNA shows in circular-dicroism experiments a signal compatible with A-form DNA. We investigated the mechanical properties and stability conditions of GC-rich DNA and compared these with a control DNA of equal GC/AT content under a variety of buffers and a wide range of forces. To do this study we used Magnetic Tweezers and AFM.

Researchers

IMDEA Nanociencia: B. Ibarra´s Group, R. Arias-Gonzalez´s Group

UAM. Science Faculty: J. Gomez-Herreros´s Group

Publications

S. Hormeno et al. Biophysical Journal 100, 1996-2006 (2011).

Mechanical Properties of High GoC-content DNA with A-type base-stacking

LINK

S. Hormeno et al. Biophysical Journal 100, 2006-2015 (2011).

Condensation prevails over B-A transition in the structure of DNA at low humidity”

LINK

S. E. Herrero-Galan et al. JACS 135(1), 122-131 (2013).

Mechanical identities of RNA and DNA double helices unveiled at the single-molecule level

LINK

Ares et al. Nanoscale 8,11818-11826 (2016).

High resolution atomic force microscopy of double-stranded RNA

LINK