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1.
Sci Rep ; 14(1): 18222, 2024 08 06.
Artículo en Inglés | MEDLINE | ID: mdl-39107370

RESUMEN

A plant's structure is the result of constant adaptation and evolution to the surrounding environment. From this perspective, our goal is to investigate the mass and radius distribution of a particular plant organ, namely the searcher shoot, by providing a Reinforcement Learning (RL) environment, that we call Searcher-Shoot, which considers the mechanics due to the mass of the shoot and leaves. We uphold the hypothesis that plants maximize their length, avoiding a maximal stress threshold. To do this, we explore whether the mass distribution along the stem is efficient, formulating a Markov Decision Process. By exploiting this strategy, we are able to mimic and thus study the plant's behavior, finding that shoots decrease their diameters smoothly, resulting in an efficient distribution of the mass. The strong accordance between our results and the experimental data allows us to remark on the strength of our approach in the analysis of biological systems traits.


Asunto(s)
Refuerzo en Psicología , Brotes de la Planta/fisiología , Hojas de la Planta/fisiología , Modelos Biológicos , Cadenas de Markov , Aprendizaje/fisiología , Fenómenos Fisiológicos de las Plantas
2.
Biochemistry ; 43(16): 4877-84, 2004 Apr 27.
Artículo en Inglés | MEDLINE | ID: mdl-15096057

RESUMEN

Telomeres are DNA-protein structures at the ends of eukaryotic chromosomes, the DNA of which comprise noncoding repeats of guanine-rich sequences. Telomeric DNA plays a fundamental role in protecting the cell from recombination and degradation. Telomeric sequences can form quadruplex structures stabilized by guanine quartets. These structures can be constructed from one, two, or four oligonucleotidic strands. Here, we report the thermodynamic characterization of the stability, analyzed by differential scanning calorimetry, of three DNA quadruplexes of different molecularity, all containing four G-tetrads. The conformational properties of these quadruple helices were studied by circular dichroism. The investigated oligomers form well-defined G-quadruplex structures in the presence of sodium ions. Two have the truncated telomeric sequence from Oxytricha, d(TGGGGT) and d(GGGGTTTTGGGG), which form a tetramolecular and bimolecular quadruplex, respectively. The third sequence, d(GGGGTTGGGGTGTGGGGTTGGGG) was designed to form a unimolecular quadruplex. The thermodynamic parameters of these quadruplexes have been determined. The tetramolecular structure is thermodynamically more stable than the bimolecular one, which, in turn, is more stable than the unimolecular one. The experimental data were discussed in light of the molecular-modeling study.


Asunto(s)
ADN/química , Conformación de Ácido Nucleico , Telómero/química , Secuencia de Bases , Rastreo Diferencial de Calorimetría , Dicroismo Circular , ADN/síntesis química , G-Cuádruplex , Espectroscopía de Resonancia Magnética , Modelos Químicos , Modelos Moleculares , Desnaturalización de Ácido Nucleico , Oligonucleótidos/síntesis química , Telómero/genética , Termodinámica
3.
Nucleosides Nucleotides Nucleic Acids ; 22(5-8): 1677-80, 2003.
Artículo en Inglés | MEDLINE | ID: mdl-14565493

RESUMEN

A NMR structural study of quadruplex [d(TGGGT)]4 containing a modified thymine is reported. The three dimensional structure of the complex is very similar to those of other parallel stranded quadruplexes. The modified thymines (T*) are able, at least in the minimised structures, to form a tetrad containing extra H-bonds through the hydroxyl groups. Nevertheless, in this new tetrad the modified thymines are slightly open towards the solvent respect to the unmodified T-tetrad.


Asunto(s)
Guanina/química , Oligodesoxirribonucleótidos/química , Secuencia de Bases , Enlace de Hidrógeno , Espectroscopía de Resonancia Magnética , Conformación de Ácido Nucleico , Oligodesoxirribonucleótidos/síntesis química
4.
Int J Biol Macromol ; 31(4-5): 131-7, 2003 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-12568920

RESUMEN

Telomeric guanine-rich sequence can adopt quadruplex structures that are important for their biological role in chromosomal stabilisation. G quartets are characterised by the cyclic hydrogen bonding of four guanine bases in a coplanar arrangement and their stability is ion-dependent. In this work we compare the stability of [d(TGGGT)](4) and [d(T*GGGT)](4) quadruplexes. The last one contains a modified thymine, where the hydroxyl group substitutes one hydrogen atom of the methyl group of the thymine in the [d(TGGGT)](4) sequence. We used a combination of spectroscopic, calorimetric and computational techniques to characterise the G-quadruplex formation. NMR and CD spectra of [d(T*GGGT)](4) were characteristic of parallel-stranded, tetramolecular quadruplex. CD and DSC melting experiments reveal that [d(T*GGGT)](4) is less stable that unmodified quadruplex. Molecular models suggest possible explanation for the observed behaviour.


Asunto(s)
ADN/química , Timina/química , Rastreo Diferencial de Calorimetría , Dicroismo Circular , Guanina/química , Espectroscopía de Resonancia Magnética , Modelos Moleculares , Conformación de Ácido Nucleico , Temperatura , Factores de Tiempo
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