Structures for polyinosinic acid and polyguanylic acid

Arnott, Struther; Chandrasekaran, R.; Marttila, Constance M.

doi:10.1042/bj1410537

Cited by 272 publications

(144 citation statements)

References 14 publications

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“…23,24,26,27 GMP is monomeric in solution, whereas G9 and poly(G) adopt tetrastranded structures. 35 Quadruplex formation has been hypothesized to affect excited-state lifetimes on the basis of work with a polyG sequence containing 20 guanines 27 which is similar to a sequence containing 20 contiguous Gs flanked by thymine residues forms a quadruplex in sodium-containing buffer. 36 Additional quantum yield (and other photophysical) measurements on quadruplexes will be required to reveal the effects of guanine content and structure on the intrinsic fluorescence.…”

Section: Discussionmentioning

confidence: 99%

Fluorescence of unmodified oligonucleotides: A tool to probe G‐quadruplex DNA structure

Méndez

Szalai

2009

Biopolymers

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Fluorescence of unmodified oligonucleotides has not been exploited for guanine‐quadruplex (G‐quadruplex) characterization. We observe that G‐rich sequences fluoresce more strongly than duplex or single‐stranded DNA but much more weakly than fluorophores like fluorescein. This increase in the intrinsic fluorescence is not due to an increase in absorption at the excitation wavelength but rather to a change in the quantum yield. We show that unlabeled oligonucleotides that form G‐quadruplexes can be differentiated on the basis of their emission spectra from similar sequences that do not contain consecutive guanines. Intermolecular quadruplexes formed by the oligonucleotides 5′‐T4GnT4‐3′ (n = 4–10) display a nonlinear, but continuous, increase in emission intensity as the G content increases. The sequence 5′‐GGGT‐3′, which has been proposed to form a monomeric quadruplex and an interlocked quadruplex (Krishnan‐Ghosh et al. J Am Chem Soc 2004, 126, 11009), was compared with the similar sequence 5′‐TGGG‐3′, the structure of which has not been characterized. Both the maximum emission intensity and the spectral shape differ for these oligonucleotides as a function of sample preparation, indicating that different types of quadruplexes form for both sequences. Our work is the first to demonstrate that the suprastructure of G‐rich sequences can be probed using fluorescence signatures of unmodified oligonucleotides. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 841–850, 2009.This article was originally published online as an accepted preprint. The ”Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

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Section: Discussionmentioning

confidence: 99%

Fluorescence of unmodified oligonucleotides: A tool to probe G‐quadruplex DNA structure

Méndez

Szalai

2009

Biopolymers

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“…This suggests that the (dG), strand is bent in three places, with three exposed and methylated loops. The fact that all four segments flanking the loops are simultaneously protected against methylation at their N7 positions can only mean (15) that these loci are shielded by formation of Hoogsteen-like hydrogen-bonded tetrads (16,17) like that shown in Fig. 2.…”

mentioning

confidence: 99%

“…4). The core of the model contains 16 guanines forming a helix of four tetrads (Fig. 2), and each of the three loops 1-3 contains three unpaired guanines.…”

mentioning

confidence: 99%

G-DNA: a twice-folded DNA structure adopted by single-stranded oligo(dG) and its implications for telomeres.

Panyutin

Kovalsky

Budowsky

et al. 1990

Proc. Natl. Acad. Sci. U.S.A.

103

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Our dimethyl sulfate modification experiments suggest that (dG). stretches within single-stranded DNA fragments, which represent the simplest model for telomeric sequences, adopt a complex intrastrand structure other than a simple hairpin. We present a molecular model for the DNA structure that conforms to dimethyl sulfate methylation data. The principal element of this G-DNA structure is a quadruple helix formed by pairwise antiparallel segments of the twicefolded (dG). stretch. This quadruple core has two wide and two narrow grooves connected by three loop-shaped segments. The strong stacking interactions of the neighboring guanine tetrads and the large number of hydrogen bonds formed can be the primary reasons that such structures are favored over a common hairpin for long (dG pPG27, which contain (dG),-(dC)" inserts at the Pst I site of pUC18 with n = 37 and 27, respectively. It has been found (11) that, after the short insert-containing restriction fragments have been denatured, the (dG),-and (dC)Q-containing strands renature much more slowly than do those of arbitrary sequence. In addition, the (dG)n strand has an abnormally high mobility in polyacrylamide gel electrophoresis (PAGE) (11). These data argue in favor of the existence within (dG),-containing single-stranded fragments of an intrastrand structure (G structure) stabilized by formation of hydrogen bonds between guanines. In this paper we describe the results of methylation experiments on the oligo(dG)-containing frag- (14). However, the G-structure methylation pattern for longer stretches-(dG)27 and (dG)37-is more complicated (Fig. 1). Clear maxima and minima of modification are seen against the background of general diminution of peak amplitude associated with overmodification (more than one dimethyl sulfate modification per fragment). The maxima between extremities are positioned at one-quarter, one-half, and three-quarters of the way along the insert. This suggests that the (dG), strand is bent in three places, with three exposed and methylated loops. The fact that all four segments flanking the loops are simultaneously protected against methylation at their N7 positions can only mean (15) that these loci are shielded by formation of Hoogsteen-like hydrogen-bonded tetrads (16,17) like that shown in Fig. 2. But in any event, the similarity of disposition of maxima and minima for the (dG)27 and (dG)37 oligomers shows that these two share a common structure, whatever §Present address:

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“…This intriguing structural motif was proposed some time ago based on fiber diffraction studies (2)(3)(4) and only recently has been rediscovered. This rekindled interest has been fueled, in part, by the recognition that telomeres, the 3' single-stranded guanine-rich overhangs found at the termini ofchromosomes, (5)(6)(7)(8) may form G-DNA type structures of potential biological significance (1,(9)(10)(11)(12)(13)(14).…”

mentioning

confidence: 99%

Thermodynamics and structure of a DNA tetraplex: a spectroscopic and calorimetric study of the tetramolecular complexes of d(TG3T) and d(TG3T2G3T).

Jin

Gaffney

Wang

et al. 1992

Proc. Natl. Acad. Sci. U.S.A.

192

127

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We report a combined thermodynamic and structural characterization of a DNA tetraplex. Using spectroscopic and calorimetric techniques, we demonstrate that d(TG3T) and d(TG3T2G3T), in the presence of K+, form stable tetramolecular complexes. From differential anning calorimetry measurements, we obtain the following thermodynamic profiles for formation of each tetraplex at 25C: AG' = -6.9 kcal/mol oftetraplex (or -2.3 kcal/mol of tetrad; 1 cal = 4.184 X), AH0 = -62.6 kcal/mol of tetraplex (or -20.9 kcal/mol of tetrad), andl S°= -186.9 cal'K-1mol' of tetraplex (or -62.3 cal'K'1 mol'1 of tetrad) for the d(TG3T) tetraplex; and AG0 = -20.2 kcal/mol of tetraplex (or -3.4 kcal/mol of tetrad), AH0 = -123.2 kcal/mol of tetraplex (or -20.5 kcal/mol of tetrad), and ASo = -346.0 calK'1mol-1 of tetraplex (or -57.7 cal K'1 mol'1 of tetrad) for the d(TG3T2G3T) tetraplex. These data demonstrate that at 25'C a G-tetrad can exhibit considerable stability, comparable to or even exceeding that of most Watson-Crick nearest-neighbor interactions, with this stability resulting from a very favorable enthalpy of formation. Temperature-dependent CD measurements reveal that the melting temperatures of both tetraplexes exhibit unusually low salt dependences. This unexpected behavior may reflect a diminished charge density due to bound K+ ions. For each complex, the Na+ and K+ forms exhibit drastically different isothermal and temperature-dependent CD profiles, with the K+ forms of each tetraplex melting more sharply and at a higher temperature than the Na+ forms. Using one-and two-dimensional NMR techniques, we show that the strands in the tetramolecular complex of d(TG3T),K+ are all parallel and that the guanine glycosidic conformations are all and.

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Structures for polyinosinic acid and polyguanylic acid

Cited by 272 publications

References 14 publications

Fluorescence of unmodified oligonucleotides: A tool to probe G‐quadruplex DNA structure

Fluorescence of unmodified oligonucleotides: A tool to probe G‐quadruplex DNA structure

G-DNA: a twice-folded DNA structure adopted by single-stranded oligo(dG) and its implications for telomeres.

Thermodynamics and structure of a DNA tetraplex: a spectroscopic and calorimetric study of the tetramolecular complexes of d(TG3T) and d(TG3T2G3T).

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