On the Helical Structure of Guanosine 5'-Monophosphate Formed at pH 5: Is It Left- or Right-Handed?

Early X-ray fiber diffraction studies have established that the spontaneous gel formation of guanosine 5'-monophosphate (5'-GMP) under slightly acidic conditions (e.g., pH 5) results from self-assembly of 5'-GMP into a helical structure in which hydrogen-bonded guanine bases form a continuous helix with 15 nucleotides per 4 turns. For more than five decades, the sense of this helix is believed to be left-handed. Using multinuclear solid-state NMR and IR spectroscopic methods, we have finally determined the long-missing structural details of this helix. First, we found that this 5'-GMP helix is right-handed containing exclusive C3'-endo sugar puckers. Second, we showed that the central channel of this helix is free of Na+ ions, which is in sharp contrast to the helix formed by 5'-GMP at pH 8 where the central channel is filled with Na+ ions.

High-resolution 39K NMR spectroscopy of bio-organic solids.

We report the first implementation of the multiple-quantum magic-angle-spinning method to obtain high-resolution (39)K NMR spectra for bio-organic solids. The observed spectral resolution in the isotropic dimension is nearly at the sub-ppm level, which approaches the intrinsic resolution limit determined primarily by quadrupole relaxation. We show that high-resolution solid-state (39)K NMR spectroscopy can be used as a new means of probing K(+) ions in biomolecular systems.

Single atom modification leads to enhanced nucleotide self-assembly: the role of cation bridging.

We report that the ability of disodium 5'-deoxy-5'-thioguanosine-5'-monophosphate, Na(2)(5'-GSMP), to self-associate into a helical G-quadruplex structure in aqueous solution at pH 8 is significantly higher than that of disodium guanosine-5'-monophosphate, Na(2)(5'-GMP), which supports our earlier hypothesis regarding the importance of cation bridging.

Quadrupole-central-transition 17O NMR spectroscopy of protein-ligand complexes in solution.

We report the first (17)O quadrupole-central-transition (QCT) NMR spectroscopic study of protein-ligand complexes in solution. This work shows that it is possible to obtain high resolution (17)O NMR spectra for (17)O-labeled ligands bound to proteins. At high magnetic fields such as 21.14 T, this (17)O QCT NMR approach should be applicable to studies of all oxygen-containing functional groups in large proteins (>30 kDa).

Probing the Na+ binding site in a calix[4]arene-guanosine conjugate dimer by solid-state 23Na NMR and quantum chemical calculation.

Using solid-state (23)Na NMR and quantum chemical calculations we have found that the Na(+) ion bound to a calix[4]arene-guanosine conjugate dimer resides slightly above the G-quartet plane and simultaneously coordinates to a water molecule in a square-pyramidal (penta-coordination) geometry.

Helical structure of disodium 5'-guanosine monophosphate self-assembly in neutral solution.

Nucleic acid molecules (DNA and RNA) are formed by linking many different basic units known as nucleotides together via covalent phosphodiester bonds. Nucleic acid molecules often form helical structures known as B-DNA (right-handed), A-DNA/RNA (right-handed), and Z-DNA (left-handed). We have found that spontaneous self-assembly of just one nucleotide, guanosine 5'-monophosphate (5'-GMP), leads to formation of a right-handed helix in neutral solution. The linkage between individual 5'-GMP molecules along the helix is provided by hydrogen bonds, as opposed to the covalent phosphodiester bonds found in regular polynucleotides. The most surprising finding is that this right-handed 5'-GMP helix has alternating C2'-endo and C3'-endo sugar puckers along the helical strand, a situation only seen to date in left-handed Z-DNA. The self-organized structure of 5'-GMP provides a perfect condition for phosphodiester bond formation which may provide a clue for formation of RNA oligomers under prebiotic conditions. We anticipate that similar helical structures could exist in other nucleic acid systems.

Direct NMR evidence for Ca2+ ion binding to G-quartets.

We report the first 1H and 43Ca NMR characterization of Ca2+ ion binding to G-quartets.

Direct 23Na NMR observation of mixed cations residing inside a G-quadruplex channel.

We report direct (23)Na NMR observation for the presence of mixed cations (Na(+)/K(+), Na(+)/Rb(+), Na(+)/Sr(2+)) inside the G-quadruplex channel formed by the self-association of guanosine 5'-monophosphate at pH 8.

Probing hydrogen bonding and ion-carbonyl interactions by solid-state 17O NMR spectroscopy: G-ribbon and G-quartet.

We report solid-state 17O NMR determination of the 17O NMR tensors for the keto carbonyl oxygen (O6) of guanine in two 17O-enriched guanosine derivatives: [6-17O]guanosine (G1) and 2',3',5'-O-triacetyl-[6-17O]guanosine (G2). In G1.2H2O, guanosine molecules form hydrogen-bonded G-ribbons where the guanine bases are linked by O6...H-N2 and N7...H-N7 hydrogen bonds in a zigzag fashion. In addition, the keto carbonyl oxygen O6 is also weakly hydrogen-bonded to two water molecules of hydration. The experimental 17O NMR tensors determined for the two independent molecules in the asymmetric unit of G1.2H2O are: Molecule A, CQ=7.8+/-0.1 MHz, etaQ=0.45+/-0.05, deltaiso=263+/-2, delta11=460+/-5, delta22=360+/-5, delta33=-30+/-5 ppm; Molecule B, CQ=7.7+/-0.1 MHz, etaQ=0.55+/-0.05, deltaiso=250+/-2, delta11=440+/-5, delta22=340+/-5, delta33=-30+/-5 ppm. In G1/K+ gel, guanosine molecules form extensively stacking G-quartets. In each G-quartet, four guanine bases are linked together by four pairs of O6...H-N1 and N7...H-N2 hydrogen bonds in a cyclic fashion. In addition, each O6 atom is simultaneously coordinated to two K+ ions. For G1/K+ gel, the experimental 17O NMR tensors are: CQ=7.2+/-0.1 MHz, etaQ=0.68+/-0.05, deltaiso=232+/-2, delta11=400+/-5, delta22=300+/-5, delta33=-20+/-5 ppm. In the presence of divalent cations such as Sr2+, Ba2+, and Pb2+, G2 molecules form discrete octamers containing two stacking G-quartets and a central metal ion, that is, (G2)4-M2+-(G2)4. In this case, each O6 atom of the G-quartet is coordinated to only one metal ion. For G2/M2+ octamers, the experimental 17O NMR parameters are: Sr2+, CQ=6.8+/-0.1 MHz, etaQ=1.00+/-0.05, deltaiso=232+/-2 ppm; Ba2+, CQ=7.0+/-0.1 MHz, etaQ=0.68+/-0.05, deltaiso=232+/-2 ppm; Pb2+, CQ=7.2+/-0.1 MHz, etaQ=1.00+/-0.05, deltaiso=232+/-2 ppm. We also perform extensive quantum chemical calculations for the 17O NMR tensors in both G-ribbons and G-quartets. Our results demonstrate that the 17O chemical shift tensor and quadrupole coupling tensor are very sensitive to the presence of hydrogen bonding and ion-carbonyl interactions. Furthermore, the effect from ion-carbonyl interactions is several times stronger than that from hydrogen-bonding interactions. Our results establish a basis for using solid-state 17O NMR as a probe in the study of ion binding in G-quadruplex DNA and ion channel proteins.

Trivalent lanthanide metal ions promote formation of stacking G-quartets.

We report the first examples of stacking G-quartet formation assisted by trivalent lanthanide metal ions (La3+, Eu3+, Tb3+, Dy3+, Tm3+).

G-quartet formation from an N2-modified guanosine derivative.

[structure: see text] We report G-quartet formation from an N2-modified lipophilic guanosine nucleoside, N2-(4-n-butylphenyl)-2',3',5'-O-triacetylguanosine. We show that, in the presence of either K+ or Na+, this guanosine derivative self-assembles into a D4-symmetric octamer consisting of two stacking all-syn G-quartets in a tail-to-tail (or head-to-head) fashion and a central ion.