Faculty Opinions recommendation of DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion.

2006 ◽  
Author(s):  
Alfred Pingoud
Keyword(s):  
Minor Groove ◽  
Base Flipping ◽  
Dna Nicking

scholarly journals Structural basis for error-free bypass of bulky adduct by DNA polymerase Polκ

2014 ◽  
Vol 70 (a1) ◽  
pp. C1401-C1401
Author(s):  
Vikash Jha ◽  
Hong Ling
Keyword(s):  
Biochemical Analysis ◽  
Minor Groove ◽  
Helical Conformation ◽  
Structural Basis ◽  
Base Flipping ◽  
Lesion Bypass ◽  
Anti Conformation ◽  
Diol Epoxides ◽  
Polycyclic Aromatic ◽  
Y Family

Humans are frequently exposed to the environmentally ubiquitous and potentially carcinigenic polycyclic aromatic hydrocarbon, benzo[a]pyrene (BP). BP is metabolized to highly reactive benzo[a]pyrene diol epoxides (BPDEs) in the cells. BPDEs react with DNA predominantly at the N2 position of guanine and form bulky adducts. The major BP adduct is (+)-trans-anti-[BP]-N2-dG (BP-N2-dG) that is carcinogenic. The bulky adduct block DNA synthesis by replicative or high-fidelity DNA polymerases. Some of the specialized lesion bypass polymerases (mostly belonging to Y-family) can replicate through this bulky adduct but often in an error prone manner, resulting in mutagenesis. Among the four human Y-family polymerases Polη, Polκ, Polι and Rev1, Polκ is unique in its ability for efficient and error-free replication through BP induced BP-N2-dG adduct. In this study, we determined the crystal structures of human Polκ (hPolκ) in ternary complex with DNA and an incoming nucleotide dCTP analogue. The crystals contain DNA with either G base or (+)-trans-anti-[BP]-N2-dG adduct at a template-primer junction and diffract to 2.5 Å and 2.8 Å, respectively. The structures reveal that hPolκ is able to accommodate the bulky adducted DNA in its minor groove without base flipping and nucleotide looping out. The bulky adduct has the polycyclic BP moiety in the minor groove in the regular helical conformation. Polκ has a unique active site that is more open at the minor groove side than other Y-family polymerases. The damaged guanine is in the anti-conformation, the dCMPNPP incoming nucleotide maintains normal Watson-Crick pairing with the G* base. This is the first structure of eukaryotic Y-family polymerase carrying the minor groove BP adduct. The structure and biochemical analysis provides a basis for understanding how hPolκ can correctly bypass and tolerate BP induced BP-N2-dG adduct in human cells.

Determination of Base Flipping Free Energy Landscapes from Nonequilibrium Stratification

2019 ◽  
Author(s):  
Xiaohui Wang ◽  
Zhaoxi Sun
Keyword(s):  
Free Energy ◽  
Energy Landscape ◽  
Sampling Technique ◽  
Umbrella Sampling ◽  
Energy Simulation ◽  
Nonlinear Dependence ◽  
Free Energy Landscape ◽  
Convergence Criterion ◽  
Base Flipping ◽  
Convergence Behavior

<p>Correct calculation of the variation of free energy upon base flipping is crucial in understanding the dynamics of DNA systems. The free energy landscape along the flipping pathway gives the thermodynamic stability and the flexibility of base-paired states. Although numerous free energy simulations are performed in the base flipping cases, no theoretically rigorous nonequilibrium techniques are devised and employed to investigate the thermodynamics of base flipping. In the current work, we report a general nonequilibrium stratification scheme for efficient calculation of the free energy landscape of base flipping in DNA duplex. We carefully monitor the convergence behavior of the equilibrium sampling based free energy simulation and the nonequilibrium stratification and determine the empirical length of time blocks required for converged sampling. Comparison between the performances of equilibrium umbrella sampling and nonequilibrium stratification is given. The results show that nonequilibrium free energy simulation is able to give similar accuracy and efficiency compared with the equilibrium enhanced sampling technique in the base flipping cases. We further test a convergence criterion we previously proposed and it comes out that the convergence behavior determined by this criterion agrees with those given by the time-invariant behavior of PMF and the nonlinear dependence of standard deviation on the sample size. </p>

scholarly journals Dissociation of minor groove binders from DNA: insights from metadynamics simulations

2008 ◽  
Vol 36 (18) ◽  
pp. 5910-5921 ◽  
Author(s):  
A. V. Vargiu ◽  
P. Ruggerone ◽  
A. Magistrato ◽  
P. Carloni
Keyword(s):  
Minor Groove ◽  
Minor Groove Binders ◽  
Groove Binders

scholarly journals Evaluation of a System to Screen for Stimulators of Non-Specific DNA Nicking by HIV-1 Integrase: Application to a Library of 50,000 Compounds

2011 ◽  
Vol 22 (2) ◽  
pp. 67-74 ◽  
Author(s):  
Malgorzata Sudol ◽  
Jennifer L Fritz ◽  
Melissa Tran ◽  
Gavin P Robertson ◽  
Julie B Ealy ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Screening ◽  
Solution Phase ◽  
The Novel ◽  
Endonuclease Activity ◽  
Viral Dna ◽  
Hit Rate ◽  
Dna Nicking ◽  
Hiv 1 ◽  
Stimulation Of

Background: In addition to activities needed to catalyse integration, retroviral integrases exhibit non-specific endonuclease activity that is enhanced by certain small compounds, suggesting that integrase could be stimulated to damage viral DNA before integration occurs. Methods: A non-radioactive, plate-based, solution phase, fluorescence assay was used to screen a library of 50,080 drug-like chemicals for stimulation of non-specific DNA nicking by HIV-1 integrase. Results: A semi-automated workflow was established and primary hits were readily identified from a graphic output. Overall, 0.6% of the chemicals caused a large increase in fluorescence (the primary hit rate) without also having visible colour that could have artifactually caused this result. None of the potential stimulators from this moderate-size library, however, passed a secondary test that included an inactive integrase mutant that assessed whether the increased fluorescence depended on the endonuclease activity of integrase. Conclusions: This first attempt at identifying integrase stimulator compounds establishes the necessary logistics and workflow required. The results from this study should encourage larger scale high-throughput screening to advance the novel antiviral strategy of stimulating integrase to damage retroviral DNA.

scholarly journals Spontaneous and frequent conformational dynamics induced by A…A mismatch in d(CAA)·d(TAG) duplex

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yogeeshwar Ajjugal ◽  
Kripi Tomar ◽  
D. Krishna Rao ◽  
Thenmalarchelvi Rathinavelan
Keyword(s):  
Mismatch Repair ◽  
Conformational Dynamics ◽  
Md Simulations ◽  
Umbrella Sampling ◽  
Base Flipping ◽  
Base Pairs ◽  
2D Noesy ◽  
Junction Formation ◽  
Nmr Techniques ◽  
Transient Events

AbstractBase pair mismatches in DNA can erroneously be incorporated during replication, recombination, etc. Here, the influence of A…A mismatch in the context of 5′CAA·5′TAG sequence is explored using molecular dynamics (MD) simulation, umbrella sampling MD, circular dichroism (CD), microscale thermophoresis (MST) and NMR techniques. MD simulations reveal that the A…A mismatch experiences several transient events such as base flipping, base extrusion, etc. facilitating B–Z junction formation. A…A mismatch may assume such conformational transitions to circumvent the effect of nonisostericity with the flanking canonical base pairs so as to get accommodated in the DNA. CD and 1D proton NMR experiments further reveal that the extent of B–Z junction increases when the number of A…A mismatch in d(CAA)·d(T(A/T)G) increases (1–5). CD titration studies of d(CAA)·d(TAG)n=5 with the hZαADAR1 show the passive binding between the two, wherein, the binding of protein commences with B–Z junction recognition. Umbrella sampling simulation indicates that the mismatch samples anti…+ syn/+ syn…anti, anti…anti & + syn…+ syn glycosyl conformations. The concomitant spontaneous transitions are: a variety of hydrogen bonding patterns, stacking and minor or major groove extrahelical movements (with and without the engagement of hydrogen bonds) involving the mismatch adenines. These transitions frequently happen in anti…anti conformational region compared with the other three regions as revealed from the lifetime of these states. Further, 2D-NOESY experiments indicate that the number of cross-peaks diminishes with the increasing number of A…A mismatches implicating its dynamic nature. The spontaneous extrahelical movement seen in A…A mismatch may be a key pre-trapping event in the mismatch repair due to the accessibility of the base(s) to the sophisticated mismatch repair machinery.

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