Extrahelical bases

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August undefined, 2024

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 … 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 …

Structural basis for broad DNA-specificity in integron

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) ... 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... how many gallons in jeep grand cherokee

Enzymatic capture of an extrahelical thymine in the search for …

WebAug 19, 2007 · Figure 1: Extrahelical uracil recognition by UNG and reaction coordinate tuning. Uracil emerges from the DNA base stack (reactant or R state) by spontaneous U•A base-pair breathing, where it... 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 the thermally induced movement of a base that is a feature of base-pair breathing 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 … how many gallons in hyundai elantra

Dynamics of uracil and 5-fluorouracil in DNA - PubMed

Archaeal DNA alkylation repair conducted by DNA glycosylase

WebFeb 6, 2009 · These studies suggest that DNA base damage can be located by repair proteins by using two mechanisms: a repair protein can probe and detect a weakened base pair that results from mutagenic or cytotoxic base damage; alternatively, a protein can passively capture and stabilize an extrahelical base lesion. WebApr 27, 2006 · These extrahelical bases, one of which is required for recombination in vivo, originate from folding of the bottom strand of attC … how many gallons in hyundai accentWebE-motif formed by extrahelical cytosine bases in DNA homoduplexes of trinucleotide and hexanucleotide repeats. Nucleic Acids Research 2024, 46 (2) , 942-955. DOI: … how many gallons in kia soul

"WebMar 29, 2005 · Base flipping is a highly conserved strategy used by enzymes to gain catalytic access to DNA bases that would otherwise be sequestered in the duplex … " - Extrahelical bases

Extrahelical bases

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 … WebFeb 18, 2011 · The extrahelical bases resulting from folding of attC bottom strands are important for the recognition by integrases. These enzymes are directly involved in the accumulation and formation of new cassette arrangements in the variable region of integrons. Thus, it is important to better understand interactions between IntIs and their …

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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 … 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 ...

WebFeb 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. WebDec 27, 2024 · A striking discovery was that 6mA might spontaneously flip out from the DNA duplex to form an extrahelical base during transient DNA melting or breathing events without the assistance by any other ...

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. WebSep 5, 1982 · In 0-10 M-NaCl D is 12 deg.C for the hybrid which is 5 to 9 deg.C higher than that ofRNA duplexes containing small numbers of extrahelical uridines (Lomant & …

WebJan 1, 2007 · The U.S. Department of Energy's Office of Scientific and Technical Information

WebJun 3, 2014 · Spontaneous 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 mismatched base is an important biophysical feature of DNA to discriminate damaged base from normal Watson–Crick paired ones. how many gallons in kegWebMay 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 ). how many gallons in keg beerWebFeb 13, 2009 · How some repair proteins, such as AGT (see figure), locate base lesions in DNA is still not fully understood.To remove a few damaged bases efficiently from the context of the entire genome, the DNA base repair proteins rely on remarkably specific detection mechanisms to locate base lesions. how many gallons in lake tahoeWebSpontaneous 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 mismatched base is an important biophysical feature of DNA to discriminate damaged base from normal Watson–Crick paired ones. how many gallons in lake erieWebJun 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 … how many gallons in kgWebApr 10, 2024 · Abstract Alkylated bases in DNA created in the presence of endogenous and exogenous alkylating agents are either cytotoxic or mutagenic, or both to a cell. Currently, cells have evolved several strategies for repairing alkylated base. One strategy is a base excision repair process triggered by a specific DNA glycosylase that is used for the repair … how many gallons in lusk reservoirWebMay 20, 2024 · The process of moving a DNA base extrahelical (base flipping) has been shown in the co-crystal structure of a UV-induced pyrimidine dimer-specific glycosylase, T4 endonuclease V, with its substrate DNA. Compared with other enzymes known to use base flipping, endonuclease V is unique in that it moves the base opposite the target how many gallons in lake george ny