A influência do esqueleto açúcar-fostato no transporte da molécula de DNA

This dissertation analyses the influence of sugar-phosphate structure in the electronic transport in the double stretch DNA molecule, with the sequence of the base pairs modeled by two types of quasi-periodic sequences: Rudin-Shapiro and Fibonacci. For the sequences, the density of state was calculated and it was compared with the density of state of a piece of human DNA Ch22. After, the electronic transmittance was investigated. In both situations, the Hamiltonians are different. On the analysis of density of state, it was employed the Dyson equation. On the transmittance, the time independent Schrödinger equation was used. In both cases, the tight-binding model was applied. The density of states obtained through Rudin-Shapiro sequence reveal to be similar to the density of state for the Ch22. And for transmittance only until the fifth generation of the Fibonacci sequence was acquired. We have considered long range correlations in both transport mechanism

Transporte eletrônico e propriedades termodinâmicas de nanobiomoléculas

We use a tight-binding formulation to investigate the transmissivity and the currentvoltage (I_V) characteristics of sequences of double-strand DNA molecules. In order to reveal the relevance of the underlying correlations in the nucleotides distribution, we compare theresults for the genomic DNA sequence with those of arti_cial sequences (the long-range correlated Fibonacci and RudinShapiro one) and a random sequence, which is a kind of prototype of a short-range correlated system. The random sequence is presented here with the same _rst neighbors pair correlations of the human DNA sequence. We found that the long-range character of the correlations is important to the transmissivity spectra, although the I_V curves seem to be mostly inuenced by the short-range correlations. We also analyze in this work the electronic and thermal properties along an _-helix sequence obtained from an _3 peptide which has the uni-dimensional sequence (Leu-Glu-Thr- Leu-Ala-Lys-Ala)3. An ab initio quantum chemical calculation procedure is used to obtain the highest occupied molecular orbital (HOMO) as well as their charge transfer integrals, when the _-helix sequence forms two di_erent variants with (the so-called 5Q variant) and without (the 7Q variant) _brous assemblies that can be observed by transmission electron microscopy. The di_erence between the two structures is that the 5Q (7Q) structure have Ala ! Gln substitution at the 5th (7th) position, respectively. We estimate theoretically the density of states as well as the electronic transmission spectra for the peptides using a tight-binding Hamiltonian model together with the Dyson's equation. Besides, we solve the time dependent Schrodinger equation to compute the spread of an initially localized wave-packet. We also compute the localization length in the _nite _-helix segment and the quantum especi_c heat. Keeping in mind that _brous protein can be associated with diseases, the important di_erences observed in the present vi electronic transport studies encourage us to suggest this method as a molecular diagnostic tool

Análise do efeito de polimorfismos não-sinônimos em genes de reparo de DNA da via BER na resposta inflamatória da meningite

In vitro and in animal models, APE1, OGG1, and PARP-1 have been proposed as being involved with inflammatory response. In this work, we have investigated if the SNPs APE1 Asn148Glu, OGG1 Ser326Cys, and PARP-1 Val762Ala are associated to meningitis and also developed a system to enable the functional analysis of polymorphic proteins. Patients with bacterial meningitis (BM), aseptic meningitis (AM) and controls (non-infected) genotypes were investigated by PIRA-PCR or PCR-RFLP. DNA damages were detected in genomic DNA by Fpg treatment. IgG and IgA were measured from plasma and the cytokines and chemokines were measured from cerebrospinal fluid samples using Bio-Plex assays. The levels of NF-κB and c-Jun were measured in CSF by dot blot assays. A significant (P<0.05) increase in the frequency of APE1 148Glu allele in BM and AM patients was observed. A significant increase in the genotypes Asn/Asn in control group and Asn/Glu in BM group was also found. For the SNP OGG1 Ser326Cys, the genotype Cys/Cys was more frequent (P<0.05) in BM group. The frequency of PARP-1 Val/Val genotype was higher in control group (P<0.05). The occurrence of combined SNPs increased significantly in BM patients, indicating that these SNPs may be associated to the disease. Increasing in sensitive sites to Fpg was observed in carriers of APE1 148Glu allele or OGG1 326Cys allele, suggesting that SNPs affect DNA repair activity. Alterations in IgG production were observed in the presence of SNPs APE1Asn148Glu, OGG1Ser326Cys or PARP-1Val762Ala. Reductions in the levels ofIL-6, IL-1Ra, MCP-1/CCL2and IL-8/CXCL8 were observed in the presence of APE1148Glu allele in BM patients, however no differences were observed in the levels of NF-κB and c-Jun considering genotypes and analyzed groups. Using APE1 as model, a system to enable the analysis of cellular effects and functional characterization of polymorphic proteins was developed using strategies of cloning APE1 cDNA in pIRES2-EGFP vector, cellular transfection of the construction obtained, siRNA for endogenous APE1 and cellular cultures genotyping. In conclusion, we obtained evidences of an effect of SNPs in DNA repair genes on the regulation of immune response. This is a pioneering work in the field that shows association of BER variant enzymes with an infectious disease in human patients, suggesting that the SNPs analyzed may affect immune response and damage by oxidative stress level during brain infection. Considering these data, new approaches of functional characterization must be developed to better analysis and interactions of polymorphic proteins in response to this context

Associação entre polimorfismos em enzimas de reparo de DNA e ocorrência de meningite bacteriana.

Despite advances in vaccine development and therapy, bacterial meningitis (BM) remains a major cause of death and long-term neurological disabilities. As part of the host inflammatory response to the invading pathogen, factors such as reactive oxygen species are generated, which may damage DNA and trigger the overactivation of DNA repair mechanisms. It is conceivable that the individual susceptibility and outcome of BM may be in part determined by non synonymous polymorphisms that may alter the function of crucial BER DNA repair enzymes as PARP-1, OGG-1 and APE-1. These enzymes, in addition to their important DNA repair function, also perform role of inflammatory regulators. In this work was investigated the non synonymous SNPs APE-1 Asn148Glu, OGG-1 Ser326Cys,PARP-1 Val762Ala, PARP-1 Pro882Leu and PARP-1 Cys908Tyr in patients with bacterial meningitis (BM), chronic meningitis (CM), aseptic meningitis (AM) and not infected (controls). As results we found increased frequency of variant alleles of PARP-1 Val762Ala (P = 0.005) and APE-1 Asn148Glu (P=0.018) in BM patients, APE-1 Asn148Glu in AM patients (P = 0.012) and decrease in the frequency of the variant allele OGG-1 Ser326Cys in patients with CM (P = 0.013), regarding the allelic frequencies in the controls. A major incidence of individuals heterozygous and/ or polymorphic homozygous in BM for PARP-1 Val762Ala (P= 0.0399, OD 4.2, 95% IC 1.213 -14.545) and PARP-1 Val762Ala/ APE-1 Asn148Glu (P = 0.0238, OD 11.111, 95% IC 1.274 - 96.914) was observed related to what was expected in a not infected population. It was also observed a major incidence of combined SNPs in the BM patients compared with the control group (P=0.0281), giving evidences that SNPs can cause some susceptibility to the disease. This combined effect of SNPs seems to regulate the principal cytokines and other factors related to BM inflammatory response and point the importance of DNA repair not only to repair activity when DNA is damaged, but to others essential functions to human organism balance.

Estudo da detecção do DNA do papiloma vírus humano (HPV) e da expressão imuno-histoquímica de proteína do ciclo celular no carcinoma epidermóide oral

Oral squamous cell carcinoma (OSCC) is the most common malignancy in oral cavity and human papillomavirus (HPV) may have an important role in its development. The aim of this experiment was to investigate the HPV DNA and viral types in 90 cases of OSCC. Moreover, a comparative analysis between the cases of OSSC with and without HPV DNA was performed by using cell cycle markers p21 and pRb in order to detect a possible correlation of these proteins and HPV infection. DNA was extracted from paraffin embedded tissue and amplified by PCR (polymerase chain reaction) with primers PCO3+ e PCO4+ for a fragment of human β-globin gene. After this procedure, PCR for HPV DNA detection was realized using a pair of generic primers GP5+ e GP6+. Immunohistochemical study was performed by streptoavidin-biotin technique and antibodies against p21 and pRb proteins were employed. Eighty-eight cases were positive for human β-globin gene and HPV DNA was found in 26 (29.5%) of then. It could not be detected significant correlation between HPV and age, sex and anatomical sites of the lesion. The most prevalent viral type was HPV 18 (80.8%). Regarding the immunohistochemical analysis, it was detected significant association between HPV presence and pRb immunoexpression (p=0,044), nevertheless, the same was not observed in relation to p21 protein (p =0,416). It can be concluded that the low detection of HPV DNA in OSCC by the present experiment suggests a possible role of the virus in the development and progression in just a subset of this disease

Conducão eletrônica e propriedades termodinâmicas da molécula de DNA

In this thesis, we study the thermo-electronic properties of the DNA molecule. For this purpose, we used three types of models with the DNA, all assuming a at geometry (2D), each built by a sequence of quasiperiodic (Fibonacci and / or Rudin-Shapiro) and a sequence of natural DNA, part of the human chromosome Ch22. The first two models have two types of components that are the nitrogenous bases (guanine G, cytosine C, adenine A and thymine T) and a cluster sugar-phosphate (SP), while the third has only the nitrogenous bases. In the first model we calculate the density of states using the formalism of Dyson and transmittance for the time independent Schr odinger equation . In the second model we used the renormalizationprocedure for the profile of the transmittance and consequently the I (current) versus V (voltage). In the third model we calculate the density of states formalism by Dean and used the results together with the Fermi-Dirac statistics for the chemical potential and the quantum specific heat. Finally, we compare the physical properties found for the quasi-periodic sequences and those that use a portion of the genomic DNA sequence (Ch22).