Fluorescence enhancement of bis-acridine orange peptide, BAO, upon binding to double stranded DNA.

Bis-acridine orange peptides carrying two acridine oranges at the epsilon-amino moieties of both terminal lysines of a tetra(lysine) chain showed a ca. 200-fold fluorescence enhancement upon addition of double stranded DNA.

Bis-intercalation-triggered fluorescence: specific detection of double stranded DNA and AT content estimation.

Detection of double stranded DNA and estimation of the AT content in DNA of unknown concentration could be achieved with a bis-acridinyl peptide carrying fluorescein, FKA.

Fluoreometric behavior of a novel bis-acridine orange bound to double stranded DNA.

Novel bis-acridine orange (1) was synthesized from Fmoc-Lys(Boc)-OH and Fmoc-Lys(AO)-OH (AO: acridine orange), with the 9-position of acridine orange (AO) linked to the epsilon-amino moiety of lysine, on the peptide synthesizer. Bis-acridine orange (1) yielded a very weak fluorescence in an aqueous media due to the intramolecular stacking, but its fluorescence was enhanced over 200-times upon binding to double-stranded DNA, irrespective of the DNA sequences. Circular dichroism (CD) spectra showed that 1 binds to double stranded DNA in its stacked conformation, concomitant with fluorescence enhancement.

Comparison of potassium ion preference of potassium-sensing oligonucleotides, PSO-1 and PSO-2, carrying the human and Oxytricha telomeric sequence, respectively.

Human [G(3)(TTAG(3))(3)] and Oxytricha [G(4)(T(4)G(4))(3)] telomere model oligonucleotides, PSO-1 and PSO-2, bearing two fluorophores, 6-carboxyfluorescein (6-FAM) and 6-carboxytetramethylrhodamine (6-TAMRA) at their 5'- and 3'-termini, respectively, were synthesized. Both of them can form an intramolecular antiparallel tetraplex upon addition of K(+), and an enhanced fluorescence resonance energy transfer (FRET) was observed. PSO-1 showed a 43,000 times higher selectivity for K(+) against Na(+). Fluorometric and circular dichroism spectrophotometric studies revealed that this system is useful for the evaluation of the interaction of different telomeric repeat oligonucleotide sequences with metal ions.

A novel potassium sensing in aqueous media with a synthetic oligonucleotide derivative. Fluorescence resonance energy transfer associated with Guanine quartet-potassium ion complex formation.

A novel potassium sensing oligonucleotide (PSO) was constructed by attaching fluorophores 6-FAM and 6-TAMRA to the 5'- and 3'-termini of d(GGG TTA GGG TTA GGG TTA GGG), respectively. The affinity of PSO for K+ was 43 000 times greater than that for Na+, high enough selectivity enabling quantitation of K+ specifically in the presence of excess Na+. Fluorescence resonance energy transfer (FRET) to 6-TAMRA from 6-FAM of PSO was observed only in the presence of K+. This phenomenon is based on the approximation of the two fluorophores upon formation of a guanine quartet mediated by K+. Furthermore, the fluorescent color of PSO changes from yellow to red upon formation of the complex, thereby enabling visualization of K+ in aqueous media.

Tetrakis-acridinyl peptide: a novel fluorometric reagent for nucleic acid analysis based on the fluorescence dequenching upon DNA binding.

Tetrakis-acridinyl peptide 1 assuming a right-handed helical stacked conformation of the acridinyl units can bind to DNA duplex with a very high affinity of 10(8) (M-bp)(-1) even at a high salt concentration of 0.2 M NaCl, irrespective of the base composition. Peptide 1 gave rise to 1600-times enhancement of its fluorescence upon binding to an AT polymer due to the collapse of this stacked structure, but the fluorescence is not enhanced with a GC polymer, though the binding constants of 1 for both polymers were the same.

Patassium sensing oligonucleotide, PSO, based on DNA tetraplex formation.

Potassium Sensing Oligonucleotide, PSO, showing a high selectivity for K+ was synthesized by connecting 6-FAM and 6-TAMRA at the 5'- and 3'-termini of d(GGG TTA GGG TTA GGG TTA GGG), respectively. Circular dichroism (CD) spectra of PSO in the absence and presence of a various amount of KCl or NaCl revealed that PSO assumes an intramolecular or intermolecular antiparallel tetraplex structure in the presence of K+ and Na+, respectively.