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

Abstract

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.

A Protein from Tetrahymena thermophila That Specifically Binds Parallel-Stranded G4-DNA

“…Telomeric and nontelomeric G-rich sequences can form G4-DNA structures [reviewed by Sundquist (1991), Henderson et al (1987), Williamson et al (1989), Sundquist and Klug (1989), Sen and Gilbert (1990), Jin et al (1992), Kang et al (1992), and Smith and Feigon (1992)l. This study demonstrates that Tetrahymenacontains an abundant protein, TGP, that binds specifically to G4 structures formed by the telomeric G-strand sequence d(TzG4)4 and not to Tet 4 intramolecular foldback monomers or to unstructured Tet 4 monomers.…”

“…Synthetic oligonucleotides containing telomeric G-strand sequences are able to form unusual structures mediated by cyclic hydrogen-bonded arrays of guanines (G-quartets) [reviewed by Sundquist (1991), Williamson et al (1989), Sundquist and Klug (1989), Kang et al (1992), and Smith and Feigon (1992)l. These structures include antiparallel, intramolecular quadruplex (G'2-DNA) (Henderson et al, 1987;Williamson et al, 1989;Sen & Gilbert, 1990;Jin et al, 1990;Kang et al, 1992) and parallel-stranded intermolecular quadruplex (G4-DNA) structures (Zimmerman et al, 1975;Sen & Gilbert, 1990;Jin et al, 1992;Aboul-ela et al, 1992;Gupta et al, 1993). Intramolecular G-DNA structures migrate faster than linear forms of the same length in nondenaturing gels (Henderson et al, 1987;Williamson et al, 1989) while intermolecular structures migrate more slowly (Sen & Gilbert, 1990;Acevedo et al, 1991;Sundquist & Klug, 1989).…”

In vitrogenerated antibodies specific for telomeric guanine-quadruplex DNA react withStylonychia lemnaemacronuclei

“…For selection, we used the biotinylated Stylonychia telomeric sequence, denoted b-sty (5Ј-TTTTTGGGGTTTTGGGGTTTTGGGGTTTTGGGG-3Ј), in the parallel quadruplex conformation. Parallel and antiparallel quadruplex structures of the sequences examined were prepared as described (11,22) and further purified to conformational homogeneity by gel filtration with a Superdex-75 column (Amersham Pharmacia). All DNA conformations were confirmed by CD spectroscopy using a Jasco 715 spectropolarimeter (11,23).…”

“…It has been shown that the G-rich overhang can adopt a variety of unusual DNA structures (4), of which guanine-quadruplex DNA and t-loops are stable in vitro under physiological conditions (5)(6)(7)(8). Parallel-stranded as well as antiparallel-stranded guaninequadruplex structures have been biophysically and structurally analyzed in detail with synthetic oligonucleotides (6)(7)(8)(9)(10)(11). It has been suggested that this structure is also involved in numerous cellular processes, including transcription and recombination, in addition to telomere function (12).…”

“…1). It is now well established that DNA sequences with multiple guanine stretches can form inter-and intramolecular, parallel or antiparallel quadruplex assemblies in vitro (6)(7)(8)(9)(10)(11).…”