Guanine-rich Oligonucleotide Research Articles

A label-free G-quadruplex-based luminescent switch-on assay for the selective detection of histidine

A label-free G-quadruplex-based luminescent switch-on assay has been developed for the selective detection of micromolar histidine in aqueous solution. In this study, an iridium(III) complex was employed as a G-quadruplex-specific luminescent probe while a guanine-rich oligonucleotide (Pu27, 5′-TG4AG3TG4AG3TG4A2G2-3′)/cupric ion (Cu2+) ensemble was employed as a recognition unit for histidine. The initial luminescence of the iridium(III) complex in the presence of G-quadruplex DNA is effectively quenched by Cu2+ ions due to the Cu2+-mediated unfolding of the G-quadruplex motif. The addition of histidine sequesters Cu2+ ions from the ensemble, thereby restoring the luminescence of the system. The assay could detect down to 1μM of histidine in aqueous media, and also exhibited good selectivity for histidine over other amino acids with the use of the cysteine, masking agent N-ethylmaleimide. Furthermore, the application of the assay for the detection of histidine in diluted urine samples was demonstrated.

A parallel G-quadruplex-selective luminescent probe for the detection of nanomolar calcium(II) ion

A parallel G-quadruplex-selective iridium(III) complex has been synthesized and employed as a luminescent probe in a label-free G-quadruplex-based detection assay for Ca2+ ions in aqueous solution. In this assay, a guanine-rich oligonucleotide (G4, 5′-G4T4G4-3′) initially exists in an antiparallel G-quadruplex conformation, resulting in a low luminescence signal. Upon incubation with Ca2+ ions, the antiparallel G-quadruplex is induced into a parallel G-quadruplex conformation, which greatly enhances the luminescence emission of the iridium(III) probe. This method was highly sensitive for Ca2+ ions with a limit of detection in the nanomolar range, and was selective for Ca2+ over other metal ions.

Potential of Mean Force Simulation by Pulling a DNA Aptamer in Complex with Thrombin

Supercomputing Center, Korea Institute of Science and Technology Information, Daejeon 305-806, KoreaReceived July 15, 2012, Accepted August 7, 2012Thrombin binding aptamter (TBA-15) is a 15-mer guanine-rich oligonucleotide. This DNA apamer specificallybinds to the thrombin protein involved in blood coagulation. Using extensive umbrella sampling moleculardynamics simulation method at all atom level, we investigated the potential of mean force (PMF) upon pullingthe DNA aptamer from the binding mode of aptamer/thrombin complex. From this calculation, the free energycost for a full dissociation of this aptamer/protein complex is 17 kcal/mol, indicating a substantial bindingaffinity of TBA-15. Interestingly, this PMF reveals noticeable plateau regions along the pulling coordinate.Possible structural changes of this complex in the plateau were investigated in details.Key Words : TBA-15, Thrombin binding aptamer, Umbralla sampling, Potential of mean forceIntroductionA single stranded guanine (G)-rich oligonucleotide is offundamental importance, since this G-rich strand constitutesan overhang of telomeres by adopting G-quadruplexes vianon-canonical base pair interactions.

A colorimetric method for the determination of lead(II) ions using gold nanoparticles and a guanine-rich oligonucleotide

We have developed a colorimetric method for the determination of Pb(II) ions. It is based on the use of gold nanoparticles and a guanine-rich synthetic oligonucleotide. On addition of Pb(II), the color of the solution turns from red to blue. The ratio of the UV-vis absorption at 630 nm and 525 nm is proportional to the concentration of Pb(II) ions in the range from 10 to 100 nM, and the detection limit is 20 nM. Other metal ions do not interfere if present in up to a 10-fold molar excess. The method was successfully applied to the detection of Pb(II) in lake water and urine. The recovery in case of spiked samples is 92%. The results show that this method is sensitive, simple and fast.

The guanine-quadruplex aptamer 93del inhibits HIV-1 replication ex vivo by interfering with viral entry, reverse transcription and integration

We have previously identified the guanine-rich oligonucleotide (ODN) 93del as a potent inhibitor in vitro of HIV-1 integrase. Moreover, low nanomolar concentrations of ODN 93del have been shown to inhibit HIV-1 replication in infected cells. To investigate the ex vivo mechanism of ODN 93del inhibition, we analysed its antiviral effects on the early steps of HIV-1 replication such as viral entry, reverse transcription and integration using quantitative PCR. In addition to the effect on viral entry previously described for other guanine-quadruplex ODNs, transfection experiments showed that ODN 93del severely affects the proviral integration step independently of the effect on viral entry. Moreover, incubation of viral particles with ODN 93del revealed a potential microbicide activity of the aptamer. Our data point to an original multimodal inhibition of HIV-1 replication by ODN 93del, strongly suggesting that targets of guanine-quartet-forming ODNs involve entry as well as other intracellular early steps of HIV-1 replication.

Detection of triple helix DNA formation of guanine-rich oligonucleotide in sodium ion abundant buffer by cross-checking FRET scheme

In this Letter, the effects of Na + and Mg 2+ on the formation of triple helix DNA were examined by cross-checking of FRET signal from the different kinds of samples. Sodium abundant solution has not been thoroughly examined for the triple helix DNA experiment, although one can often face to the biological environment which has abundant Na + ion. The result reconfirms that Mg 2+ ion helps the oligonucleotides to form both double helix and triple helix DNA. It was conjectured and confirmed that Na + plays a complex role, being configured by the polyelectrolyte effect and the effect of K + on guanine-rich oligonucleotide.

Allosteric Control of Self‐Assembly: Modulating the Formation of Guanine Quadruplexes through Orthogonal Aromatic Interactions

All four one: The covalent attachment (A) of a porphyrin head group onto a guanine-rich oligonucleotide strand can enhance the self-assembly of DNA quadruplexes through porphyrin-based π–π interactions (B). Modulation of these allosteric interactions, by addition of a porphyrin-complexing cyclodextrin derivative, allows for a high degree of control over the formation and disassembly of the guanine quadruplexes (C and D).

Guanine rich oligonucleotide–amino acid/peptide conjugates: preparation and characterization

Covalent addition of aminoacyl or peptidyl groups could improve the performance of RNA/DNA molecules either in catalysis or in other attributes such as their ability to interact with membranes. This can explain the transformation of the RNA world first into a peptidyl-RNA world and eventually into a RNA–protein world. Subsequently, the emergence of DNA as more stable storage of genetic information than RNA finally gave shape to present day DNA–RNA–Protein world. For this reason, this paper reports a stepwise study, of the direct incorporation of amino acid/peptide onto synthetic amino modified deoxyoligonucleotide. The amino acid/peptide has been covalently linked to the primary amine of amino modified oligonucleotide, which is separated from the oligomer by a spacer arm of 10 atoms. The yield depends on the presence of bulky amino acid side chains that possibly hinder the attack of incoming nucleophile. On the other hand, the use of relatively high concentrations of EDC has improved the conjugation yield remarkably and complete conjugation can be achieved within few hours. Such a facile incorporation of amino acids or peptides may help oligonucleotides with greater cell membrane permeability, stability and reactivity.

Guanine-rich oligonucleotide modified at the 5′ terminal by dimethoxytrityl residue inhibits HIV-1 replication by specific interaction with the envelope glycoprotein

Previous studies have shown that a guanine-rich oligonucleotide SA-1042, DmTr-TGGGAGGTGGGTCTG, neutralizes HIV-1 infectivity, blocks syncytium formation and inhibits the binding of recombinant gp120 to immobilized soluble CD4 in vitro (Furukawa et al., 1994). We have now investigated the precise mode of action of SA-1042. We show here that SA-1042 specifically antagonizes the binding of anti-V3 loop antibodies or anti-CD4 binding-site antibodies to recombinant gp120, and also blocks the binding of an anti-V3 loop antibody to the V3 peptide (gp120HIB: aa302-324). In contrast, SA-1042 does not inhibit gp120 binding of monoclonal antibodies directed to other regions of gp120, such as the conserved N-terminal regions (gp120HIB: aa35-108 or gp120HIB: aa72-130) or the C-terminal region (gp120HIB: aa481-496). Furthermore, SA-1042 does not interfere with the binding of monoclonal antibodies directed to other molecules, gp41, CD4, CD11a, CD18, CD26, CD44 or CD54. These data suggest that SA-1042 exerts its antiviral effects by targeting the V3 loop as well as the CD4 binding site on gp120.