Publications by Marco Pasi | EPFL Graph Search

Sequence-dependent structural properties of B-DNA: what have we learned in 40 years?

John Maddocks, Daiva Petkeviciute, Paolo Carloni, Marco Pasi, Rahul Sharma

The structure of B-DNA, the physiological form of the DNA molecule, has been a central topic in biology, chemistry and physics. Far from uniform and rigid, the double helix was revealed as a flexible and structurally polymorphic molecule. Conformational ch ...

Springernature2021

The static and dynamic structural heterogeneities of B-DNA: extending Calladine-Dickerson rules

John Maddocks, Daiva Petkeviciute, Alessandro Samuele Patelli, Marco Pasi

We present a multi-laboratory effort to describe the structural and dynamical properties of duplex B-DNA under physiological conditions. By processing a large amount of atomistic molecular dynamics simulations, we determine the sequence-dependent structura ...

Oxford University Press (OUP)2019

Analyzing ion distributions around DNA: sequence-dependence of potassium ion distributions from microsecond molecular dynamics

John Maddocks, Marco Pasi

Microsecond molecular dynamics simulations of B-DNA oligomers carried out in an aqueous environment with a physiological salt concentration enable us to perform a detailed analysis of how potassium ions interact with the double helix. The oligomers studied ...

Oxford University Press2015

Analyzing ion distributions around DNA

John Maddocks, Marco Pasi

We present a new method for analyzing ion, or molecule, distributions around helical nucleic acids and illustrate the approach by analyzing data derived from molecular dynamics simulations. The analysis is based on the use of curvilinear helicoidal coordin ...

Oxford University Press2014

cgDNA: a software package for the prediction of sequence-dependent coarse-grain free energies of B-form DNA

John Maddocks, Daiva Petkeviciute, Marco Pasi

cgDNA is a package for the prediction of sequence-dependent configuration-space free energies for B-form DNA at the coarse-grain level of rigid bases. For a fragment of any given length and sequence, cgDNA calculates the configuration of the associated fre ...

Oxford Univ Press2014

mu ABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA

John Maddocks, Daiva Petkeviciute, Jonathan Mitchell, Marco Pasi

We present the results of microsecond molecular dynamics simulations carried out by the ABC group of laboratories on a set of B-DNA oligomers containing the 136 distinct tetranucleotide base sequences. We demonstrate that the resulting trajectories have ex ...

Oxford Univ Press2014