Using the databases of proteins and linkers, a search has been undertaken with the aim to find linker segments adopting the polyproline II conformation in DNA-protein complexes. Seventy three linker-DNA complexes were found. It was shown that the mean length of polyproline II segment comprises six residues, praline being not dominant. The symmetry of praline disposition in these regions prevents the formation of the cooperative water net involving amide groups. An example of specific distribution of proline in some proteins of the motility apparatus is presented.
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Quantifying the Chirality of Vibrational Modes in Helical Molecular Chains.
Phys Rev Lett
December 2024
Tel Aviv University, University of Pennsylvania, Department of Chemistry, Philadelphia, Pennsylvania 19104, USA and School of Chemistry, Tel Aviv 69978, Israel.
Chiral phonons have been proposed to be involved in various physical phenomena, yet the chirality of molecular normal modes has not been well defined mathematically. Here we examine two approaches for assigning and quantifying the chirality of molecular normal modes in double-helical molecular wires with various levels of twist. First, associating with each normal mode a structure obtained by imposing the corresponding motion on a common origin, we apply the continuous chirality measure (CCM) to quantitatively assess the relationship between the chirality-weighted normal mode spectrum and the chirality of the underlying molecular structure.
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ACS Nano
January 2025
School of Science and Engineering, Shenzhen Institute of Aggregate Science and Technology, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Guangdong 518172, P.R. China.
Helical structures such as right-handed double helix for DNA and left-handed α-helix for proteins in biological systems are inherently chiral. Importantly, chirality at the nanoscopic level plays a vital role in their macroscopic chiral functionalities. In order to mimic the structures and functions of natural chiral nanoarchitectures, a variety of chiral nanostructures obtained from artificial helical polymers are prepared, which can be directly observed by atomic force microscopy (AFM), scanning tunneling microscopy (STM), scanning electron microscopy (SEM), and transmission electron microscopy (TEM).
View Article and Find Full Text PDFHierarchical chirality observed from chiral supramolecular assembling of racemic and enantiopure helicene derivatives on silica nanohelix surfaces.
Nanoscale
January 2025
CBMN, CNRS, UMR 5248, University of Bordeaux, 33600 Pessac, France.
Cast films of racemic helicene derivatives adsorbed onto the surface of nanometric silica helices with controlled handedness exhibited distinct CD signals, whereas no CD signal was observed in the absence of silica nanohelices. These CD signals originate from the helical supramolecular assemblies formed by the racemic mixture of helicenes, with no evidence of enantiospecific adsorption. Interestingly, when enantiomerically pure forms of these helicenes were drop-cast onto the silica helices, different CD spectra were observed depending on the combination of the helicenes' handedness with that of the silica nanohelices.
View Article and Find Full Text PDFSingle-Molecule Electrical Conductance in Z-form DNA:RNA.
Small
December 2024
Department of Chemistry, University of Massachusetts Lowell, Lowell, MA, 01854, USA.
Nucleic acids have emerged as new materials with promising applications in nanotechnology, molecular electronics, and biosensing, but their electronic properties, especially at the single-molecule level, are largely underexplored. The Z-form is an exotic left-handed helical oligonucleotide conformation that may be involved in critical biological processes such as the regulation of gene expression and epigenetic processes. In this work, the electrical conductance of individual Guanine Cytosine (GC)-rich DNA:RNA molecules is measured in physiological buffer and 2,2,2-Trifluoroethanol (TFE) solvent, corresponding to the natural (right-handed helix) A-form typical in DNA:RNA hybrids and the (left-handed) Z-form conformations, respectively.
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Chemistry
December 2024
Department of Chemical Sciences (DiSC), University of Padova, Via F. Marzolo 1, Padova, 35131, Italy.
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