Through-bond correlation of sugar and base protons in unlabeled nucleic acids

Nuclear magnetic resonance and mass spectrometry studies of 2′,3′,5′-O-triacetylguanosine self-assembly in the presence of alkaline earth metal ions (Ca2+, Sr2+, Ba2+)

We report structural determination of cation-templated self-assembly of a guanosine derivative, 2′,3′,5′-O-triacetylguanosine (TAG), in the presence of three alkaline earth metal ions (Ca2+, Sr2+, and Ba2+) in CDCl3. Using a combination of nuclear magnetic resonance (NMR) and electrospray ionization mass spectrometry (ESI-MS) methods, we have found that TAG molecules form discrete octamers in the form of [TAG]8M2+ (M2+ = Ca2+, Sr2+, and Ba2+), which is composed of two G-quartets and a sandwiched metal ion. We have determined the ability of the three alkaline earth metal ions to promote TAG self-assembly (relative binding affinity) to be Sr2+ ≫ Ba2+ > Ca2+. More importantly, we have used two-dimensional (2D) NMR methods to determine the structural details of [TAG]8Sr2+. In particular, we found that each octamer consists of an all-anti G-quartet stacking on top of an all-syn G-quartet in a tail-to-head fashion with a twist angle of 45° between the two G-quartets. This TAG octamer structure represents a unique case quite different from other lipophilic guanosine octamers reported in the literature.

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.

NMR methods for studying quadruplex nucleic acids

Solution NMR spectroscopy has traditionally played a central role in examining quadruplex structure, dynamics, and interactions. Here, an overview is given of the methods currently applied to structural, dynamics, thermodynamics, and kinetics studies of nucleic acid quadruplexes and associated cations.

An interlocked dimeric parallel-stranded DNA quadruplex: a potent inhibitor of HIV-1 integrase

We report on the NMR-based solution structure of the 93del d(GGGGTGGGAGGAGGGT) aptamer, a potent nanomolar inhibitor of HIV-1 integrase. This guanine-rich DNA sequence adopts an unusually stable dimeric quadruplex architecture in K+ solution. Within each 16-nt monomer subunit, which contains one A.(G.G.G.G) pentad sandwiched between two G.G.G.G tetrads, all G-stretches are parallel, and all guanines are anti with the exception of G1, which is syn. Dimer formation is achieved through mutual pairing of G1 of one monomer, with G2, G6, and G13 of the other monomer, to complete G.G.G.G tetrad formation. There are three single-nucleotide double-chain-reversal loops within each monomer fold, such that the first (T5) and third (A12) loops bridge three G-tetrad layers, whereas the second (A9) loop bridges two G-tetrad layers and participates in A.(G.G.G.G) pentad formation. Results of NMR and of integrase inhibition assays on loop-modified sequences allowed us to propose a strategy toward the potential design of improved HIV-1 integrase inhibitors. Finally, we propose a model, based on molecular docking approaches, for positioning the 93del dimeric DNA quadruplex within a basic channel/canyon formed between subunits of a dimer of dimers of HIV-1 integrase.

Propeller-type parallel-stranded G-quadruplexes in the human c-myc promoter

The nuclease-hypersensitivity element III1 in the c-myc promoter is a good anticancer target since it largely controls transcriptional activation of the important c-myc oncogene. Recently, the guanine-rich strand of this element has been shown to form an equilibrium between G-quadruplex structures built from two different sets of G-stretches; two models of intramolecular fold-back antiparallel-stranded G-quadruplexes, called "basket" and "chair" forms, were proposed. Here, we show by NMR that two sequences containing these two sets of G-stretches form intramolecular propeller-type parallel-stranded G-quadruplexes in K(+)-containing solution. The two structures involve a core of three stacked G-tetrads formed by four parallel G-stretches with all anti guanines and three double-chain-reversal loops bridging three G-tetrad layers. The central loop contains two or six residues, while the two other loops contain only one residue.

Two-repeat human telomeric d(TAGGGTTAGGGT) sequence forms interconverting parallel and antiparallel G-quadruplexes in solution: distinct topologies, thermodynamic properties, and folding/unfolding kinetics

We demonstrate by NMR that the two-repeat human telomeric sequence d(TAGGGTTAGGGT) can form both parallel and antiparallel G-quadruplex structures in K(+)-containing solution. Both structures are dimeric G-quadruplexes involving three stacked G-tetrads. The sequence d(TAGGGUTAGGGT), containing a single thymine-to-uracil substitution at position 6, formed a predominantly parallel dimeric G-quadruplex with double-chain-reversal loops; the structure was symmetric, and all guanines were anti. Another modified sequence, d(UAGGGT(Br)UAGGGT), formed a predominantly antiparallel dimeric G-quadruplex with edgewise loops; the structure was asymmetric with six syn guanines and six anti guanines. The two structures can coexist and interconvert in solution. For the latter sequence, the antiparallel form is more favorable at low temperatures (<50 degrees C), while the parallel form is more favorable at higher temperatures; at temperatures lower than 40 degrees C, the antiparallel G-quadruplex folds faster but unfolds slower than the parallel G-quadruplex.