6-TAMRA (6-Carboxytetramethylrhodamine)

Excavating an active site: the nucleobase specificity of ribonuclease A

Ribonuclease A (RNase A) catalyzes the cleavage of RNA after pyrimidine nucleotides. When bound in the active site, the base of a pyrimidine nucleotide forms hydrogen bonds with the side chain of Thr45. Here, the role of Thr45 was probed by using the wild-type enzyme, its T45G variant, X-ray diffraction analysis, and synthetic oligonucleotides as ligands and substrates. Catalytic specificity was determined with the fluorogenic substrate: 6-carboxyfluorescein approximately dArXdAdA approximately 6-carboxytetramethylrhodamine (6-FAM approximately dArXdAdA approximately 6-TAMRA), where X = C, U, A, or G. Wild-type RNase A cleaves 10(6)-fold faster when X = C than when X = A. Likewise, its affinity for the non-hydrolyzable oligonucleotide 6-FAM approximately d(CAA) is 50-fold greater than for 6-FAM approximately d(AAA). T45G RNase A cleaves 6-FAM approximately dArAdAdA approximately 6-TAMRA 10(2)-fold faster than does the wild-type enzyme. The structure of crystalline T45G RNase A, determined at 1.8-A resolution by X-ray diffraction analysis, does not reveal new potential interactions with a nucleobase. Indeed, the two enzymes have a similar affinity for 6-FAM approximately d(AAA). The importance of pentofuranosyl ring conformation to nucleotide specificity was probed with 6-FAM approximately d(AU(F)AA), where U(F) is 2'-deoxy-2'-fluorouridine. The conformation of the pentofuranosyl ring in dU(F) is known to be more similar to that in rU than dU. The affinity of wild-type RNase A for 6-FAM approximately d(AU(F)AA) is 50-fold lower than for 6-FAM approximately d(AUAA). This discrimination is lost in the T45G enzyme. Together, these data indicate that the side chain of Thr45 plays multiple roles-interacting favorably with pyrimidine nucleobases but unfavorably with purine nucleobases. Moreover, a ribose-like ring disfavors the interaction of Thr45 with a pyrimidine nucleobase, suggesting that Thr45 enhances catalysis by ground-state destabilization.

Dye structure affects Taq DNA polymerase terminator selectivity

All DNA sequencing methods have benefited from the development of new F667Y versions of Taq DNA polymerase. However, terminator chemistry methods show less uniform peak height patterns when compared to primer chemistry profiles suggesting that the dyes and/or their linker arms affect enzyme selectivity. We have measured elementary nucleotide rate and binding constants for representative rhodamine- and fluorescein-labeled terminators to determine how they interact with F667 versions of Taq Pol I. We have also developed a rapid gel-based selectivity assay that can be used to screen and to quantify dye-enzyme interactions with F667Y versions of the enzyme. Our results show that 6-TAMRA-ddTTP behaves like unlabeled ddTTP, while 6-FAM-ddTTP shows a 40-fold reduction in the rate constant for polymerization without affecting ground-state nucleotide binding. Detailed mechanism studies indicate that both isomers of different fluorescein dyes interfere with a conformational change step which the polymerase undergoes following nucleotide binding but only when these dyes are attached to pyrimidines. When these same dyes are attached to purines by the same propargylamino linker arm, they show no effect on enzyme selectivity. These studies suggest that it may be possible to develop fluorescein terminators for thermocycle DNA sequencing methods for polymerases that do not discriminate between deoxy- and dideoxynucleotides.

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.

Labelling peptides with fluorescent probes for incorporation into degradable polymers

Two peptides, atrial natriuretic peptide (ANP) and salmon calcitonin (sCT) were conjugated with a fluorescent, amine-reactive probe 5-(and 6-)carboxytetramethylrhodamine,-succinimidylester (5-(6)-TAMRA-SE). The labelling reaction was followed by HPLC and found to be complete after 2 h. The labelled peptides were purified by gel filtration chromatography and characterised by [1H]NMR, UV/VIS and fluorescence spectroscopy. NMR-spectra confirmed the conjugation of dye to the peptides. Two absorption maxima between 500 and 600 nm were recorded in the UV/VIS-spectra. The fluorescence spectra were found to be pH-dependent, which allowed the measurement of pH in aqueous solution. The labelled peptides were encapsulated into poly(lactic acid) (PLA) microspheres using a double emulsion technique. Probe attachment permitted location of the peptides in the polymer.