Showing papers by "Fabrizio Cleri published in 2020"

Detection of single DNA mismatches by force spectroscopy in short DNA hairpins

Abstract: Identification of defective DNA structures is a difficult task, since small differences in base-pair bonding are hidden in the local structural variability of a generally random base-pair sequence. Defects, such as base mismatches, missing bases, crosslinks, and so on, occur in DNA with high frequency and must be efficiently identified and repaired to avoid dire consequences such as genetic mutations. Here, we focus on the detection of base mismatches, which is local deviations from the ideal Watson-Crick pairing rule, which may typically originate from DNA replication process, foreign chemical attack, or ionizing radiation. Experimental detection of a mismatch defect demands the ability to measure slight deviations in the free energy and molecular structure. We introduce different mismatches in short DNA hairpins (10 or 20 base pairs plus a 4-base loop) sandwiched between dsDNA handles to be used in single-molecule force spectroscopy with optical tweezers. We perform both hopping and force-pulling experiments to measure the excess free energies and deduce the characteristic kinetic signatures of the mismatch from the force-distance curves. All-atom molecular dynamics simulations lend support to the detailed interpretation of the experimental data. Such measurements, at the lowest sensitivity limits of this experimental technique, demonstrate the capability of identifying the presence of mismatches in a random complementary dsDNA sequence and provide lower bounds for the ability to distinguish different structural defects.

A stochastic force model for the ballistic-diffusive transition of heat conduction

Abstract: We theoretically study the heat conduction in a harmonic chain with a stochastic force field, in contact with two Langevin thermal baths at different temperatures. In particular, we investigate the interplay between the thermal baths properties and the size of the system. To this aim, we introduce a stochastic force field, which is simple enough to be energy-conserving for each particle of the chain, but sufficiently aleatory to induce the ballistic to diffusive transition in the conductive behavior of the chain. When this stochastic force field is absent, we observe a ballistic behavior strongly dependent on the characteristic collision frequency of the thermal baths for any size of the system. On the other hand, when the stochastic force field is activated, the diffusive behavior is established and the effect of the thermal baths is removed in the thermodynamic limit.

DNA Aptamers Block the Receptor Binding Domain at the Spike Protein of SARS-CoV-2

Abstract: DNA aptamers are versatile molecular species obtained by the folding of short single-stranded nucleotide sequences, with highly specific recognition capabilities against proteins. Here we test the ability of selected DNA aptamers in interacting with the spike (S-)protein of the SARS-CoV-2 viral capsid. The S-protein, a trimer made up of several subdomains, develops the crucial function of recognizing the ACE2 receptors on the surface of human cells, and sub- sequent fusioning of the virus membrane with the host cell membrane. In order to do this, the S1 domain of one protomer switches between a closed conformation, in which the binding site is inaccessible to the cell receptors, and an open conformation, in which ACE2 can bind, thereby initiating the entry process of the viral genetic material in the host cell. Here we show by means of state-of-the-art molecular simulations that small DNA aptamers can recognize the S-protein of SARS-CoV-2. Moreover, their interaction with different regions of the S-protein can effectively block, or at least considerably slow down the opening process of the S1 domain, thereby largely reducing the probability of virus-cell binding. We also provide evidence that binding of the human ACE2 receptor may be drastically affected under such conditions. Given the facility and low cost of fabrication of specific aptamers, the present findings could open the way to both an innovative viral screening technique with sub-nanomolar sensitivity, and to an effective and low impact curative strategy.