Stabilization of a G-Quadruplex from Unfolding by Replication Protein A Using Potassium and the Porphyrin TMPyP4

Prakash, Aishwarya; Kieken, Fabien; Marky, Luis A.; Borgstahl, Gloria E. O.

doi:10.4061/2011/529828

Cited by 16 publications

(18 citation statements)

References 57 publications

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“…According to QGRS mapper [ 47 ], the G-rich sequence used in [ 22 ] is able to form a quadruplex structure. The similarity to RPA protein OB-fold supports our results of the quadruplex preferences, as RPA was shown to bind and unwind quadruplex DNA [ 58 , 59 ]. In our study, we showed greater binding of full length IFI16 protein to quadruplex DNA arising from G-rich single stranded than to double stranded DNA from the same sequence.…”

Section: Discussionsupporting

confidence: 77%

IFI16 Preferentially Binds to DNA with Quadruplex Structure and Enhances DNA Quadruplex Formation

et al. 2016

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Interferon-inducible protein 16 (IFI16) is a member of the HIN-200 protein family, containing two HIN domains and one PYRIN domain. IFI16 acts as a sensor of viral and bacterial DNA and is important for innate immune responses. IFI16 binds DNA and binding has been described to be DNA length-dependent, but a preference for supercoiled DNA has also been demonstrated. Here we report a specific preference of IFI16 for binding to quadruplex DNA compared to other DNA structures. IFI16 binds to quadruplex DNA with significantly higher affinity than to the same sequence in double stranded DNA. By circular dichroism (CD) spectroscopy we also demonstrated the ability of IFI16 to stabilize quadruplex structures with quadruplex-forming oligonucleotides derived from human telomere (HTEL) sequences and the MYC promotor. A novel H/D exchange mass spectrometry approach was developed to assess protein interactions with quadruplex DNA. Quadruplex DNA changed the IFI16 deuteration profile in parts of the PYRIN domain (aa 0–80) and in structurally identical parts of both HIN domains (aa 271–302 and aa 586–617) compared to single stranded or double stranded DNAs, supporting the preferential affinity of IFI16 for structured DNA. Our results reveal the importance of quadruplex DNA structure in IFI16 binding and improve our understanding of how IFI16 senses DNA. IFI16 selectivity for quadruplex structure provides a mechanistic framework for IFI16 in immunity and cellular processes including DNA damage responses and cell proliferation.

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Section: Discussionsupporting

confidence: 77%

IFI16 Preferentially Binds to DNA with Quadruplex Structure and Enhances DNA Quadruplex Formation

et al. 2016

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“…A second property of hRev1 that contributes to the dissolution of the G4 DNA structure is its ability to bind to ssDNA. In this way, hRev1 is acting in a manner analogous to RPA ( 45–48 ). The added effect of hRev1 binding to ssDNA on G4 disruption is manifest in the DMS footprinting results, but it is also apparent in the stopped-flow fluorescence assays where more pronounced changes in the amplitude of the signal are observed when the amount of enzyme is increased.…”

Section: Discussionmentioning

confidence: 99%

Human Rev1 polymerase disrupts G-quadruplex DNA

Eddy¹,

Ketkar²,

Zafar³

et al. 2013

Nucleic Acids Research

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The Y-family DNA polymerase Rev1 is required for successful replication of G-quadruplex DNA (G4 DNA) in higher eukaryotes. Here we show that human Rev1 (hRev1) disrupts G4 DNA structures and prevents refolding in vitro. Nucleotidyl transfer by hRev1 is not necessary for mechanical unfolding to occur. hRev1 binds G4 DNA substrates with Kd,DNA values that are 4–15-fold lower than those of non-G4 DNA substrates. The pre-steady-state rate constant of deoxycytidine monophosphate (dCMP) insertion opposite the first tetrad-guanine by hRev1 is ∼56% as fast as that observed for non-G4 DNA substrates. Thus, hRev1 can promote fork progression by either dislodging tetrad guanines to unfold the G4 DNA, which could assist in extension by other DNA polymerases, or hRev1 can prevent refolding of G4 DNA structures. The hRev1 mechanism of action against G-quadruplexes helps explain why replication progress is impeded at G4 DNA sites in Rev1-deficient cells and illustrates another unique feature of this enzyme with important implications for genome maintenance.

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“…These were dependent on replication polarity, suggesting that secondary structure formation can alter the binding of RPA at the replication fork in vivo (43). Similarly, Prakash et al found that RPA could stabilize G-quadruplex DNA against unfolding (55), suggesting an additional, previously unknown function of RPA in binding to non-B-DNA structures in vivo.…”

Section: Discussionmentioning

confidence: 99%

Oligodeoxynucleotide Binding to (CTG) · (CAG) Microsatellite Repeats Inhibits Replication Fork Stalling, Hairpin Formation, and Genome Instability

Liu

Chen

Leffak

2013

Molecular and Cellular Biology

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(CTG) n · (CAG) n trinucleotide repeat (TNR) expansion in the 3= untranslated region of the dystrophia myotonica protein kinase (DMPK) gene causes myotonic dystrophy type 1. However, a direct link between TNR instability, the formation of noncanonical (CTG) n · (CAG) n structures, and replication stress has not been demonstrated. In a human cell model, we found that (CTG) 45 · (CAG) 45 causes local replication fork stalling, DNA hairpin formation, and TNR instability. Oligodeoxynucleotides (ODNs) complementary to the (CTG) 45 · (CAG) 45 lagging-strand template eliminated DNA hairpin formation on leading-and laggingstrand templates and relieved fork stalling. Prolonged cell culture, emetine inhibition of lagging-strand synthesis, or slowing of DNA synthesis by low-dose aphidicolin induced (CTG) 45 · (CAG) 45 expansions and contractions. ODNs targeting the laggingstrand template blocked the time-dependent or emetine-induced instability but did not eliminate aphidicolin-induced instability. These results show directly that TNR replication stalling, replication stress, hairpin formation, and instability are mechanistically linked in vivo.

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Stabilization of a G-Quadruplex from Unfolding by Replication Protein A Using Potassium and the Porphyrin TMPyP4

Cited by 16 publications

References 57 publications

IFI16 Preferentially Binds to DNA with Quadruplex Structure and Enhances DNA Quadruplex Formation

IFI16 Preferentially Binds to DNA with Quadruplex Structure and Enhances DNA Quadruplex Formation

Human Rev1 polymerase disrupts G-quadruplex DNA

Oligodeoxynucleotide Binding to (CTG) · (CAG) Microsatellite Repeats Inhibits Replication Fork Stalling, Hairpin Formation, and Genome Instability

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