CRNs Exposed: A Method for the Systematic Exploration of Chemical Reaction Networks

Formal methods have enabled breakthroughs in many fields, such as in hardware verification, machine learning and biological systems. The key object of interest in systems biology, synthetic biology, and molecular programming is chemical reaction networks (CRNs) which formalizes coupled chemical reactions in a well-mixed solution. CRNs are pivotal for our understanding of biological regulatory and metabolic networks, as well as for programming engineered molecular behavior. Although it is clear that small CRNs are capable of complex dynamics and computational behavior, it remains difficult to explore the space of CRNs in search for desired functionality. We use Alloy, a tool for expressing structural constraints and behavior in software systems, to enumerate CRNs with declaratively specified properties. We show how this framework can enumerate CRNs with a variety of structural constraints including biologically motivated catalytic networks and metabolic networks, and seesaw networks motivated by DNA nanotechnology. We also use the framework to explore analog function computation in rate-independent CRNs. By computing the desired output value with stoichiometry rather than with reaction rates (in the sense that X ? Y+Y computes multiplication by 2), such CRNs are completely robust to the choice of reaction rates or rate law. We find the smallest CRNs computing the max, minmax, abs and ReLU (rectified linear unit) functions in a natural subclass of rate-independent CRNs where rate-independence follows from structural network properties

Synthesis and characterization of a metal-salen base pair for the assembly of programmed metal arrays inside the DNA double helix

Base pairing in natural oligonucleotides relies on hydrogen bonding and pi-stacking. Applying coordinative interactions between ligand-like nucleobases and metal cations is a new way of assembling artificial oligonucleotide duplexes. The incorporation of numerous metal-base pairs into oligonucleotides may lead to interesting compounds for nano-technological applications. In this thesis, the synthesis of the salen-metal base pair is described, which comprises preparation of a suitable protected salicylic aldehyde precursor and an organo-cuprate mediated C-glycosidation as the key step. An x-ray structure of the monomeric copper-salen base pair shows a very good geometrical match with natural Watson-Crick base pairs. Up to 10 consecutive salicylic aldehyde-nucleobases could be incorporated into DNA oligonucleotides by means of phosphoramidite chemistry. The synthesized double strands with one ligand show typical B-DNA CD-spectra and distinct melting characteristics. Addition of excess ethylenediamine and 1 eq of Mn2+ or Cu2+ increase the melting temp. by 28 °C and 42 °C, respectively. The complexation of these and other metals was examined by UV-, CD- and EPR-spectroscopy and high res. ESI mass spectrometry. It was possible to stack 10 manganese atoms inside the double helix and to prepare sequence specifically arrays of up to 5 copper ions plus 5 mercury ions inside one duplex

Macromoléculas y ligandos: péptido-nucleótidos y b-aminoácidos morfánicos. Síntesis, modelización molecular y evaluación biológica

[EN] The thesis presents a combined theoretical and experimental research in organic chemistry and biochemistry. Six different chapters, covering macromolecules and ligands preparation and simulation, are described: - [1] New Mechanistical Insights in the Asymmetric Michael Addition of Chiral Lithium Amides. It has been lapsed 20 years without any revising ot the mechanis originally proposed by Davies in 1994 about the conjugate addition of chiral liyhium amides to unsaturated esters. New ideas based in QM/DFT state-of-the-art theories are proposed. - [2] Asymmetric Synthesis of Morphan Type b-Amino Acids. The synthesis of several morphan structures, 2-azabiciclo[3.3.1]nonane scaffold, are discussed, several of them being b-Amino acids. - [3] Structure-based Design and Synthesis of Novel mu Opioid Receptor Ligands. The morphan core is used in a structure-based design using Docking approaches and MD simulations to discover new potential opioid ligands. The leads are synthesized in few steps taking the initial morphan b-amino acid obtained in chapter 2. - [4] Biological Evaluation of Novel mu Opioid Receptor Ligands. The synthesized compounds in chapter 3 are submiitted to biological trials, which describes the acitivity of these series of candidates. - [5] Asymmetric Synthesis of Flexible Peptide-Nucleotides (PNA). Several peptide-nucleotides were prepared following asymmetric Michael additions together with several nucleobase insertion protocols to synthesize PNA-monomers. - [6] Molecular Dynamics Simulations of Flexible Peptide-Nucleotides. The Leumman¿s PNA-monomer are theoretically studied through MD simulations to gain insigth in the hybridization properties with natural nucleic acid systems

Statistical models for genome sequence mapping

In this work we present a mapper, an algorithm to find short DNA sequences in large reference texts. Our algorithm uses the standard seed-and-extend approach, utilized by most modern mappers, combined with a novel genome annotation called neighborhood annotation. The neighborhood annotation is a data structure that contains information of similarity between sequences of the same reference. Based on this annotation, we build a statistical model to aid the processes of seeding and mapping quality estimation. Overall, our algorithm achieves higher sensitivity and more accurate estimation of mapping reliability with simulated Illumina reads, at the same speed compared to the state-of-the art algorithms. The C source code of the algorithm implementation is available at http://github.com/ezorita/mapper.En este proyecto presentamos un algoritmo de mapping. Los mappers son algoritmos utilizados para encontrar secuencias cortas de ADN en textos de referencia mucho más largos. Nuestro algoritmo utiliza la técnica estándar de seed-and-extend, utilizada por la mayoria de mappers actuales, combinada con una nueva anotación del genoma: el neighborhood annotation. Esta anotación es una estructura de datos que almacena información sobre las similitudes entre las secuencias del texto de referencia. Basandonos en esta estructura, hemos diseñado un modelo estadístico que utilizamos para favorecer los procesos de seeding y de estimación de la calidad de mapping. Finalmente, hemos implementado y testeado el rendimiento de nuestro algoritmo en secuencias simuladas de Illumina. Los resultados obtenidos muestran una mejor sensitividad y estimaciones más precisas de la fiabilidad de mapping, a la misma velocidad que los mappers del estado del arte. El código fuente de la implementación en C está disponible en open-source en http://github.com/ezorita/mapper.En aquest projecte hi presentem un algoritme de mapping. Els mappers són algoritmes que s'utilitzen per trobar seqüències curtes d'ADN en textos de referència molt grans. El nostre algoritme utilitza la tècnica estàndard de seed-and-extend, utilitzada per la majoria de mappers actuals, combinada amb una nova anotació del genoma que hem anomenat neighborhood annotation. Aquesta anotació consisteix en una estructura de dades que emmagatzema informació sobre les similaritats entre les seqüències del text de referència. Basant-nos en aquesta estructura, hem dissenyat un model estadístic que utilitzem per assistir els processos de seeding i d'estimació de la qualitat de mapping. Finalment, hem implementat i mesurat el rendiment del nostre algoritme en seqüenciacions simulades d'Illumina. Els resultats obtinguts determinen millor sensitivitat i estimacions més acurades de la fiabilitat de mapping, a la mateixa velocitat que els mappers de l'estat de l'art. El codi font de la implementació en C està disponible en open-source al web http://github.com/ezorita/mapper

Thermodynamically based DNA strand design

We describe a new algorithm for design of strand sets, for use in DNA computations or universal microarrays. Our algorithm can design sets that satisfy any of several thermodynamic and combinatorial constraints, which aim to maximize desired hybridizations between strands and their complements, while minimizing undesired cross-hybridizations. To heuristically search for good strand sets, our algorithm uses a conflict-driven stochastic local search approach, which is known to be effective in solving comparable search problems. The PairFold program of Andronescu et al. [M. Andronescu, Z. C. Zhang and A. Condon (2005) J. Mol. Biol., 345, 987–1001; M. Andronescu, R. Aguirre-Hernandez, A. Condon, and H. Hoos (2003) Nucleic Acids Res., 31, 3416–3422.] is used to calculate the minimum free energy of hybridization between two mismatched strands. We describe new thermodynamic measures of the quality of strand sets. With respect to these measures of quality, our algorithm consistently finds, within reasonable time, sets that are significantly better than previously published sets in the literature

Derivation of nearest-neighbor DNA parameters in magnesium from single-molecule experiments

DNA hybridization is an essential molecular reaction in biology with many applications. The nearest-neighbor (NN) model for nucleic acids predicts DNA thermodynamics using energy values for the different base pair motifs. These values have been derived from melting experiments in monovalent and divalent salt and applied to predict melting temperatures of oligos within a few degrees. However, an improved determination of the NN energy values and their salt dependencies in magnesium is still needed for current biotechnological applications seeking high selectivity in the hybridization of synthetic DNAs. We developed a methodology based on single molecule unzipping experiments to derive accurate NN energy values and initiation factors for DNA. A new set of values in magnesium is derived, which reproduces unzipping data and improves melting temperature predictions for all available oligo lengths, in a range of temperature and salt conditions where correlation effects between the magnesium bound ions are weak. The NN salt correction parameters are shown to correlate to the GC content of the NN motifs. Our study shows the power of single-molecule force spectroscopy assays to unravel novel features of nucleic acids such as sequence-dependent salt corrections