Biomedical subjects

D A Mac Dónaill

Publications and source records attributed to D A Mac Dónaill.

3 recordsLinked to original sources

PubMed2001

Lanthanide macrocyclic quinolyl conjugates as luminescent molecular-level devices.

The Eu(III) tetraazamacrocyclic complexes [Eu.1] and [Eu.2], and the Tb(III) and Yb(III) complexes [Tb.1] and [Yb.2], have been synthesized as luminescent molecular-level devices. The Eu complexes exhibit unique dual pH switching behavior in water under ambient conditions. The delayed Eu emission is reversibly switched on in acid, with an enhancement factor of several hundred for [Eu.1]. These observations are consistent with the protonation of the quinoline aryl nitrogen moiety (pK(a) approximately equal to 5.9 for [Eu.1]). The fluorescence emission spectra of these complexes are unaffected by acid, but pronounced changes occur in alkaline solution due to the deprotonation of the aryl amide nitrogen (pK(a) approximately 9.4 for [Eu.1]). [Tb.1] shows a more intriguing pH dependence; Tb emission is switched "on" only in the presence of H+ and in the absence of molecular oxygen, whereas the fluorescence emission properties are similar to those observed with [Eu.1]. This behavior can be conveniently described as a molecular-level logic gate, corresponding to a two-input INHIBIT function, A wedge B'. The analogous [Yb.2] complex shows no such pH or O(2) dependence.

Journal Article↗

PubMed2001

Representation of amino acids as five-bit or three-bit patterns for filtering protein databases.

MOTIVATION: We propose representing amino acids by bit-patterns so they may be used in a filter algorithm for similarity searches over protein databases, to rapidly eliminate non-homologous regions of database sequences. The filter algorithm would be based on dynamic programming optimization. It would have the advantage over previous filter algorithms that its substitution scoring function distinguishes between conservative and non-conservative amino acid substitutions. RESULTS: Simulated annealing was used to search for the best five-bit or three-bit patterns to represent amino acids, where similar amino acids were given similar bit-patterns. The similarity between amino acids was estimated from the BLOSUM45 matrix. Representing amino acids by these five-bit and three-bit patterns, the Escherichia coli PhoE precursor and the bacteriophage PA2 LC precursor were aligned. The alignments were nearly the same as that obtained when BLOSUM45 was used to score substitutions. AVAILABILITY: The C code of the optimization algorithm for searching for the optimal bit-pattern representation of amino acids is available from the authors upon request.

Algorithms↗

PubMed1995

On the application of integer arithmetic in nucleotide sequence analysis.

A method exploiting quaternary integer arithmetic for the rapid comparison of nucleotide sequences is proposed. A central feature of the method is the identification of a suitable integer arithmetic operation which, operating on two numerical strings (representing two sequences), yields an output string unambiguously related to the number of matching nucleotides in the compared sequences. The number of matching nucleotide bases in compared sequences can be determined without having to make individual base by base comparisons. The method is a general extension of the algorithm previously described in the code UNIREP. The rules governing integer arithmetic as applied to nucleotide sequences are discussed.

Algorithms↗