Specificity of hydroxylmethyluracil-containing DNA for transcription factor 1: Structural insights

Vu, Hai Minh; Pasternack, Laura B.; Kearns, David R.

doi:10.1002/(sici)1097-0282(1999)52:1<57::aid-bip3>3.0.co;2-k

Cited by 4 publications

(3 citation statements)

References 43 publications

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“…This interesting preference for HmU-containing sequences is probably not a result of direct DNA−protein contacts involving HmU. Instead, HmU was found to confer more flexibility to the DNA and thus increase binding of TF1 (which is known to bend DNA) to the HmU-containing site relative to thymine-containing DNA ( , ). NMR studies done by Vu et al suggest that the extra flexibility conferred by HmU in the TF1 DNA-binding sequence is due to intra -strand hydrogen bonds formed by HmU and its neighboring adenine, which weakens the inter -strand Watson−Crick hydrogen bonds of HmU and its base pairing partner, adenine ().…”

Section: Discussionmentioning

confidence: 99%

“…This interesting preference for HmU-containing sequences is probably not a result of direct DNA-protein contacts involving HmU. Instead, HmU was found to confer more flexibility to the DNA and thus increase binding of TF1 (which is known to bend DNA) to the HmU-containing site relative to thymine-containing DNA (76,77) sequence is due to intra-strand hydrogen bonds formed by HmU and its neighboring adenine, which weakens the interstrand Watson-Crick hydrogen bonds of HmU and its base pairing partner, adenine (77). Despite these nondeleterious and even beneficial (in the case of SPO1 phage) effects of HmU in DNA, higher organisms have repair activities that remove HmU paired with A (51-56).…”

Section: Implications Of U:a Base Pairs In Dnamentioning

confidence: 98%

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Endogenous DNA Lesions Can Inhibit the Binding of the AP-1 (c-Jun) Transcription Factor

et al. 2002

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The repair of DNA damage, caused by both endogenous and exogenous sources, is necessary to remove lesions that either miscode or block DNA or RNA polymerases. We propose that damage also must be repaired to maintain sequence-specific DNA-protein interactions. In this paper, we have systematically studied two lesions that interfere with one important DNA landmark, the thymine methyl group. Oxidation of the thymine methyl group in DNA generates 5-hydroxymethyluracil (HmU) whereas the misincorporation of dUMP into DNA generates uracil (U), replacing the methyl group with a hydrogen. Both substitutions are shown to inhibit binding of the AP-1 (c-Jun) transcription factor. The energy cost of the perturbation, approximately 0.4 kcal/mol, is similar in magnitude for both U and HmU substitutions and is additive when multiple substitutions are present. A third lesion, substitution of the central C:G base pair of the AP-1 DNA binding domain with the pro-mutagenic U:G mispair, unexpectedly increases AP-1 binding, allowing the transcription factor to interfere with uracil DNA glycosylase activity. Our results support the hypothesis that an additional role for DNA repair systems is to maintain the integrity of sequence-specific DNA-protein interactions, a role of particular importance in long-lived organisms.

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Section: Discussionmentioning

confidence: 99%

Section: Implications Of U:a Base Pairs In Dnamentioning

confidence: 98%

Endogenous DNA Lesions Can Inhibit the Binding of the AP-1 (c-Jun) Transcription Factor

et al. 2002

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“…Can't you see it?' 80 In a final dream Đào dreams that she has found and put on the lei with Sinh's fingers dangling from it: 'She stepped back to look at her own monstrous visage in the mirror. Singh's nails twinkled at her décolletage.…”

Section: Questions Ofmentioning

confidence: 99%

Australian Writing and the Contemporary: Are We There Yet?

Lawrence

2016

CSR

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Australia’s geographical location (within ‘Asia’)—seen as a negative into the twenty-first century when the nation defined itself as culturally and aspirationally linked to the major Euro-American metropolitan cultural centres (the ‘West’)—must now be reevaluated. After two hundred years of white settlement and of turning its back on the region in which it is located, some Australian writers are writing texts that illuminate an aspect of Australian literature that is in transition, becoming, by definition, in, of, and with the region as well as in, of, and with present time. Art historian Terry Smith’s theory of the three currents of contemporary art, particularly the third current, suggests a new paradigm, a potential break from modernism, and a different kind of entanglement and interconnection in a world that is witnessing shifts in world power, voluntary and involuntary mass movements of people, and real time global communication technologies. Adrian Snodgrass and David Coyne’s application of hermeneutical theory to the architectural design studio via the metaphor of excursion and return illuminates some imaginative intersections, understandings and energies in three texts by Australian authors—Michelle De Kretser, Chi Vu and Jennifer Mackenzie. In Smith’s terms too, the texts perform original leaps of the imagination in their diversity, freshness, and ability to surprise and invite questions about literature’s potential to stir up prior understandings and invite new ways of being in the present. In terms of Giorgio Agamben’s definition of the contemporary, the three texts bring the reader to a plurality and intercultural connectedness that we have yet to fully recognise and live. They represent a line of flight towards a literary imaginary in Australian writing that is contemporary, locally grounded, but also regionally and globally entangled.

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Solution structure of a mutant of transcription factor 1: implications for enhanced DNA binding

et al. 2000

Journal of Molecular Biology

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Specificity of hydroxylmethyluracil-containing DNA for transcription factor 1: Structural insights

Cited by 4 publications

References 43 publications

Endogenous DNA Lesions Can Inhibit the Binding of the AP-1 (c-Jun) Transcription Factor

Endogenous DNA Lesions Can Inhibit the Binding of the AP-1 (c-Jun) Transcription Factor

Australian Writing and the Contemporary: Are We There Yet?

Solution structure of a mutant of transcription factor 1: implications for enhanced DNA binding

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