Sterochemically modified polyamides for recognition in the minor groove of DNA

The design of synthetic molecules that recognize specific sequences of DNA is an ongoing challenge in molecular medicine. Cell-permeable small molecules targeting predetermined DNA sequences offer a potential approach for offsetting the abnormal effects of misregulated gene-expression. Over the past twenty years, Professor Peter B. Dervan has developed a set of pairing rules for the rational design of minor groove binding polyamides containing pyrrole (Py), imidazole (Im), and hydroxypyrrole (Hp). Polyamides have illustrated the capability to permeate cells and inhibit transcription of specific genes in vivo. This provides impetus to identify structural elements that expand the repetoire of polyamide motifs with recognition properties comparable to naturally occurring DNA binding proteins. Through the introduction of chiral amino acids, we have developed chiral polyamides with stereochemically regulated binding characteristics. In addition, chiral substituents have facilitated the development of new polyamide motifs that broaden binding site sizes targetable by this class of ligands.

The application of metallointercalators in recognition of and charge transport in nucleic acids

Metal complexes that utilize the 9,10-phenanthrene quinone diimine (phi) moiety bind to DNA through the major groove. These metallointercalators can recognize DNA sites and perform reactions on DNA as a substrate. The site-specific metallointercalator Λ-1-Rh(MGP)_2phi^(5+) competitively disrupts the major groove binding of a transcription factor, yAP-1, from an oligonucleotide that contains a common binding site. The demonstration that metal complexes can prevent transcription factor binding to DNA site-specifically is an important step in using metallointercalators as therapeutics.

The distinctive photochemistry of metallointercalators can also be applied to promote long range charge transport in DNA. Experiments using duplexes with regions 4 to 10 nucleotides long containing strictly adenine and thymine sequences of varying order showed that radical migration is more dependent on the sequence of bases, and less dependent on the distance between the guanine doublets. This result suggests that mechanistic proposals of long range charge transport must involve all the bases.

RNA/DNA hybrids show charge migration to guanines from a remote site, thus demonstrating that nucleic acid stacking other than B-form can serve as a radical bridge. Double crossover DNA assemblies also provide a medium for charge transport at distances up to 100 Å from the site of radical introduction by a tethered metal complex. This radical migration was found to be robust to mismatches, and limited to individual, electronically distinct base stacks. In single DNA crossover assemblies, which have considerably greater flexibility, charge migration proceeds to both base stacks due to conformational isomers not present in the rigid and tightly annealed double crossovers.

Finally, a rapid, efficient, gel-based technique was developed to investigate thymine dimer repair. Two oligonucleotides, one radioactively labeled, are photoligated via the bases of a thymine-thymine interface; reversal of this ligation is easily visualized by gel electrophoresis. This assay was used to show that the repair of thymine dimers from a distance through DNA charge transport can be accomplished with different photooxidants.

Thus, nucleic acids that support long range charge transport have been shown to include A-track DNA, RNA/DNA hybrids, and single and double crossovers, and a method for thymine dimer repair detection using charge transport was developed. These observations underscore and extend the remarkable finding that DNA can serve a medium for charge transport via the heteroaromatic base stack.

Mechanisms of substrate selection by the signal recognition particle

The signal recognition particle (SRP) targets membrane and secretory proteins to their correct cellular destination with remarkably high fidelity. Previous studies have shown that multiple checkpoints exist within this targeting pathway that allows ‘correct cargo’ to be quickly and efficiently targeted and for ‘incorrect cargo’ to be promptly rejected. In this work, we delved further into understanding the mechanisms of how substrates are selected or discarded by the SRP. First, we discovered the role of the SRP fingerloop and how it activates the SRP and SRP receptor (SR) GTPases to target and unload cargo in response to signal sequence binding. Second, we learned how an ‘avoidance signal’ found in the bacterial autotransporter, EspP, allows this protein to escape the SRP pathway by causing the SRP and SR to form a ‘distorted’ complex that is inefficient in delivering the cargo to the membrane. Lastly, we determined how Trigger Factor, a co-translational chaperone, helps SRP discriminate against ‘incorrect cargo’ at three distinct stages: SRP binding to RNC; targeting of RNC to the membrane via SRP-FtsY assembly; and stronger antagonism of SRP targeting of ribosomes bearing nascent polypeptides that exceed a critical length. Overall, results delineate the rich underlying mechanisms by which SRP recognizes its substrates, which in turn activates the targeting pathway and provides a conceptual foundation to understand how timely and accurate selection of substrates is achieved by this protein targeting machinery.

Rewriting Schemes for Flash Memory

Flash memory is a leading storage media with excellent features such as random access and high storage density. However, it also faces significant reliability and endurance challenges. In flash memory, the charge level in the cells can be easily increased, but removing charge requires an expensive erasure operation. In this thesis we study rewriting schemes that enable the data stored in a set of cells to be rewritten by only increasing the charge level in the cells. We consider two types of modulation scheme; a convectional modulation based on the absolute levels of the cells, and a recently-proposed scheme based on the relative cell levels, called rank modulation. The contributions of this thesis to the study of rewriting schemes for rank modulation include the following: we

•propose a new method of rewriting in rank modulation, beyond the previously proposed method of “push-to-the-top”;

•study the limits of rewriting with the newly proposed method, and derive a tight upper bound of 1 bit per cell;

•extend the rank-modulation scheme to support rankings with repetitions, in order to improve the storage density;

•derive a tight upper bound of 2 bits per cell for rewriting in rank modulation with repetitions;

•construct an efficient rewriting scheme that asymptotically approaches the upper bound of 2 bit per cell.

The next part of this thesis studies rewriting schemes for a conventional absolute-levels modulation. The considered model is called “write-once memory” (WOM). We focus on WOM schemes that achieve the capacity of the model. In recent years several capacity-achieving WOM schemes were proposed, based on polar codes and randomness extractors. The contributions of this thesis to the study of WOM scheme include the following: we

•propose a new capacity-achievingWOM scheme based on sparse-graph codes, and show its attractive properties for practical implementation;

•improve the design of polarWOMschemes to remove the reliance on shared randomness and include an error-correction capability.

The last part of the thesis studies the local rank-modulation (LRM) scheme, in which a sliding window going over a sequence of real-valued variables induces a sequence of permutations. The LRM scheme is used to simulate a single conventional multi-level flash cell. The simulated cell is realized by a Gray code traversing all the relative-value states where, physically, the transition between two adjacent states in the Gray code is achieved by using a single “push-to-the-top” operation. The main results of the last part of the thesis are two constructions of Gray codes with asymptotically-optimal rate.

Representações sociais da Aids para pessoas que vivem com HIV e suas interfaces cotidianas

O presente estudo teve como objetivo descrever o conteúdo das representações sociais acerca da Aids para os usuários soropositivos em acompanhamento ambulatorial da rede pública de saúde e analisar a interface das representações sociais da Aids com o cotidiano dos indivíduos que vivem com o HIV, especialmente no que concerne à sua organização e ao processo de adesão ao tratamento. Trata-se de um estudo exploratório-descritivo, pautado na abordagem qualitativa e orientado pela Teoria das Representações Sociais. Os sujeitos consistiram em 30 usuários em acompanhamento ambulatorial de um Hospital Público Municipal localizado na cidade do Rio de Janeiro referenciado para clientes soropositivos ao HIV/Aids. Os dados foram coletados por meio de entrevista e analisados através da análise de conteúdo. Como resultados, emergiram 6 categorias, quais sejam: Elementos de memória da Ancoragem da Aids na sociedade e o seu processo de transformação, onde foi explicitada a ancoragem da Aids no outro, na África, no macaco, no homossexual e uma nova ancoragem apresentada consiste na cronicidade do diabetes, deixando a síndrome de ser sinônimo de morte; Transmissão e Prevenção da Aids segundo as pessoas que convivem com a síndrome, na qual os sujeitos apresentaram quase todas as formas cientificamente comprovadas quanto aos meios de transmissão do vírus HIV; O cotidiano dos indivíduos soropositivos permeado pelo processo de vulnerabilidade ao HIV, no âmbito do qual entende-se que o reconhecimento do risco individual frente à epidemia irá influenciar, sobretudo, as práticas e os comportamentos das pessoas; Discriminação e ocultamento no conviver com o HIV, onde se apresenta como estratégias de sobrevivência social o ocultamento do estado de soropositividade ao HIV. Assim, podem continuar a vida como pessoas consideradas normais, sem serem acusadas e discriminadas, sejam no âmbito familiar, social ou no trabalho; além disso, os sujeitos do estudo declararam que eram preconceituosos antes do diagnóstico; o processo de adesão ao tratamento na cotidianidade de indivíduos soropositivos, observando-se, nesta categoria, que um dos grandes motivadores da adesão ao tratamento consiste no fato dos usuários acreditarem no resultado positivo da terapêutica; o enfrentamento cotidiano experiênciado pelos sujeitos que convivem com o HIV, onde a forma como os sujeitos organizam o seu cotidiano para enfrentar e conviver com o HIV reflete diretamente em suas atitudes e em suas práticas, tanto no processo da adesão, como nas relações sociais (o outro) e, principalmente, na relação individual (o eu). Conclui-se que a representação social da Aids apresenta-se multifacetada e dependente do contexto histórico e social no qual o indivíduo está inserido, seus valores, cultura, nível de informação e conhecimento.