Dna

Potaman, Vladimir N.; Sinden, Richard R.

doi:10.1007/0-387-29148-2_1

Cited by 12 publications

(4 citation statements)

References 95 publications

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“…As an exception, it is worth noticing ref where authors studied the geometry dependence of the splitting, and also ref in which the distance dependence of CT states in heterodimers was examined. In living organisms, NAs mostly exist in the canonical forms indeed, but occurrence of some other conformations is also possible, depending on the sequence and local environment conditions . DNA in cell is wound around nucleosomes, being in partially distorted conformation relative to the B form.…”

Section: Introductionmentioning

confidence: 99%

Noncanonical Stacking Geometries of Nucleobases as a Preferred Target for Solar Radiation

2015

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Direct DNA absorption of UVB photons in a spectral range of 290-320 nm of terrestrial solar radiation is responsible for formation of cyclobutane pyrimidine dimers causing skin cancer. Formation of UVB-induced lesions is not random, and conformational features of their hot spots remain poorly understood. We calculated the electronic excitation spectra of thymine, cytosine, and adenine stacked dimers with ab initio methods in a wide range of conformations derived from PDB database and molecular dynamics trajectory of thymine-containing oligomer. The stacked dimers with reduced interbase distances in curved, hairpin-like, and highly distorted DNA and RNA structures exhibit excitonic transitions red-shifted up to 0.6 eV compared to the B-form of stacked bases, which makes them the preferred target for terrestrial solar radiation. These results might have important implications for predicting the hot spots of UVB-induced lesions in nucleic acids.

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Section: Introductionmentioning

confidence: 99%

Noncanonical Stacking Geometries of Nucleobases as a Preferred Target for Solar Radiation

2015

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“…In nature, there are a wide range of helices observed in biopolymer secondary structure. From 3.6 residues-per-turn α-helices in proteins to 10.5 residues-per-turn double helices in B-DNA, biopolymers adopt a wide range of helical secondary structures. Inspired by the diversity of helices observed in nature, we designed a parameter scan in a 1b1s model to explore the different helix types accessible within these toy models.…”

Section: Methodsmentioning

confidence: 99%

Folding Coarse-Grained Oligomer Models with PyRosetta

Fobe

Walker

Meek

et al. 2022

J. Chem. Theory Comput.

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Non-biological foldamers are a promising class of macromolecules that share similarities to classical biopolymers such as proteins and nucleic acids. Currently, designing novel foldamers is a non-trivial process, often involving many iterations of trial synthesis and characterization until folded structures are observed. In this work, we aim to tackle these foldamer design challenges using computational modeling techniques. We developed CG PyRosetta, an extension to the popular protein folding python package, PyRosetta, which introduces coarse-grained (CG) residues into PyRosetta, enabling the folding of toy CG foldamer models. Although these models are simplified, they can help explore overarching physical hypotheses about how oligomers can form. Through systematic variation of CG parameters in these models, we can investigate various folding hypotheses at the CG scale to inform the design process of new foldamer chemistries. In this study, we demonstrate CG PyRosetta’s ability to identify minimum energy structures with a diverse structural search over a range of simple models, as well as two hypothesis-driven parameter scans investigating the effects of side-chain size and internal backbone angle on secondary structures. We are able to identify several types of secondary structures from single- and double-helices to sheet-like and knot-like structures. We show how side-chain size and backbone bond angle both play an important role in the structure and energetics of these toy models. Optimal side-chain sizes promote favorable packing of side chains, while specific backbone bond angles influence the specific helix type found in folded structures.

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“…From 3.6 residues-per-turn α-helices in proteins to 10.5 residues-per-turn double helices in B-DNA, 75 biopolymers adopt a wide range of helical secondary structures. Inspired by the diversity of helices observed in nature, we designed a parameter scan to explore the different helix types accessible with a simple 1b1s model.…”

Section: Internal Bond-angle Effect On Secondary Structurementioning

confidence: 99%

Folding Coarse-Grained Oligomer Models with PyRosetta

Fobe

Walker

Meek

et al. 2022

Preprint

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Non-biological foldamers are a promising class of macromolecules that share similarities to classical biopolymers such as proteins and nucleic acids. Currently, designing novel foldamers is a non-trivial process, often involving many iterations of trial synthesis and characterization until folded structures are observed. In this work, we aim to tackle these foldamer design challenges using computational modeling techniques. We developed CG PyRosetta, an extension to the popular protein folding python package, PyRosetta, which introduces coarse-grained (CG) residues into PyRosetta, enabling the folding of toy CG foldamer models. Through systematic variation of CG parameters in these models, we can investigate various folding hypotheses and generate folding principles at the CG scale to inform the design process of new foldamer chemistries. We demonstrate CG PyRosetta’s ability to identify minimum energy structures with a diverse structural search over a range of simple models and two hypothesis-driven parameter scans investigating the effects of side-chain size and internal backbone angle on secondary structure. We are able to identify several types of secondary structures from single- and double-helices to sheet-like and knot-like structures. We show how side-chain size and backbone bond angle both play an important role in the structure and energetics of these toy models. Optimal side-chain sizes promote favorable packing of side-chains, while specific backbone bond-angles influence the specific helix type found in folded structures.

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Dna

Cited by 12 publications

References 95 publications

Noncanonical Stacking Geometries of Nucleobases as a Preferred Target for Solar Radiation

Noncanonical Stacking Geometries of Nucleobases as a Preferred Target for Solar Radiation

Folding Coarse-Grained Oligomer Models with PyRosetta

Folding Coarse-Grained Oligomer Models with PyRosetta

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