Stacking of the mutagenic DNA base analog 5-bromouracil

Holroyd, Leo F.; Mourik, Tanja van

doi:10.1007/s00214-013-1431-z

Cited by 10 publications

(13 citation statements)

References 47 publications

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“…The 5X‐uracils with X = F, Cl, Br, or I are employed to increase the sensitivity of DNA against ionising radiation and play roles in cancer treatment. 5‐Bromouracil is a known mutagen; the last years our group has been interested in the mutagenic mechanism of this base, including the role of hydration . Ho et al have shown that a halogen bond formed between a brominated uracil and an oxygen on a phosphate group can be engineered to direct the conformation of a DNA Holliday junction .…”

Section: Introductionmentioning

confidence: 99%

Competition between hydrogen and halogen bonding in halogenated 1‐methyluracil: Water systems

Hogan

Mourik

2016

J Comput Chem

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The competition between hydrogen‐ and halogen‐bonding interactions in complexes of 5‐halogenated 1‐methyluracil (XmU; X = F, Cl, Br, I, or At) with one or two water molecules in the binding region between C5‐X and C4O4 is investigated with M06‐2X/6‐31+G(d). In the singly‐hydrated systems, the water molecule forms a hydrogen bond with C4O4 for all halogens, whereas structures with a halogen bond between the water oxygen and C5‐X exist only for X = Br, I, and At. Structures with two waters forming a bridge between C4O and C5‐X (through hydrogen‐ and halogen‐bonding interactions) exist for all halogens except F. The absence of a halogen‐bonded structure in singly‐hydrated ClmU is therefore attributed to the competing hydrogen‐bonding interaction with C4O4. The halogen‐bond angle in the doubly‐hydrated structures (150–160°) is far from the expected linearity of halogen bonds, indicating that significantly non‐linear halogen bonds may exist in complex environments with competing interactions. © 2016 Wiley Periodicals, Inc.

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Section: Introductionmentioning

confidence: 99%

Competition between hydrogen and halogen bonding in halogenated 1‐methyluracil: Water systems

Hogan

Mourik

2016

J Comput Chem

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“…All other stacks have a rise value around 3.2 -3.3 Å. This is slightly shorter than the average distance between consecutive bases in B-DNA (3.4 Å [36]), but about 0.1-0.2 Å longer than in stacks optimised at the same level of theory but in the absence of the sugar-phosphate backbone [20][21][22]. In some stacks (for example A/T), replacing T by E leads to a slight increase in stacking energy.…”

Section: Stacked Basesmentioning

confidence: 93%

“…Adjacent purine bases stack α/β, whereas a 5'-pyrimidine/3'-purine pair stacks β/β and a 5'-pyrimidine/3'-purine pair stacks α/α. Previously, we had denoted these as face-to-face (α/α or β/β) or faceto-back (α/β or β/α) in stacked DNA base pairs [20][21][22]. Note that if there is no information on which base is on the 3' or 5' side (like in isolated stacked base pairs), then there is no distinction between α/α and β/β or between α/β and β/α.…”

Section: Methodsmentioning

confidence: 99%

“…As isolated stacks preferably adopt relative orientations (twist angles) that are not feasible in DNA [20][21][22], we first optimised the structures of the corresponding dinucleotides (the stacked bases connected by the sugarphosphate backbone). We considered dinucleotides with T or E at the 3'-end and one of the five bases at the 5'-end as well as dinucleotides with T or E at the 5'-end and the other base at the 3'-end.…”

Section: Methodsmentioning

confidence: 99%

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Stacking with the unnatural DNA base 6-ethynylpyridone

Gibson

Mourik

2017

Chemical Physics Letters

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It was previously reported that the incorporation of 6-ethynylpyridone (E) into a DNA duplex (replacing T in a T:A base pair) leads to DNA duplexes that are more stable than the T:Acontaining duplexes. DFT calculations at the M06-2X/6-31+G(d) and BLYP-D3/6-31+G(d) levels on various base pairs, stacked bases and stacked base pairs in continuum solvation water suggest that the observed increased stability of E:A-containing duplexes is due to the combined effects of stronger base pairing and enhanced stacking of the E:A base pair.

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“…Thus a newly developed hybrid meta functional method 17 M06-2X within the scope of Kohn-Sham density functional theory (DFT) is adopted to calculate the cellulose building blocks in this work. This method has been successfully applied to the hydrogen bonding and noncovalent interactions such as cellulose-based and organic materials according to the previous calculations [17][18][19] . The geometrical optimizations, energies and electronic properties are all computed with Gaussioan09 package 20 under the framework of linear combination of atomic orbital (LCAO) theory.…”

Section: Introductionmentioning

confidence: 99%

First-Principle Simulations on the Elongation of Polymerized Cellulose Building Blocks

Hongcun¹,

Wang²,

Wu³

2014

Asian J. Chem.

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This work presents first-principle simulations on the elongation effect of cellulose building blocks with different lengths. The models of finite oligomers and infinite polymers are both considered. The hydrogen bonding, total energies and electronic properties of the polymerized cellulose structures are investigated. The simulations confirm the hydrogen bonding in these cellulose building blocks. Due to the sizedependent effects at nanometer scale, the longer cellulose chains exhibit lower energies than the short. A quantitative relation of energy respect to number of glucose is obtained. It is found that the lengths of chains, the configuration and solvent effects are important factors for the electronic properties of the cellulose polymers. The energy band structures and Young's modulus of the cellulose polymers are also investigated based on first-principle calculations.

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Stacking of the mutagenic DNA base analog 5-bromouracil

Cited by 10 publications

References 47 publications

Competition between hydrogen and halogen bonding in halogenated 1‐methyluracil: Water systems

Competition between hydrogen and halogen bonding in halogenated 1‐methyluracil: Water systems

Stacking with the unnatural DNA base 6-ethynylpyridone

First-Principle Simulations on the Elongation of Polymerized Cellulose Building Blocks

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