Four hundred twenty-eight high-resolution DNA–protein complexes were chosen for a bioinformatics study. Although 164 crystal structures (38% of those searched) contained no interactions, 574 discrete π–contacts between the aromatic amino acids and DNA nucleobases or deoxyribose identified using strict criteria, including visual inspection. The abundance structure interactions determined by unequivocally classifying contacts as either π–π stacking, T-shaped sugar–π contacts. Three forty-four...

5-Methylcytosine (5mC) in DNA CpG islands is an important epigenetic biomarker for mammalian gene regulation. It oxidized to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) by the ten-eleven translocation (TET) family enzymes, which are α-ketoglutarate (α-KG)/Fe(II)-dependent dioxygenases. In this work, we demonstrate that marker 5mC modified 5hmC, 5fC, 5caC vitro another class of α-KG/Fe(II)-dependent proteins—the repair enzymes AlkB family, include...

Insertion of an indanone handle into DNA oligonucleotides permits base-catalyzed aldol to create fluorescent molecular rotor (FMR) chalcones with turn-on fluorescence and brightness suitable for biosensing applications.

The structures and binding energies of a series C−H···X hydrogen-bonded complexes involving acetylene, ethylene, ethane as proton donors the first- second-row hydrides CH4, NH3, OH2, FH, PH3, SH2, ClH acceptors have been determined. Geometries were optimized with both MP2 B3-LYP methods in conjuction 6-311+G(3df,2p) basis set. In general, we note good agreement between structures. However, for some very weakly bound larger differences exist, particularly r(H···X) distance, these instances...

Detailed (gas-phase) MP2/6-31G*(0.25) potential energy surface scans and CCSD(T) calculations at the complete basis set (CBS) limit were used to analyze (face-to-face) stacking (edge-to-face) T-shaped interactions between histidine (modeled as imidazole) DNA nucleobases. For first time, a variety of relative monomer arrangements both neutral protonated natural nucleobases considered determine effects charge on optimum dimer geometry binding strength. Our results reveal that protonation...

The stacking and T-shaped interactions between the natural DNA or RNA nucleobases (adenine, cytosine, guanine, thymine, uracil) all aromatic amino acids (histidine, phenylalanine, tyrosine, tryptophan) were investigated using ab initio quantum mechanical calculations. We characterized potential energy surface of nucleobase-amino acid dimers MP2/6-31G*(0.25) method. stabilization energies in with strongest further examined at CCSD(T)/CBS level theory. Results highest theory possible for these...

The present work analyzed 120 high-resolution X-ray crystal structures and identified 335 RNA–protein π-interactions (154 nonredundant) between a nucleobase aromatic (W, H, F, or Y) acyclic (R, E, D) π-containing amino acid. Each contact was critically (including using visual inspection protocol) to determine the most prevalent composition, structure, strength of at interfaces. These contacts commonly involve F U, with U:F interactions comprising one-fifth total number found. Furthermore,...

Endonuclease V (EndoV) is a single-metal-dependent enzyme that repairs deaminated DNA nucleobases in cells by cleaving the phosphodiester bond, and this has proven to be powerful tool biotechnology medicine. The catalytic mechanism used EndoV must understood design new disease detection therapeutic solutions further exploit interdisciplinary applications. This study mixed molecular dynamics (MD) quantum mechanics/molecular mechanics (QM/MM) approach compare eight distinct pathways provides...

QM cluster and QM/MM calculations reveal that the single-metal dependent endonuclease I- Ppo I prefers direct metal coordination to leaving group of substrate break extremely stable phosphodiester bond in DNA.

Abstract The thrombin binding aptamer (TBA) is a prototypical platform used to understand the impact of chemically-modified nucleotides on stability and target affinity. To provide structural insight into experimentally-observed effects modification size, location, number performance, long time-scale molecular dynamics (MD) simulations were performed multiple orientations TBA–thrombin complexes that contain large, flexible tryptophan thymine derivative (T-W) or truncated analogue (T-K)....

Aldol condensation between phenolic aldehydes and a latent enolate indanone handle within DNA oligonucleotides provides access to fluorescent nucleobase GFP-surrogates with smart features for ratiometric detection strategies.

The geometries, relative energies, and hyperfine coupling constants of dehydrogenated, hydrogenated, hydroxylated radiation products, as well the anion cation, thymine (T), 1-methylthymine (1-MeT), uracil (U) are calculated through use density functional theory. results for T 1-MeT subsequently compared to accurate ENDOR experiments performed by Sagstuen co-workers (Sagstuen, E.; Hole, E. O.; Nelson, W. H.; Close, D. M. J. Phys. Chem. 1989, 93, 5974 references therein). theoretical support...

The geometries, spin density distributions, and hyperfine coupling constants (HFCC) in possible radiation products of guanine are studied through the use functional theory. Numerous hydrogenated, dehydrogenated, hydroxylated radicals examined compared to those obtained from detailed ESR/ENDOR studies on single crystals different derivatives. calculated couplings for anion deviate observed experimentally. possibility that radical assigned experimentally may fact be hydrogenated at O6 position...

The present work characterizes the gas-phase stacking interactions between four aromatic amino acid residues (histidine, phenylalanine, tyrosine, and tryptophan) adenine or 3-methyladenine due to proposed utilization of these by enzymes that repair DNA alkylation damage. MP2 potential energy surfaces stacked dimers are considered as a function variables (vertical displacement, angle rotation, horizontal tilt angle) using variety basis sets. It is found maximum interaction decreases with...

Despite remarkable stability, the phosphodiester bond of nucleic acids is hydrolytically cleaved in critical biological processes. Although this reaction commonly accepted to take place via a two-metal-assisted mechanism, recent experimental evidence suggests that several enzymes use single-metal ion, but precise catalytic mechanism unknown. In present work, we employ multiscale computational approach decipher cleavage for unique pathway by focusing on human APE1 repair enzyme, which...

Abstract A set of >300 nonredundant high-resolution RNA–protein complexes were rigorously searched for π-contacts between an amino acid side chain (W, H, F, Y, R, E and D) RNA nucleobase (denoted π–π interaction) or ribose moiety sugar–π). The resulting dataset >1500 visually inspected classified based on the interaction type, acids components involved. More than 80% structures contained at least one π-interaction, with contacts making up 59% identified interactions. sugar–π...

Reactive oxygen species damage DNA and result in health issues. The major product, 8-oxo-7,8-dihydroguanine (8oG), is repaired by human adenine glycosylase homologue (MUTYH). Although MUTYH misfunction associated with a genetic disorder called MUTYH-associated polyposis (MAP) potential target for cancer drugs, the catalytic mechanism required to develop disease treatments debated literature. This study uses molecular dynamics simulations quantum mechanics/molecular mechanics techniques...

Density functional theory is used to investigate various hydrogenated, dehydrogenated, and hydroxylated radicals formed upon irradiation of adenine. The relative energies, geometries, hyperfine coupling constants possible are discussed. couplings compared experimental data in order confirm the assignment particular specific radicals. C8-hydrogenated N9-dehydrogenated lowest energy their respective classes. Several degrees geometrical distortion exhibited adenine For example, C2- only...

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSodium Dodecyl sulfate Micellar Aggregation Numbers in the Presence of CyclodextrinsDavid J. Jobe, Vincent C. Reinsborough, and Stacey D. WetmoreCite this: Langmuir 1995, 11, 7, 2476–2479Publication Date (Print):July 1, 1995Publication History Published online1 May 2002Published inissue 1 July 1995https://pubs.acs.org/doi/10.1021/la00007a027https://doi.org/10.1021/la00007a027research-articleACS PublicationsRequest reuse permissionsArticle...

The (gas-phase) MP2/6-31G*(0.25) π···π stacking interactions between the five natural bases and aromatic amino acids calculated using (truncated) monomers composed of conjugated rings and/or (extended) containing biological backbone (either protein or deoxyribose sugar) were previously compared. Although preliminary energetic results indicated that strengthens, while sugar either strengthens weakens, interaction truncated models, reasons for these effects unknown. present work explains...

The ability of a dinucleoside monophosphate to mimic the conformation B-DNA was tested using combination different phosphate models (anionic, neutral, counterion), environments (gas, water), and density functionals (B3LYP, MPWB1K, M06-2X) with 6-31G(d,p) basis set. Three sequences (5′-GXPy-3′, where XPy = T, U or BrU) were considered, which vary in (natural modified) 3′ pyrimidine nucleobase (XPy). These bases selected due their presence natural DNA, structural similarity T and/or...