Energy Hyperspace for Stacking Interaction in AU/AU Dinucleotide Step: Dispersion-Corrected Density Functional Theory Study

Double helical structures of DNA and RNA are mostly determined by base pair stacking interactions, which give them the base sequence-directed features, such as small roll values for the purine-pyrimidine steps. Earlier attempts to characterize stacking interactions were mostly restricted to calculations on fiber diffraction geometries or optimized structure using ab initio calculations lacking variation in geometry to comment on rather unusual large roll values observed in AU/AU base pair step in crystal structures of RNA double helices. We have generated stacking energy hyperspace by modeling geometries with variations along the important degrees of freedom, roll, and slide, which were chosen via statistical analysis as maximally sequence dependent. Corresponding energy contours were constructed by several quantum chemical methods including dispersion corrections. This analysis established the most suitable methods for stacked base pair systems despite the limitation imparted by number of atom in a base pair step to employ very high level of theory. All the methods predict negative roll value and near-zero slide to be most favorable for the purine-pyrimidine steps, in agreement with Calladine's steric clash based rule. Successive base pairs in RNA are always linked by sugar-phosphate backbone with C3-endo sugars and this demands C1-C1 distance of about 5.4 angstrom along the chains. Consideration of an energy penalty term for deviation of C1-C1 distance from the mean value, to the recent DFT-D functionals, specifically B97X-D appears to predict reliable energy contour for AU/AU step. Such distance-based penalty improves energy contours for the other purine-pyrimidine sequences also. (c) 2013 Wiley Periodicals, Inc. Biopolymers 101: 107-120, 2014.

Beyond Watson and Crick : programming the self-assembly and reconfiguration of DNA nanostructures based on stacking interactions

Life is the result of the execution of molecular programs: like how an embryo is fated to become a human or a whale, or how a person’s appearance is inherited from their parents, many biological phenomena are governed by genetic programs written in DNA molecules. At the core of such programs is the highly reliable base pairing interaction between nucleic acids. DNA nanotechnology exploits the programming power of DNA to build artificial nanostructures, molecular computers, and nanomachines. In particular, DNA origami—which is a simple yet versatile technique that allows one to create various nanoscale shapes and patterns—is at the heart of the technology. In this thesis, I describe the development of programmable self-assembly and reconfiguration of DNA origami nanostructures based on a unique strategy: rather than relying on Watson-Crick base pairing, we developed programmable bonds via the geometric arrangement of stacking interactions, which we termed stacking bonds. We further demonstrated that such bonds can be dynamically reconfigurable.

The first part of this thesis describes the design and implementation of stacking bonds. Our work addresses the fundamental question of whether one can create diverse bond types out of a single kind of attractive interaction—a question first posed implicitly by Francis Crick while seeking a deeper understanding of the origin of life and primitive genetic code. For the creation of multiple specific bonds, we used two different approaches: binary coding and shape coding of geometric arrangement of stacking interaction units, which are called blunt ends. To construct a bond space for each approach, we performed a systematic search using a computer algorithm. We used orthogonal bonds to experimentally implement the connection of five distinct DNA origami nanostructures. We also programmed the bonds to control cis/trans configuration between asymmetric nanostructures.

The second part of this thesis describes the large-scale self-assembly of DNA origami into two-dimensional checkerboard-pattern crystals via surface diffusion. We developed a protocol where the diffusion of DNA origami occurs on a substrate and is dynamically controlled by changing the cationic condition of the system. We used stacking interactions to mediate connections between the origami, because of their potential for reconfiguring during the assembly process. Assembling DNA nanostructures directly on substrate surfaces can benefit nano/microfabrication processes by eliminating a pattern transfer step. At the same time, the use of DNA origami allows high complexity and unique addressability with six-nanometer resolution within each structural unit.

The third part of this thesis describes the use of stacking bonds as dynamically breakable bonds. To break the bonds, we used biological machinery called the ParMRC system extracted from bacteria. The system ensures that, when a cell divides, each daughter cell gets one copy of the cell’s DNA by actively pushing each copy to the opposite poles of the cell. We demonstrate dynamically expandable nanostructures, which makes stacking bonds a promising candidate for reconfigurable connectors for nanoscale machine parts.

Comparison of the thermodynamics and base-pair dynamics of a full LNA:DNA duplex and of the isosequential DNA:DNA duplex

Locked nucleic acids (LNA), conformationally restricted nucleotide analogues, are known to enhance pairing stability and selectivity toward complementary strands. With the aim to contribute to a better understanding of the origin of these effects, the structure, thermal stability, hybridization thermodynamics, and base-pair dynamics of a full-LNA:DNA heteroduplex and of its isosequential DNA:DNA homoduplex were monitored and compared. CD measurements highlight differences in the duplex structures: the homoduplex and heteroduplex present B-type and A-type helical conformations, respectively. The pairing of the hybrid duplex is characterized, at all temperatures monitored (between 15 and 37 degrees C), by a larger stability constant but a less favorable enthalpic term. A major contribution to this thermodynamic profile emanates from the presence of a hairpin structure in the LNA single strand which contributes favorably to the entropy of interaction but leads to an enthalpy penalty upon duplex formation. The base-pair opening dynamics of both systems was monitored by NMR spectroscopy via imino protons exchange measurements. The measurements highlight that hybrid G-C base-pairs present a longer base-pair lifetime and higher stability than natural G-C base-pairs, but that an LNA substitution in an A-T base-pair does not have a favorable effect on the stability. The thermodynamic and dynamic data confirm a more favorable stacking of the bases in the hybrid duplex. This study emphasizes the complementarities between dynamic and thermodynamical studies for the elucidation of the relevant factors in binding events.

Clustering-Based Ensemble Method as an Alternative to Stacking

One of the most popular techniques of generating classifier ensembles is known as stacking which is based on a meta-learning approach. In this paper, we introduce an alternative method to stacking which is based on cluster analysis. Similar to stacking, instances from a validation set are initially classified by all base classifiers. The output of each classifier is subsequently considered as a new attribute of the instance. Following this, a validation set is divided into clusters according to the new attributes and a small subset of the original attributes of the instances. For each cluster, we find its centroid and calculate its class label. The collection of centroids is considered as a meta-classifier. Experimental results show that the new method outperformed all benchmark methods, namely Majority Voting, Stacking J48, Stacking LR, AdaBoost J48, and Random Forest, in 12 out of 22 data sets. The proposed method has two advantageous properties: it is very robust to relatively small training sets and it can be applied in semi-supervised learning problems. We provide a theoretical investigation regarding the proposed method. This demonstrates that for the method to be successful, the base classifiers applied in the ensemble should have greater than 50% accuracy levels.

Synthesis, characterization, and structure of a new cobalt(II) Schiff-base complex with quinoxaline- 2-carboxalidine-2-amino-5-methylphenol

The mononuclear cobalt(II) complex [CoL2] H2O (where HL is quinoxaline-2-carboxalidine- 2-amino-5-methylphenol) has been prepared and characterized by elemental analysis, conductivity measurement, IR, UV-Vis spectroscopy, TG-DTA, and X-ray structure determination. The crystallographic study shows that cobalt(II) is distorted octahedral with each tridentate NNO Schiff base in a cis arrangement. The crystal exhibits a 2-D polymeric structure parallel to [010] plane, formed by O-H...N and O-H... O intermolecular hydrogen bonds and pye stacking interactions, as a racemic mixture of optical enantiomers. The ligand is a Schiff base derived from quinoxaline-2-carboxaldehyde

Controle da porosidade e das características ácido-base de óxidos mistos derivados da hidrotalcita para aplicação em catálise

Pós-graduação em Química - IQ

Base-Paired and Base-Stacked Structures of the Anti-HIV Drug Lamivudine: A Nucleoside DNA-Mimicry with Unprecedented Topology

We have prepared a DNA-mimicry of nucleosides in which the anti-HIV drug lamivudine (beta-L-2',3'-dideoxy-3'-thiacytidine, 3TC) self-assembles into a base-paired and helically base-stacked hexagonal structure. Face-to-face and face-to-tail stacked 3TC=3TC dimers base-paired through two hydrogen bonds between neutral cytosines by either N-H center dot center dot center dot O or N-H center dot center dot center dot N atoms give rise to a right-handed DNA-mimicry of lamivudine with an unusual highly symmetric hexagonal lattice and topology. In addition, a base-paired and base-stacked supramolecular architecture of lamivudine hemihydrochloride hemihydrate was also obtained as a result of our crystal screenings. This structure is formed through partially face-to-face stacked lamivudine pairs held together by protonated and neutral fragments. However, no helical stacking occurs in this structure in which lamivudine also adopts unusual conformations as the C1'-endo and C1'-exo sugar puckers and cytosine orientations intermediate between the anti and syn conformations. As a conclusion drawn from the nucleoside duplex, the hexagonal DNA-mimicry of lamivudine reveals that such double-stranded helices can be assembled without counterions and organic solvents but with higher crystallographic symmetry instead, because only water crystallizes together with lamivudine in this structure.

Bipyridyl- and biphenyl-DNA: A recognition motif based on interstrand aromatic stacking

The synthesis and incorporation into oligonucleotides of C-nucleosides containing the two aromatic, non-hydrogen-bonding nucleobase substitutes biphenyl (I) and bipyridyl (Y) are described. Their homo- and hetero-recognition properties in different sequential arrangements were then investigated via UV-melting curve analysis, gel mobility assays, CD- and NMR spectroscopy. An NMR analysis of a dodecamer duplex containing one biphenyl pair in the center, as well as CD data on duplexes with multiple insertions provide further evidence for the zipper-like interstrand stacking motif that we proposed earlier based on molecular modeling. UV-thermal melting experiments with duplexes containing one to up to seven I- or Y base pairs revealed a constant increase in T(m) in the case of I and a constant decrease for Y. Mixed I/Y base pairs lead to stabilities in between the homoseries. Insertion of alternating I/abasic site- or Y/abasic site pairs strongly decreases the thermal stability of duplexes. Asymmetric distribution of I- or Y residues on either strand of the duplex were also investigated in this context. Duplexes with three natural base pairs at both ends and 50 % of I pairs in the center are still readily formed, while duplexes with blunt ended I pairs tend to aggregate unspecifically. Duplexes with one natural overhang at the end of a I-I base pair tract can both aggregate or form ordered duplexes, depending on the nature of the natural bases in the overhang

Polímeros de coordenação à base de cobalto(II) e N,N'-bis(4-piridil)-1,4,5,8-naftaleno diimida como ligante e suas propriedade estruturais, espectroscópicas e fotoelétricas

Polímeros de coordenação têm atraído a atenção de pesquisadores na última década por conta de sua incrível versatilidade e virtualmente infinito número de possibilidades de combinação de ligantes orgânicos e centros metálicos. Estes compostos normalmente herdam as características magnéticas, eletrônicas e espectroscópicas de seus componentes base. Entretanto, apesar do crescente número de trabalhos na área, ainda são raros os polímeros de coordenação que apresentem condutividade elétrica. Para este fim, utilizou-se a N,N\'-bis(4-piridil)-1,4,5,8-naftaleno diimida, ou NDI-py, que pertence a uma classe de compostos rígidos, planares, quimicamente e termicamente estáveis e que já foram extensamente estudados por suas propriedades fotoeletroquímicas e semicondução do tipo n. O primeiro polímero de coordenação sintetizado, MOF-CoNDI-py-1, indicou ser um polímero linear, de estrutura 1D. O segundo, MOF-CoNDI-py-2, que conta com ácido tereftálico como ligante suporte, é um sólido cristalino com cela unitária monoclínica pertencente ao grupo espacial C2/c, determinado por difração de raios-X de monocristal. A rede apresenta um arranjo trinuclear de íons Co(II) alto spin com coordenados em uma geometria de octaedro distorcido, enquanto os ligantes NDI-py se encontram em um arranjo paralelo na estrutura, em distâncias apropriadas para transferência eletrônica. Com o auxílio de cálculo teóricos a nível de DFT, foi realizado um estudo aprofundado dos espectros eletrônicos e vibracionais, com atribuição das transições observadas, tanto para o MOF-CoNDI-py-2 quanto para o ligante NDI-py livre. A rede de coordenação absorve em toda a região do espectro eletrônico analisada, de 200 nm a 2500 nm, além de apresentar luminescência com característica do ligante. Dispositivos eletrônicos fabricados com um cristal do MOF-CoNDI-py-2 revelaram condutividades da ordem de 7,9 10-3 S cm -1, a maior já observada para um MOF. Além de elevada, a condutividade elétrica dos cristais demonstrou-se altamente anisotrópica, sendo significativamente menos condutor em algumas direções. Os perfis de corrente versus voltagem foram analisados em termos de mecanismos de condutividade, sendo melhores descritos por um mecanismo limitado pelo eletrodo to tipo Space-Charge Limited Current, concordando com a proposta de condutividade através dos planos de NDI-py na rede. A condutividade dos cristais também é fortemente dependente de luz, apresentando fotocondução quando irradiado por um laser vermelho, de 632 nm, enquanto apresenta um comportamento fotorresistivo frente a uma fonte de luz branca. Estes resultados, combinados, trazem um MOF em uma estrutura incomum e com elevada condutividade elétrica, modulada por luz, em medidas diretas de corrente. Não existem exemplos conhecidos de MOFs na literatura com estas características.

Sedimentology of a Middle Jurassic Base-of-Slope environment, Cutri Formation, Mallorca

The Cutri Formation’s, type location, exposed in the NW of Mallorca, Spain has previously been described by Álvaro et al., (1989) and further interpreted by Abbots (1989) unpublished PhD thesis as a base-of-slope carbonate apron. Incorporating new field and laboratory analysis this paper enhances this interpretation. From this analysis, it can be shown without reasonable doubt that the Cutri Formation was deposited in a carbonate base-of-slope environment on the palaeowindward side of a Mid-Jurassic Tethyan platform. Key evidence such as laterally extensive exposures, abundant deposits of calciturbidtes and debris flows amongst hemipelagic deposits strongly support this interpretation.