Groove Binding Ligands for the Interaction with Parallel-Stranded ps-Duplex DNA and Triplex DNA

DNA adopts different conformations not only based on novel base pairs, but also with different chain polarities. Besides several duplex structures (A, B, Z, parallel stranded (ps)-DNA, etc.), DNA also forms higher-order structures like triplex, tetraplex, and i-motif. Each of these structures has its own biological significance. The ps-duplexes have been found to be resistant to certain nucleases and endonucleases. Molecules that promote triple-helix formation have significant potential. These investigations have many therapeutic advantages which may be useful in the regulation of the expression of genes responsible for certain diseases by locking either their transcription (antigene) or translation (antisense). Each DNA minor groove binding ligand (MGBL) interacts with DNA through helical minor groove recognition in a sequence-specific manner, and this interferes with several DNA-associated processes. Incidentally, these ligands interact with some non-B-DNA and with higher-order DNA structures including ps-DNA and triplexes. While the design and recognition of minor grooves of duplex DNA by specific MGBLs have been a topic of many reports, limited information is available on the binding behavior of MGBLs with nonduplex DNA. In this review, we summarize various attempts of the interaction of MGBLs with ps-DNA and DNA triplexes.

Comparative studies on parallel and antiparallel duplex and triplex DNA

Parallel strand models for base sequences d(A)(10). d(T)(10), d(AT)(5) . d(TA)(5), d(G(5)C(5)). d(C(5)G(5)), d(GC)(5) . d(CG)(5) and d(CTATAGGGAT). d(GATATCCCTA), where reverse Watson-Crick A-T pairing with two H-bonds and reverse Watson-Crick G-C pairing with one H-bond or with two H-bonds were adopted, and three models of d(T)(14). d(A)(14). d(T)(14) triple helix with different strand orientations were built up by molecular architecture and energy minimization. Comparisons of parallel duplex models with their corresponding B-DNA models and comparisons among the three triple helices showed: (i) conformational energies of parallel AT duplex models were a little lower, while for GC duplex models they were about 8% higher than that of their corresponding B-DNA models; (ii) the energy differences between parallel and B-type duplex models and among the three triple helices arose mainly from base stacking energies, especially for GC base pairing; (iii) the parallel duplexes with one H-bond G-C pairs were less stable than those with two H-bonds G-C pairs. The present paper includes a brief discussion about the effect of base stacking and base sequences on DNA conformations. (C) 1997 Academic Press Limited.

Theoretical studies on conformation comparison of braid-like and triplex DNA

Based on the experimental data of scanning tunneling microscopy (STM), models of three-stranded braid-like DNAs composed by three kinds of base triplets AAA, TAT and GCA were constructed. We investigated the braid-like DNAs and their comparative tripler DNAs using a molecular mechanics method. The three strands of braid-like DNAs are proven equivalent, while those of tripler DNAs are not. The conformational energies for braid-like DNAs were found to be higher than that for tripler DNAs. Each period in one strand of braid-like DNA has 18 nucleotides, half of which are right-handed, while the other half are left-handed. Additional discussions concerning sugar puckering modes and the H-bonds are also included. (C) 1999 Elsevier Science B.V. All rights reserved.

Stability and molecular modeling of triplex DNA inhibiting DNA binding protein binding to the core promoter of hepatitis B virus.

Two three-dimensional structure models of the 21nt oligodeoxyribonucleotides, CPI (G3TG-2TGT2G5TG2TGT) and CP3 (TGTG2TGST2GTG2TG3), were constructed by InsightII (MSI) software in IRIS Indigo2 (SGI) workstation using the crystal structure of TAT tripler formation as the template. The initial structures subsequently were minimized by molecular mechanics. The final structures were believed as the dominant conformation. The results showed that the energy of CP1 is lower than that of CP3, and the former is more stable than the latter. Moreover, the results further proved that the 21nt oligodeoxyribo-nucleotide CP1 stably combines with the core promoter (Cp) fragment of hepatitis B virus (HBV) to form a tripler DNA, and CP1 specifically inhibits a specific cellular factor (DNA binding protein) binding to Cp fragment. These results indicated that specific repression of gene transcription of HBV DNA might be possible by tripler-formation DNA.

Interactions of mitoxantrone with duplex and triplex DNA studied by electrospray ionization mass spectrometry

We have examined interactions between mitoxantrone (MXT) and DNA duplexes or triplexes with different base compositions by using electrospray ionization mass spectrometry (ESI-MS), respectively. MXT interacts preferentially with DNA duplexes compared to the triplexes. In the mass spectrum of the duplex-MXT mixture, the complex peaks dominated in the ratios of duplex/MXT of 1:1, 1:2 and 1:3, and the 1:2 duplex/MXT peak was the most abundant. In contrast, only 1:1 triplex-MXT complexes were observed in the mass spectrum of the triplex-MXT mixture, and the most intensive peak was a free triplex ion without MXT.

Spectral and electrochemical detection of protonated triplex formation by a small-molecule anticancer agent

Triplex helical formation has been the focus of considerable interest because of possible applications in developing new molecular biology tools as well as therapeutic agents and the possible relevance of H-DNA structures in biology system. We report here that a small-molecule anticancer agent, coralyne, has binding preference to the less stable protonated triplex d(C+-T)(6):d(A-G)(6).d(C-T)(6) over duplex d(A-G)(6).d(C-T)(6) and shows different spectral and electrochemical characteristics when binding to triplex and duplex DNA, indicating that electrochemical technique can detect the less stable protonated triplex formation.

Carbon nanotubes selective destabilization of duplex and triplex DNA and inducing B-A transition in solution

Single-walled carbon nanotubes (SWNTs) have been considered as the leading candidate for nano-device applications ranging from gene therapy and novel drug delivery to membrane separations. The miniaturization of DNA-nanotube devices for biological applications requires fully understanding DNA-nanotube interaction mechanism. We report here, for the first time, that DNA destabilization and conformational transition induced by SWNTs are sequence-dependent. Contrasting changes for SWNTs binding to poly[dGdC]:poly[dGdC] and poly[dAdT]:poly[dAdT] were observed. For GC homopolymer, DNA melting temperature was decreased 40 degrees C by SWNTs but no change for AT-DNA. SWNTs can induce B-A transition for GC-DNA but AT-DNA resisted the transition. Our circular dichroism, competitive binding assay and triplex destabilization studies provide direct evidence that SWNTs induce DNA B-A transition in solution and they bind to the DNA major groove with GC preference.

Triplex selective 2-(2-naphthyl)quinoline compounds: Origins of affinity and new design principles

A novel competition dialysis assay was used to investigate the structural selectivity of a series of substituted 2-(2-naphthyl)quinoline compounds designed to target triplex DNA. The interaction of 14 compounds with 13 different nucleic acid sequences and structures was studied. A striking selectivity for the triplex structure poly dA:[poly dT](2) was found for the majority of compounds studied. Quantitative analysis of the competition dialysis binding data using newly developed metrics revealed that these compounds are among the most selective triplex-binding agents synthesized to date. A quantitative structure-affinity relationship (QSAR) was derived using triplex binding data for all 14 compounds used in these studies. The QSAR revealed that the primary favorable determinant of triplex binding free energy is the solvent accessible surface area. Triplex binding affinity is negatively correlated with compound electron affinity and the number of hydrogen bond donors. The QSAR provides guidelines for the design of improved triplex-binding agents.

Mycobacterium triplex pulmonary infection in an immunocompetent patient

We present the case of a 47-year-old immunocompetent patient with clinical evidence of pulmonary mycobacterial disease which was found to be due to Mycobacterium triplex. This novel organism is an uncommon, emerging, pathogen for which few reports of clinical infection exist in the medical literature. © 2002 The British Infection Society.

Contribution of ocular B-mode and triplex Doppler in the evaluation of 10 Poodle dogs with cataracts

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Ecobiometria e Triplex Doppler para a avaliação da vitalidade fetal em Cebus apella

Os objetos do trabalho foram: 1) realizar a ecobiometria do concepto para acompanhar o crescimento fetal e determinar a idade gestacional em Cebus apella; 2) descrever o momento em que os órgãos do feto são observados; 3) realizar a sexagem fetal; 4) avaliar o fluxo sanguíneo das artérias uterinas (AU) e umbilical (Aum), mensurando os índices de resistividade (IR) e pulsatilidade (IP); 5) observar a presença ou ausência da incisura protodiastólica (IPD) e do componente diastólico nas ondas de fluxo sanguíneo das AU e Aum, respectivamente, durante a gestação em C. apella. Seis fêmeas adultas da espécie C. apella foram selecionadas e, posteriormente, condicionadas para os procedimentos de colpocitologia ou contenção química. Para o monitoramento do ciclo reprodutivo das fêmeas e crescimento folicular, foram realizados exames colpocitológicos e ultrassonografia (US), respectivamente, para a escolha do melhor dia da monta natural ou inseminação artificial. Vinte dias após a cópula ou inseminação, era realizado o diagnóstico da gestação por meio da US. O dia de cada exame em relação ao parto foi contado em retrospecto (nascimento = dia 0). Os exames ultrassonográficos foram feitos nos dias -133, -113, -83, -53, -21 e -1 antes do parto. A US bidimensional em modo B foi utilizada para mensurar o saco gestacional do dia - 133 até -113; os diâmetros biparietal, fronto-occiptal, circunferência da cabeça e circunferência abdominal do dia -113 a -1; e comprimento do fêmur do dia -53 até -23, mostrando o aumento desses parâmetros com o avanço da gestação. O coração e o estômago começaram a ser visualizados no dia -113 e, os demais órgãos e a sexagem no dia -83. O Triplex Doppler foi empregado para avaliar o fluxo sanguíneo durante o período gestacional, mostrando uma diminuição nos IR e IP das AU e Aum, do dia -133 a -1, bem como observar o desaparecimento da IPD (dia -1) e aparecimento do componente diastólico (dia -53) na onda de fluxo sanguíneo das AU e Aum, respectivamente. Entre os dias -113 a -1, a média da freqüência cardíaca fetal, obtida pelo Triplex Doppler, foi de 189 ± 2,43 bpm. O presente trabalho permitiu determinar a idade gestacional, avaliar o crescimento anatômico do feto, descrever o momento em que os órgãos são visualizados e realizar a sexagem em C. apella. Constatou-se, também, que o fluxo sanguíneo das AU e Aum são importantes parâmetros para avaliar a vitalidade fetal em C. apella.

Triplex Doppler da artéria renal e a relação entre a ecobiometria dos rins com distância atlanto-coccígea e altura em Canis familiaris

O objetivo do trabalho foi estabelecer a relação entre a ecobiometria renal com medidas de conformação corporal como a distância atlanto-coccígea (DAC) e a altura (H) de cães adultos saudáveis, obtendo-se parâmetros de normalidade para avaliar o tamanho e volume renal, bem como estabelecer valores de referência para avaliar a perfusão sanguínea dos rins por meio do índice de resistividade (IR) e do índice de pulsatilidade (IP) do ramo principal da artéria renal. No estudo foram utilizados 22 cães adultos sem raça definida, sendo 11 machos e 11 fêmeas. Os animais foram previamente aferidos quanto a DAC e a H. Os exames ultra-sonográficos foram realizados com um aparelho HDI 4000 PHILIPS munido de um transdutor microconvexo multifreqüêncial (5-8 MHz), dispositivos Doppler Colorido e Doppler de Fluxo. Os animais foram posicionados em decúbito lateral direito ou esquerdo, de acordo com o rim a ser avaliado. Os diâmetros longitudinal (DL) e dorsoventral (DDV) dos rins foram mensurados na secção longitudinal e, o diâmetro transversal (DT) foi aferido no plano transversal. O volume (V) foi calculado automaticamente pelo software do ultra-som. Com o uso do Triplex Doppler, o IR e o IP das artérias renais direita e esquerda foram obtidos. Todos os dados foram apresentados em média ± EPM. Análises de regressão linear foram realizadas tendo o DL, DDV, DT e V como variáveis dependentes e a DAC e H como variáveis independentes. Os IR e IP dos rins direito e esquerdo foram comparados pelo teste t de Student. A DAC variou de 54-78cm para machos e 37-71cm para fêmeas e a altura variou entre 34-64 cm para os machos e 24-57cm para as fêmeas. As médias obtidas para DL, DDV, DT e V dos rins esquerdo e direito foram: 5,24±0,27cm, 3,07±0,15cm, 3,07±0,9cm, 28,01±3,4mL e 4,50±0,19cm, 2,88±0,14cm, 2,71±0,15cm, 21,27±2,6mL, respectivamente. As análises de regressão linear entre as medidas lineares e volume renal com a DAC e a H foram significativas para os interceptos e coeficientes de regressão (P<0,01). Houve diferenças estatísticas quando comparado os IR e IP entre os rins direito e esquerdo (P=0,001), sendo que as médias para IR e IP dos rins esquerdo e direito foram 0,62±0,08; 1,34±0,18 e 0,70±0,06; 1,62±0,13; respectivamente. Os dados obtidos no presente trabalho podem auxiliar na avaliação do tamanho, volume e perfusão dos rins de cães adultos.