Extrahelical bases

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August undefined, 2024

WebFeb 18, 2011 · Integron integrases (IntIs) bind specifically to the bottom strand of attC sites. The extrahelical bases resulting from folding of attC bottom strands are important … WebJun 20, 2024 · Base-flipping dynamics from an intrahelical to an extrahelical state exerted by thymine DNA glycosylase during DNA repair process. Thymine DNA glycosylase …

Enzymatic capture of an extrahelical thymine in the search …

WebE-motif formed by extrahelical cytosine bases in DNA homoduplexes of trinucleotide and hexanucleotide repeats. Nucleic Acids Research 2024, 46 (2) , 942-955. DOI: … WebJan 1, 2007 · The U.S. Department of Energy's Office of Scientific and Technical Information csse comprehension

Damage detection and base flipping in direct DNA alkylation repair

WebJan 5, 2024 · extrahelical (not comparable) Beyond, or temporarily removed from the double helix, of a nucleic acid molecule; Usage notes . Used especially to describe … Weboff) and extrahelical base (k on* [E] and k off*), and the rate of site repair if X is a damaged base (k repair). For completeness, a kinetic step for enzyme translocation along the DNA is also shown WebSpontaneous flipping of a single DNA base to an extrahelical position is a fundamental issue in DNA biophysics. The dynamics of such spontaneous flipping of a lesion or … marco gelfi

Base-flipping dynamics from an intrahelical to an …

Archaeal DNA alkylation repair conducted by DNA glycosylase

WebApr 27, 2006 · The extrahelical base G20″ is buried in a deep hydrophobic pocket, located in subunits A/C bound to the other VCR bs duplex, thus forming a set of trans -interactions that hold the synaptic... WebFeb 22, 2007 · Biological assembly 1 assigned by authors. Macromolecule Content Total Structure Weight: 31.21 kDa Atom Count: 2,582 Modelled Residue Count: 242 Deposited Residue Count: 242 Unique protein chains: 1 Unique nucleic acid chains: 2 Display Files Download Files 2OYT Crystal Structure of UNG2/DNA (TM) PDB DOI: … marco genchi uniprWebFeb 8, 2011 · Each of these enzymes uses an extrahelical base recognition mechanism, and previous studies with UNG have shown that extrahelical recognition is facilitated by destabilized base pairs possessing kinetically enhanced base pair opening rates. marco gemini official

"WebAbstract. The efficient enzymatic detection of damaged bases concealed in the DNA double helix is an essential step during DNA repair in all cells. Emergent structural … " - Extrahelical bases

Extrahelical bases

The Origins of High-Affinity Enzyme Binding to an Extrahelical …

WebOct 25, 2024 · When the proper base is flipped or not flipped, as encoded by the specific interactions of the finger loop with DNA, the downstream effect of the SRA-DNA interaction is recognized. Our analysis of published SRA–DNA complexes revealed a variety of extrahelical bases, bound DNA sequences, and SRA:DNA stoichiometries (Table 1). In … WebMar 25, 2008 · The free energies projected onto d 1 and d 2 (the unstacking step) were essentially the same for the two bases, with the extrahelical conformation somewhat lower in free energy than the intrahelical conformation. That the protein significantly stabilizes a base separated state (compare with SI Fig. 8) ...

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WebApr 26, 2006 · The left (L) and right (R) IntI-binding sites are boxed and the extrahelical bases are shown. The inactive IntI monomers (purple) bound to L are inactivated by conformational changes resulting... WebFeb 20, 2007 · The enzyme uracil DNA glycosylase (UNG) excises unwanted uracil bases in the genome using an extrahelical base recognition mechanism. Efficient removal of uracil is essential for prevention of C-to-T transition mutations arising from cytosine deamination, cytotoxic U*A pairs arising from incorporation of dUTP in DNA, and for …

WebMay 20, 2004 · The G7:G7′ base pair is severely tilted with respect to the main helix axis, but is stacked well on the spatially adjacent C5:G8′ and G8:C5′ base pairs. The ribbon trace emphasizes the structural distortion induced by the extrahelical position of C6 and C6′ bases in the minor groove (Fig. (Fig.6A), 6 A), and the unusually narrow major ... WebJun 20, 2024 · The former NMR studies suggest that UDG captures the damaged bases in a passive scenario whereby the extrahelical bases emerge spontaneously by thermal …

WebMay 14, 2024 · The former NMR studies suggest that UDG captures the damaged bases in a passive scenario whereby the extrahelical bases emerge spontaneously by thermal motions of DNA chains as UDG is searching for the lesions ( 23, 58 ), while an active role of UDG has also been proposed by other biochemical studies ( 46, 48 ). WebSep 5, 1982 · The base alterations induced by four alkylating agents, methyl methanesulfonate (MMS), ethyl methanesulfonate (EMS), N-nitroso-N-methylurea …

WebAug 19, 2007 · The implication was that spontaneous thermally induced opening of T•A and U•A base pairs exposes an extrahelical state that sets in motion the remainder of the base-flipping process.

csse finvizWebFig. 3 Global architecture of the Fpg extrahelical base binding pocket. As indicated, the cFapydG (green)-containing DNA (gray) is stabilized in extrahelical conformation in a large Fpg cavity. The accessibility surfaces of the protein clearly show that this cavity is highly exposed to water molecules. csse familiarisation paperWebJan 5, 2024 · extrahelical (not comparable) Beyond, or temporarily removed from the double helix, of a nucleic acid molecule; Usage notes . Used especially to describe the thermally induced movement of a base that is a feature of base-pair breathing marco gennaro