93 research outputs found
Adenine versus guanine DNA adducts of aristolochic acids: role of the carcinogen-purine linkage in the differential global genomic repair propensity
Sherpa Romeo green journal: open accessComputational modeling is employed to provide
a plausible structural explanation for the
experimentally-observed differential global genome
repair (GGR) propensity of the ALII-N2-dG and ALIIN6-
dA DNA adducts of aristolochic acid II. Our modeling
studies suggest that an intrinsic twist at the
carcinogen–purine linkage of ALII-N2-dG induces
lesion site structural perturbations and conformational
heterogeneity of damaged DNA. These structural
characteristics correlate with the relative repair
propensities of AA-adducts, where GGR recognition
occurs for ALII-N2-dG, but is evaded for intrinsically
planar ALII-N6-dA that minimally distorts DNA and
restricts the conformational flexibility of the damaged
duplex. The present analysis on the ALII adduct
model systems will inspire future experimental studies
on these adducts, and thereby may extend the
list of structural factors that directly correlate with
the propensity for GGR recognition.Ye
DNA base sequence effects on bulky lesion-induced conformational heterogeneity during DNA replication
4-Aminobiphenyl (ABP) and its structure analog 2-aminofluorene (AF) are well-known carcinogens. In the present work, an unusual sequence effect in the 5′-CTTCTG1G2TCCTCATTC-3′ DNA duplex is reported for ABP- and AF-modified G. Specifically, the ABP modification at G1 resulted in a mixture of 67% major groove B-type (B) and 33% stacked (S) conformers, while at the ABP modification at G2 exclusively resulted in the B-conformer. The AF modification at G1 and G2 lead to 25%:75% and 83%:17% B:S population ratios, respectively. These differences in preferred conformation are due to an interplay between stabilizing (hydrogen bonding and stacking that is enhanced by lesion planarity) and destabilizing (solvent exposure) forces at the lesion site. Furthermore, while the B-conformer is a thermodynamic stabilizer and the S-conformer is a destabilizer in duplex settings, the situation is reversed at the single strands/double strands (ss/ds) junction. Specifically, the twisted biphenyl is a better stacker at the ss/ds junction than the coplanar AF. Therefore, the ABP modification leads to a stronger strand binding affinity of the ss/ds junction than the AF modification. Overall, the current work provides conformational insights into the role of sequence and lesion effects in modulating DNA replication
Computational evaluation of nucleotide insertion opposite expanded and widened DNA by the translesion synthesis polymerase Dpo4
Open accessExpanded (x) and widened (y) deoxyribose nucleic acids (DNA) have an extra benzene
ring incorporated either horizontally (xDNA) or vertically (yDNA) between a natural pyrimidine
base and the deoxyribose, or between the 5- and 6-membered rings of a natural purine. Far-reaching
applications for (x,y)DNA include nucleic acid probes and extending the natural genetic code.
Since modified nucleobases must encode information that can be passed to the next generation in
order to be a useful extension of the genetic code, the ability of translesion (bypass) polymerases
to replicate modified bases is an active area of research. The common model bypass polymerase
DNA polymerase IV (Dpo4) has been previously shown to successfully replicate and extend past a
single modified nucleobase on a template DNA strand. In the current study, molecular dynamics
(MD) simulations are used to evaluate the accommodation of expanded/widened nucleobases in the
Dpo4 active site, providing the first structural information on the replication of (x,y)DNA. Our results
indicate that the Dpo4 catalytic (palm) domain is not significantly impacted by the (x,y)DNA bases.
Instead, the template strand is displaced to accommodate the increased C1’–C1’ base-pair distance.
The structural insights unveiled in the present work not only increase our fundamental understanding
of Dpo4 replication, but also reveal the process by which Dpo4 replicates (x,y)DNA, and thereby
will contribute to the optimization of high fidelity and efficient polymerases for the replication of
modified nucleobases.Ye
Structural and energetic characterization of the major DNA adduct formed from the food mutagen ochratoxin A in the NarI hotspot sequence: influence of adduct ionization on the conformational preferences and implications for the NER propensity
Sherpa Romeo green journal, open accessThe nephrotoxic food mutagen ochratoxin A (OTA)
produces DNA adducts in rat kidneys, the major lesion
being the C8-linked-2 -deoxyguanosine adduct
(OTB-dG). Although research on other adducts
stresses the importance of understanding the structure
of the associated adducted DNA, site-specific
incorporation of OTB-dG into DNA has yet to be attempted.
The present work uses a robust computational
approach to determine the conformational
preferences of OTB-dG in three ionization states at
three guanine positions in the NarI recognition sequence
opposite cytosine. Representative adducted
DNA helices were derived from over 2160 ns of simulation
and ranked via free energies. For the first
time, a close energetic separation between three distinct
conformations is highlighted, which indicates
OTA-adducted DNA likely adopts a mixture of conformations
regardless of the sequence context. Nevertheless,
the preferred conformation depends on
the flanking bases and ionization state due to deviations
in discrete local interactions at the lesion
site. The structural characteristics of the lesion thus
discerned have profound implications regarding its
repair propensity andmutagenic outcomes, and support
recent experiments suggesting the induction of
double-strand breaks and deletion mutations upon
OTA exposure. This combined structural and energetic
characterization of the OTB-dG lesion in DNA
will encourage future biochemical experiments on
this potentially genotoxic lesion.Ye
DNA-protein pi-interactions in nature: abundance, structure, composition and strength of contacts between aromatic amino acids and DNA neucleobases or deoxyribose sugar
Sherpa Romeo green journal, open accessFour 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 pi-
contacts between the aromatic amino acids and the
DNA nucleobases or deoxyribose were identified using
strict criteria, including visual inspection. The
abundance and structure of the interactions were determined
by unequivocally classifying the contacts
as either pi–pi stacking, Pi–pi T-shaped or sugar–
pi contacts. Three hundred forty-four nucleobase–
amino acid pi–pi contacts (60% of all interactions
identified) were identified in 175 of the crystal structures
searched. Unprecedented in the literature, 230
DNA–protein sugar–pi contacts (40% of all interactions
identified) were identified in 137 crystal structures,
which involve C–H···pi and/or lone–pair···pi interactions,
contain any amino acid and can be classified
according to sugar atoms involved. Both pi–pi
and sugar–pi interactions display a range of relative
monomer orientations and therefore interaction energies
(up to –50 (–70) kJ mol−1 for neutral (charged)
interactions as determined using quantum chemical
calculations). In general, DNA–protein pi-interactions
are more prevalent than perhaps currently accepted
and the role of such interactions in many biological
processes may yet to be uncovered.Ye
Lewis acid behavior of MoF5 and MoOF4: syntheses and characterization of MoF5(NCCH3), MoF5(NC5H5)n, and MoOF4(NC5H5)n (n- 1, 2)
Accepted author manuscriptThe Lewis acid–base adducts MoF5(NC5H5)n and MoOF4(NC5H5)n (n = 1, 2) were synthesized from the reactions of MoF5 and MoOF4 with C5H5N and structurally characterized by X-ray crystallography. Whereas the crystal structures of MoF5(NC5H5)2 and MoOF4(NC5H5)2 are isomorphous containing pentagonal-bipyramidal molecules, the fluorido-bridged, heptacoordinate [MoF5(NC5H5)]2 dimer differs starkly from monomeric, hexacoordinate MoOF4(NC5H5). For the weaker Lewis base CH3CN, only the 1:1 adduct, MoF5(NCCH3), could be isolated. All adducts were characterized by Raman spectroscopy in conjunction with vibrational frequency calculations. Multinuclear NMR spectroscopy revealed an unprecedented isomerism of MoOF4(NC5H5)2 in solution, with the pyridyl ligands occupying adjacent or nonadjacent positions in the equatorial plane of the pentagonal bipyramid. Paramagnetic MoF5(NC5H5)2 was characterized by electron paramagnetic resonance (EPR) spectroscopy as a dispersion in solid adamantane as well as in a diamagnetic host lattice of MoOF4(NC5H5)2; EPR parameters were computed using ZORA with the BPW91 functional using relativistic all-electron wave functions for Mo and simulated using EasySpin. Density functional theory calculations (B3LYP) and natural bond orbital analyses were conducted to elucidate the distinctive bonding and structural properties of all adducts reported herein and explore fundamental differences observed in the Lewis acid behavior of MoF5 and MoOF4.Ye
Structural and biochemical impact of C8-aryl-guanine adducts within the NarI recognition DNA sequence: influence of aryl ring size on targeted and semi-targeted mutagenicity
Chemical mutagens with an aromatic ring system may be enzymatically transformed to afford aryl radical species that preferentially react at the C8-site of 2′-deoxyguanosine (dG). The resulting carbon-linked C8-aryl-dG adduct possesses altered biophysical and genetic coding properties compared to the precursor nucleoside. Described herein are structural and in vitro mutagenicity studies of a series of fluorescent C8-aryl-dG analogues that differ in aryl ring size and are representative of authentic DNA adducts. These structural mimics have been inserted into a hotspot sequence for frameshift mutations, namely, the reiterated G3-position of the NarI sequence within 12mer (NarI(12)) and 22mer (NarI(22)) oligonucleotides. In the NarI(12) duplexes, the C8-aryl-dG adducts display a preference for adopting an anti-conformation opposite C, despite the strong syn preference of the free nucleoside. Using the NarI(22) sequence as a template for DNA synthesis in vitro, mutagenicity of the C8-aryl-dG adducts was assayed with representative high-fidelity replicative versus lesion bypass Y-family DNA polymerases, namely, Escherichia coli pol I Klenow fragment exo− (Kf−) and Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4). Our experiments provide a basis for a model involving a two-base slippage and subsequent realignment process to relate the miscoding properties of C-linked C8-aryl-dG adducts with their chemical structure
Structural and biochemical impact of C8-aryl-guanine adducts within the Narl recognition DNA sequence: influence of aryl ring size on targeted and semi-targeted mutagenicity
Sherpa Romeo green journal, open accessChemical mutagens with an aromatic ring system
may be enzymatically transformed to afford aryl radical
species that preferentially react at the C8-site
of 2 -deoxyguanosine (dG). The resulting carbonlinked
C8-aryl-dG adduct possesses altered biophysical
and genetic coding properties compared to the
precursor nucleoside. Described herein are structural
and in vitro mutagenicity studies of a series of
fluorescent C8-aryl-dG analogues that differ in aryl
ring size and are representative of authentic DNA
adducts. These structural mimics have been inserted
into a hotspot sequence for frameshift mutations,
namely, the reiterated G3-position of the NarI sequence
within 12mer (NarI(12)) and 22mer (NarI(22))
oligonucleotides. In the NarI(12) duplexes, the C8-
aryl-dG adducts display a preference for adopting an
anti-conformation opposite C, despite the strong syn
preference of the free nucleoside. Using the NarI(22)
sequence as a template for DNA synthesis in vitro,
mutagenicity of the C8-aryl-dG adducts was assayed
with representative high-fidelity replicative versus
lesion bypass Y-family DNA polymerases, namely,
Escherichia coli pol I Klenow fragment exo− (Kf−)
and Sulfolobus solfataricus P2 DNA polymerase IV
(Dpo4). Our experiments provide a basis for a model
involving a two-base slippage and subsequent realignment
process to relate the miscoding properties of C-linked C8-aryl-dG adducts with their chemical
structures.Ye
Stabilization of [WF5]+ by bidentate N-donor ligands
Accepted author manuscriptTransition-metal hexafluorides do not exhibit fluoride-ion donor properties in the absence of donor ligands. We report the first synthesis of donor-stabilized [MF5]+ derived from a transition-metal hexafluoride via fluoride-ion abstraction using WF6(L) (L=2,2′-bipy, 1,10-phen) and SbF5(OSO) in SO2. The [WF5(L)][Sb2F11] salts and [WF5(1,10-phen)][SbF6]⋅SO2 have been characterized by X-ray crystallography, Raman spectroscopy, and multinuclear NMR spectroscopy. The reaction of WF6(2,2′-bipy) with an equimolar amount of SbF5(OSO) reveals an equilibrium between [WF5(2,2′-bipy)]+ and the [WF4(2,2′-bipy)2]2+ dication, as determined by 19F NMR spectroscopy. The geometries of the cations in the solid state are reproduced by gas-phase geometry optimizations (DFT-B3LYP), and NBO analyses reveal that the positive charges of the cations are stabilized primarily by compensatory σ-electron donation from the N-donor ligands.Ye
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