NMR evaluation of ammonium ion movement within a unimolecular G-quadruplex in solution

d[G4(T4G4)3] has been folded into a unimolecular G-quadruplex in the presence of 15NH4+ ions. NMR spectroscopy confirmed that its topology is the same as the solution state structure determined earlier by Wang and Patel (J. Mol. Biol., 1995; 251: 76–94) in the presence of Na+ ions. The d[G4(T4G4)3] G-quadruplex exhibits four G-quartets with three 15NH4+-ion-binding sites (O1, I and O2). Quantitative analysis utilizing 15NH4+ ions as a NMR probe clearly demonstrates that there is no unidirectional 15NH4+ ion movement through the central cavity of the G-quadruplex. 15NH4+ ions move back and forth between the binding sites within the G-quadruplex and exchange with ions in bulk solution. 15NH4+ ion movement is controlled by the thermodynamic preferences of individual binding sites, steric restraints of the G-quartets for 15NH4+ ion passage and diagonal versus edge-type arrangement of the T4 loops. The movement of 15NH4+ ions from the interior of the G-quadruplex to bulk solution is faster than exchange within the G-quadruplex. The structural details of the G-quadruplex define stiffness of individual G-quartets that intimately affects 15NH4+ ion movement. The stiffness of G-quartets and steric hindrance imposed by thymine residues in the loops contribute to the 5-fold difference in the exchange rate constants through the outer G-quartets

Solution Structure of a Prion Protein Aptamer Analogue

It has previously been shown that r(GGA)4 folds into a G-quadruplex structure, which binds to the normal cellular form of the prion protein (PrPC) with high affinity. The current study utilizes CD and NMR spectroscopy to show that a dimeric parallel G-quadruplex structure is formed by r(GGA)2 in a KCl solution. Each r[(GGA)2]2 G-quadruplex unit exhibits two G-quartets, one of which is hydro- gen bonded to two additional adenines forming a hexade. Through stacking of hexade planes, two G-quadruplex units interact with each other and form a symmetric dimer, r[(GGA)2]4. The topolo¬gy of r[(GGA)2]4 is in agreement with the fold of r[(GGA)4]2, however, subtle differences are found in the region responsible for PrPC binding

Impact of oxidative lesions on the human telomeric G-quadruplex

Telomere attrition is closely associated with cell aging and exposure to reactive oxygen species (ROS). While oxidation products of nucleotides have been studied extensively in the past, the underlying secondary/tertiary structural changes in DNA remain poorly understood. In this work, we systematically probed guanine positions in the human telomeric oligonucleotide sequence (hTel) by substitutions with the major product of ROS, 8-oxo-7,8-dihydroguanine (oxoG), and evaluated the G-quadruplex forming ability of such oligonucleotides. Due to reduced hydrogen-bonding capability caused by oxoG, a loss of G-quadruplex structure was observed for most oligonucleotides containing oxidative lesions. However, some positions in the hTel sequence were found to tolerate substitutions with oxoG. Due to oxoG’s preference for the syn conformation, distinct responses were observed when replacing guanines with different glycosidic conformations. Accommodation of oxoG at sites originally in syn or anti in nonsubstituted hTel G-quadruplex requires a minor structural rearrangement or a major conformational shift, respectively. The system responds by retaining or switching to a fold where oxoG is in syn conformation. Most importantly, these G-quadruplex structures are still stable at physiological temperatures and should be considered detrimental in higher-order telomere structures

8-oxoguanine forms quartets with a large central cavity

[Image: see text] Oxidation of a guanine nucleotide in DNA yields an 8-oxoguanine nucleotide ((oxo)G) and is a mutagenic event in the genome. Due to different arrangements of hydrogen-bond donors and acceptors, (oxo)G can affect the secondary structure of nucleic acids. We have investigated base pairing preferences of (oxo)G in the core of a tetrahelical G-quadruplex structure, adopted by analogues of d(TG(4)T). Using spectroscopic methods, we have shown that G-quartets can be fully substituted with (oxo)G nucleobases to form an (oxo)G-quartet with a revamped hydrogen-bonding scheme. While an (oxo)G-quartet can be incorporated into the G-quadruplex core without distorting the phosphodiester backbone, larger dimensions of the central cavity change the cation localization and exchange properties

8-oxoguanine forms quartets with a large central cavity

Oxidation of a guanine nucleotide in DNA yields an 8-oxoguanine nucleotide ($^{oxo}$G) and is a mutagenic event in the genome. Due to different arrangements of hydrogen-bond donors and acceptors, $^{oxo}$G can affect the secondary structure of nucleic acids. We have investigated base pairing preferences of $^{oxo}$G in the core of a tetrahelical G-quadruplex structure, adopted by analogues of d(TG$_4$T). Using spectroscopic methods, we have shown that G-quartets can be fully substituted with $^{oxo}$G nucleobases to form an $^{oxo}$G-quartet with a revamped hydrogen-bonding scheme. While an $^{oxo}$G-quartet can be incorporated into the G-quadruplex core without distorting the phosphodiester backbone, larger dimensions of the central cavity change the cation localization and exchange properties

Relative volumes of autocorrelation peaks as a function of mixing time (τ) at 283 K () and 313 K ()

<p><b>Copyright information:</b></p><p>Taken from "NMR evaluation of ammonium ion movement within a unimolecular G-quadruplex in solution"</p><p>Nucleic Acids Research 2007;35(8):2554-2563.</p><p>Published online 4 Apr 2007</p><p>PMCID:PMC1895886.</p><p>© 2007 The Author(s)</p> Black filled squares, blue open triangles and red open circles represent the experimental points for the autocorrelation peaks I, O and O, respectively. Curves represent the best fits of the experimental data to

Relative volumes of cross-peaks as a function of mixing time (τ) at 283 K () and 313 K ()

<p><b>Copyright information:</b></p><p>Taken from "NMR evaluation of ammonium ion movement within a unimolecular G-quadruplex in solution"</p><p>Nucleic Acids Research 2007;35(8):2554-2563.</p><p>Published online 4 Apr 2007</p><p>PMCID:PMC1895886.</p><p>© 2007 The Author(s)</p> Red open circles and black filled squares represent experimental data points for OI and OI cross-peaks, respectively. Curves represent the best fits of the experimental data to

Relative volumes of OB (red open circles) and OB (black filled squares) cross-peaks as a function of mixing time (τ) at 293 K

<p><b>Copyright information:</b></p><p>Taken from "NMR evaluation of ammonium ion movement within a unimolecular G-quadruplex in solution"</p><p>Nucleic Acids Research 2007;35(8):2554-2563.</p><p>Published online 4 Apr 2007</p><p>PMCID:PMC1895886.</p><p>© 2007 The Author(s)</p> Curves represent the best fit of the experimental data to