Biophysical Characterization of an Ensemble of Intramolecular i-Motifs Formed by the Human c-MYC NHE III1 P1 Promoter Mutant Sequence

Dettler, Jamie M.; Buscaglia, Robert; Cui, Jingjing; Cashman, Derek J.; Blynn, Meredith; Lewis, Edwin A.

doi:10.1016/j.bpj.2010.04.042

Cited by 40 publications

(40 citation statements)

References 37 publications

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“…The nonlinear regression fitting was done using CHASM data analysis program developed in our laboratory [24]. The ITC fitting procedures used here have been described previously [17,19,25–27]. …”

Section: Methodsmentioning

confidence: 99%

Bcl-2 Promoter Sequence G-Quadruplex Interactions with Three Planar and Non-Planar Cationic Porphyrins: TMPyP4, TMPyP3, and TMPyP2

Nagesh

Lewis

2013

PLoS ONE

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The interactions of three related cationic porphyrins, TMPyP4, TMPyP3 and TMPyP2, with a WT 39-mer Bcl-2 promoter sequence G-quadruplex were studied using Circular Dichroism, ESI mass spectrometry, Isothermal Titration Calorimetry, and Fluorescence spectroscopy. The planar cationic porphyrin TMPyP4 (5, 10, 15, 20-meso-tetra (N-methyl-4-pyridyl) porphine) is shown to bind to a WT Bcl-2 G-quadruplex via two different binding modes, an end binding mode and a weaker mode attributed to intercalation. The related non-planar ligands, TMPyP3 and TMPyP2, are shown to bind to the Bcl-2 G-quadruplex by a single mode. ESI mass spectrometry experiments confirmed that the saturation stoichiometry is 4:1 for the TMPyP4 complex and 2:1 for the TMPyP2 and TMPyP3 complexes. ITC experiments determined that the equilibrium constant for formation of the (TMPyP4)1/DNA complex (K1 = 3.7 × 106) is approximately two orders of magnitude greater than the equilibrium constant for the formation of the (TMPyP2)1/DNA complex, (K1 = 7.0 × 104). Porphyrin fluorescence is consistent with intercalation in the case of the (TMPyP4)3/DNA and (TMPyP4)4/DNA complexes. The non-planar shape of the TMPyP2 and TMPyP3 molecules results in both a reduced affinity for the end binding interaction and the elimination of the intercalation binding mode.

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Section: Methodsmentioning

confidence: 99%

Bcl-2 Promoter Sequence G-Quadruplex Interactions with Three Planar and Non-Planar Cationic Porphyrins: TMPyP4, TMPyP3, and TMPyP2

Nagesh

Lewis

2013

PLoS ONE

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“…It is well known that CD spectrum for a typical i‐motif DNA structure exhibits a positive peak at (or near) 286 nm followed by a negative peak at 265 nm while the B‐DNA like structure exhibits a positive peak at (or near) 275 nm and negative peak at 254 nm. [ ] Figure A shows the CD spectra of 4 μM 11Py in sodium cacodylate buffer at varied pH (4.5, 5.7 and 7.0), containing 100 mM NaCl. At acidic pH, the CD spectrum of 11Py showed signature peak of i‐motif formation .…”

Section: Resultsmentioning

confidence: 99%

“…Later, several proteins have been identified that could shift the pKa of the formation of i‐motif to a more basic value and hence, can stabilize the i‐motif structure at either near neutral or neutral pH . Recent reports suggest that molecular crowding environment raise the p K a value of cytosine at N3 position which can fold the (CCT) 8 triple repeat DNAs or C‐rich sequences located in promoter region of c‐myc at neutral pH into i‐motif structure . Zhao et al (2008) reported the formation of stable i‐motif structure using single‐walled carbon nanotubes as a mimicking agent …”

Section: Resultsmentioning

confidence: 99%

Magnesium and molecular crowding of the cosolutes stabilize the i‐motif structure at physiological pH

et al. 2017

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Most of the important genomic regions, especially the G,C rich gene promoters, consist of sequences with potential to form G,C-tetraplexes on both the DNA strands. In this study, we used three C-rich oligonucleotides (11Py, 21Py, and HTPy), of which 11Py and 21Py are located at various transcriptional regulatory elements of the human genome while HTPy sequence is a C-rich strand of human telomere sequence. These C-rich oligonucleotides formed i-motif structures, verified by Circular Dichroism (CD), UV absorption melting experiments, and native gel electrophoresis. The CD spectra revealed that 11Py and 21Py form i-motif structures at acidic pH values of 4.5 and 5.7 in the presence of 100 mM NaCl but remain unstructured at pH 7.0. However, 21Py can form stable i-motif structure even at neutral pH in presence of 1 mM MgCl . UV-thermal melting studies showed stabilization of 21Py i-motif at pH 5.7 in the presence of Na or K with increasing concentration of MgCl or CaCl from 1 to 10 mM. Significant shift in the CD peak of HTPy sequence was observed as the positive peak from 286 nm shifted to 276 nm while the negative peak from 265 to 254 nm. Further, inevitable necessity of 1 mM Mg to form i-motif structure at neutral pH was observed. Under similar ionic conditions and neutral pH, all the three C-rich sequences were able to form stable i-motif structures (11Py, 21Py) or altered i-motif/homoduplex structures (HTPy) in the presence of MgCl and cell mimicking molecular crowding conditions of 40 wt% PEG 200. It is concluded that presence of Mg ions and molecular crowding agents induce and stabilize i-motif structures at physiological solution environment.

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“…6 E). Thus, these results indicate that factors such as the superhelical density of the DNA, the binding of specific proteins, and macromolecular crowding conditions inside the cell could facilitate the formation of i-motif structures under physiological conditions (101,102).…”

Section: The I-motif Blocks Primer Extension By Dna Polymerasementioning

confidence: 96%

Probing the Potential Role of Non-B DNA Structures at Yeast Meiosis-Specific DNA Double-Strand Breaks

Kshirsagar

Khan

Hosur

et al. 2017

Biophysical Journal

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A plethora of evidence suggests that different types of DNA quadruplexes are widely present in the genome of all organisms. The existence of a growing number of proteins that selectively bind and/or process these structures underscores their biological relevance. Moreover, G-quadruplex DNA has been implicated in the alignment of four sister chromatids by forming parallel guanine quadruplexes during meiosis; however, the underlying mechanism is not well defined. Here we show that a G/C-rich motif associated with a meiosis-specific DNA double-strand break (DSB) in Saccharomyces cerevisiae folds into G-quadruplex, and the C-rich sequence complementary to the G-rich sequence forms an i-motif. The presence of G-quadruplex or i-motif structures upstream of the green fluorescent protein-coding sequence markedly reduces the levels of gfp mRNA expression in S. cerevisiae cells, with a concomitant decrease in green fluorescent protein abundance, and blocks primer extension by DNA polymerase, thereby demonstrating the functional significance of these structures. Surprisingly, although S. cerevisiae Hop1, a component of synaptonemal complex axial/lateral elements, exhibits strong affinity to G-quadruplex DNA, it displays a much weaker affinity for the i-motif structure. However, the Hop1 C-terminal but not the N-terminal domain possesses strong i-motif binding activity, implying that the C-terminal domain has a distinct substrate specificity. Additionally, we found that Hop1 promotes intermolecular pairing between G/C-rich DNA segments associated with a meiosis-specific DSB site. Our results support the idea that the G/C-rich motifs associated with meiosis-specific DSBs fold into intramolecular G-quadruplex and i-motif structures, both in vitro and in vivo, thus revealing an important link between non-B form DNA structures and Hop1 in meiotic chromosome synapsis and recombination.

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Biophysical Characterization of an Ensemble of Intramolecular i-Motifs Formed by the Human c-MYC NHE III1 P1 Promoter Mutant Sequence

Cited by 40 publications

References 37 publications

Bcl-2 Promoter Sequence G-Quadruplex Interactions with Three Planar and Non-Planar Cationic Porphyrins: TMPyP4, TMPyP3, and TMPyP2

Bcl-2 Promoter Sequence G-Quadruplex Interactions with Three Planar and Non-Planar Cationic Porphyrins: TMPyP4, TMPyP3, and TMPyP2

Magnesium and molecular crowding of the cosolutes stabilize the i‐motif structure at physiological pH

Probing the Potential Role of Non-B DNA Structures at Yeast Meiosis-Specific DNA Double-Strand Breaks

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