Chemical-induced formation of BZ-junction with base extrusion

Subramani, Vinod Kumar; Ravichandran, S.; Bansal, Varun; Kim, Kyeong Kyu

doi:10.1016/j.bbrc.2018.12.045

Cited by 17 publications

(12 citation statements)

References 25 publications

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“…3D. It is worth noting that such base extrusions at the B-Z junction have been reported in earlier investigations (PDB ID: 2ACJ 32,33 ). The backbone conformational angles (ε, ζ, α, γ) at C 7 A 8 , A 8 A 9 , A 9 C 10 , G 21 T 22 , T 22 A 23 and G 24 T 25 base steps predominantly favor BIII and ZI conformations.…”

Section: Resultssupporting

confidence: 72%

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

Ajjugal

Tomar

Rao

et al. 2021

Sci Rep

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Base 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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Section: Resultssupporting

confidence: 72%

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

Ajjugal

Tomar

Rao

et al. 2021

Sci Rep

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“…Previous studies had shown similar binding affinities for small cations such as [Co(NH 3 ) 6 ] 3+ with respect to DNA and heparin [10] . DNA binding of [Co(NH 3 ) 6 ] 3+ has been well studied, especially the ability to induce B → Z conformational changes in canonical DNA sequences [23, 24] . Gel retardation assays confirmed the ability of WC to bind to nucleic acids and inhibit migration of plasmid pSP73 and tRNA, again more efficiently than [Co(NH 3 ) 6 ] 3+ (Figure S16).…”

Section: Resultssupporting

confidence: 53%

“…[10] DNAbinding of [Co(NH 3 ) 6 ] 3+ has been well studied, especially the ability to induce B!Z conformational changes in canonical DNA sequences. [23,24] Gel retardation assays confirmed the ability of WC to bind to nucleic acids and inhibit migration of plasmid pSP73 and tRNA, again more efficiently than [Co(NH 3 ) 6 ] 3+ (Figure S16). Thel ow mm concentrations needed for WC are similar to those for heparin binding,s uggesting similar binding affinities of WC to both biomolecules,a ss een previously for [Co(NH 3 ) 6 ] 3+ and [CoCl(NH 3 ) 5 ] 2+ .…”

Section: Antiproliferative Effects and Morphologymentioning

confidence: 85%

On the Biology of Werner's Complex

et al. 2021

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WernersC omplex, as ac ationic coordination complex (CCC), has hitherto unappreciated biological properties derived from its binding affinity to highly anionic biomolecules such as glycosaminoglycans (GAGs) and nucleic acids.C ompetitive inhibitor and spectroscopic assays confirm the high affinity to GAGs heparin, heparan sulfate (HS), and its pentasaccharide mimetic Fondaparinux (FPX). Functional consequences of this affinity include inhibition of FPX cleavage by bacterial heparinase and mammalian heparanase enzymes with inhibition of cellular invasion and migration. WernersC omplex is av ery efficient condensing agent for DNAa nd tRNA. In proof-of-principle for translational implications,i ti sd emonstrated to displaya ntiviral activity against human cytomegalovirus (HCMV) at micromolar concentrations with promising selectivity.E xploitation of non-covalent hydrogen-bonding and electrostatic interactions has motivated the unprecedented discovery of these properties, opening new avenues of researchf or this iconic compound.

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“…Helical conformation variance is also induced by the sequence of the bases [ 10 ], e.g., the A-form can be induced by purine-based fragments, while the B-DNA is mostly favored by mixed bases. The transition between DNA-forms is caused by chemicals interactions [ 11 ], such as with ruthenium and spermidine, as well as by methylation events [ 12 ], where a methyl group is added to the fifth carbon of the cytosine residue. The recognition and interaction of the double-strand with proteins during relevant cellular processes can be maximized, optimized, and produced by local variations to the B-form of the nucleic acid, as reported for a large number of DNA-binding proteins [ 13 , 14 , 15 ].…”

Section: Overview Of Nucleic Acidsmentioning

confidence: 99%

DNA Studies: Latest Spectroscopic and Structural Approaches

et al. 2021

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This review looks at the different approaches, techniques, and materials devoted to DNA studies. In the past few decades, DNA nanotechnology, micro-fabrication, imaging, and spectroscopies have been tailored and combined for a broad range of medical-oriented applications. The continuous advancements in miniaturization of the devices, as well as the continuous need to study biological material structures and interactions, down to single molecules, have increase the interdisciplinarity of emerging technologies. In the following paragraphs, we will focus on recent sensing approaches, with a particular effort attributed to cutting-edge techniques for structural and mechanical studies of nucleic acids.

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Chemical-induced formation of BZ-junction with base extrusion

Cited by 17 publications

References 25 publications

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

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

On the Biology of Werner's Complex

DNA Studies: Latest Spectroscopic and Structural Approaches

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