Multifunctional G-Quadruplex Aptamers and Their Application to Protein Detection

Two significant G-quadruplex aptamers named AGRO100 and T30695 are identified as multi functional aptamers that can bind the protein ligands nucleolin or HIV-1 integrase and hemin. Besides their strong binding to target proteins, both AGRO100 and T30695 exhibit high hemin-binding affinities comparable to that of the known aptamer (termed PS2M) selected by the in vitro evolution process. Most importantly, their corresponding hemin-DNA complexes reveal excellent peroxidase-like activities. higher than that of the reported hemin-PS2M DNAzyme. This enables these multifunctional aptamers to be applied to the sensitive detection of proteins. which is demonstrated by applying AGRO100 to the chemiluminescence detection of nucleolin expressed at the surface of HeLa cells. Based on the specific AGRO100-nucleolin interaction, the surface-expressed nucleolin of HeLa cells is labeled in situ with the hemin-AGRO100 DNAzyme, and then determined in the luminol-H2O2 system.

Bimolecular quadruplexes and their transitions to higher-order molecular structures detected by ESI-FTICR-MS

Four individual quadruplexes, which are self-assembled in ammonium acetate solution from telomeric sequences of closely related DNA strands - d(G(4)T(4)G(4)), d(G(3)T(4)G(4)), d(G(3)T(4)G(3)), and d(G(4)T(4)G(3)) - have been detected in the gas phase using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS). The bimolecular quadruplexes associate with the same number of NH4+ in the gas phase as NMR shows that they do in solution. The quadruplex structures formed in solution are maintained in the gas phase. Furthermore, the mass spectra show that the bimolecular quadruplexes generated by the strands d(G(3)T(4)G(3)) and d(G(4)T(4)G(3)) are unstable, being converted into trimolecular and tetramolecular structures with increasing concentrations of NH4+ in the solution. Circular dichroism (CD) spectra reveal structural changes during the process of strand stoichiometric transitions, in which the relative orientation of strands in the quadruplexes changes from an antiparallel to a parallel arrangement. Such changes were observed for the strand d(G(4)T(4)G(3)), but not for the strand d(G(3)T(4)G(3)). The present work provides a significant insight into the formation of various DNA quadruplexes, especially the higher-order species.

Potassium-Lead-Switched G-Quadruplexes: A New Class of DNA Logic Gates

A cation-driven allosteric G-quadruplex DNAzyme (PW17) was utilized to devise a conceptually new class of DNA logic gate based on cation-tuned ligand binding and release. K+ favors the binding of hemin to parallel-stranded PW17, thereby promoting the DNAzyme activity, whereas Pb2+ induces PW17 to undergo a parallel-to-antiparallel conformation transition and thus drives hemin to release from the G-quadruplex, deactivating the DNAzyme. Such a K+-Pb2+ switched G-quadruplex, in fact, functions as a two-input INHIBIT logic gate. With the introduction of another input EDTA, this G-quadruplex can be further utilized to construct a reversibly operated IMPLICATION gate.

Chiral metallo-supramolecular complexes selectively recognize human telomeric G-quadruplex DNA

Here, we report the first example that one enantiomer of a supramolecular cylinder can selectively stabilize human telomeric G-quadruplex DNA. The P-enantiomer of this cylinder has a strong preference for G-quadruplex over duplex DNA and, in the presence of sodium, can convert G-quadruplexes from an antiparallel to a hybrid structure. The compound's chiral selectivity and its ability to discriminate quadruplex DNA have been studied by DNA melting, circular dichroism, gel electrophoresis, fluorescence spectroscopy and S1 nuclease cleavage.

Molecular Dynamics Simulation of Peeling a DNA Molecule on Substrate

Molecular dynamics (MD) simulations are performed to study adhesion and peeling of a short fragment of single strand DNA (ssDNA) molecule from a graphite surface. The critical peel-off force is found to depend on both the peeling angle and the elasticity of ssDNA. For the short ssDNA strand under investigation, we show that the simulation results can be explained by a continuum model of an adhesive elastic band on substrate. The analysis suggests that it is often the peak value, rather than the mean value, of adhesion energy which determines the peeling of a nanoscale material.

Metric representation of DNA sequences

A metric representation of DNA sequences is borrowed from symbolic dynamics. In view of this method, the pattern seen in the chaos game representation of DNA sequences is explained as the suppression of certain nucleotide strings in the DNA sequences. Frequencies of short nucleotide strings and suppression of the shortest ones in the DNA sequences can be determined by using the metric representation.

Recurrence plot analysis of DNA sequences

Recurrence plot technique of DNA sequences is established on metric representation and employed to analyze correlation structure of nucleotide strings. It is found that, in the transference of nucleotide strings, a human DNA fragment has a major correlation distance, but a yeast chromosome's correlation distance has a constant increasing. (C) 2004 Elsevier B.V All rights reserved.

Large three-photon absorption and intramolecular charge transfer of the bis-donor fluorene-based molecules

Three-photon absorption (3PA) of two fluorene-based molecules with D-pi-D structural motifs (abbreviated as BPAF and BCZF) has been determined by using a Q-switched Nd: YAG laser pumped with 38 ps pulses at 1064 nm in DMF. The measured 3PA cross-sections are 222 and 140 x 10(-78) cm(6) s(2) for BPAF and BCZF, respectively. AM1 calculations show that attaching different donors changes the charge density distribution of the fluorene skeleton, and it is observed that the 3PA cross-section can be enhanced with increasing intramolecular charge transfer character, measured by the parameter Delta p(1)/Delta p(2)/Delta p(1)'. (c) 2005 Elsevier B.V. All fights reserved.