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Description: Rifazone-8{sub 2} (R-8{sub 2}), a new rifamycin derivative, is shown to preferentially inhibit the growth of virus-transformed chick cells in culture. Macromolecular synthesis and glucose uptake of transformed cells are also appreciably decreased in the presence of low concentrations of R-8{sub 2} where the normal cells appear unaffected. While R-8{sub 2} is shown to be a selective inhibitor of RNA-directed DNA polymerase in vitro, its action on the growth of transformed cells may involve some other mechanism.
Date: March 28, 1974
Creator: Bissell, Mina J.; Hatie, Carroll; Tischler, Allan N. & Calvin, Melvin.
Partner: UNT Libraries Government Documents Department

Single molecule study of a processivity clamp sliding on DNA

Description: Using solution based single molecule spectroscopy, we study the motion of the polIII {beta}-subunit DNA sliding clamp ('{beta}-clamp') on DNA. Present in all cellular (and some viral) forms of life, DNA sliding clamps attach to polymerases and allow rapid, processive replication of DNA. In the absence of other proteins, the DNA sliding clamps are thought to 'freely slide' along the DNA; however, the abundance of positively charged residues along the inner surface may create favorable electrostatic contact with the highly negatively charged DNA. We have performed single-molecule measurements on a fluorescently labeled {beta}-clamp loaded onto freely diffusing plasmids annealed with fluorescently labeled primers of up to 90 bases. We find that the diffusion constant for 1D diffusion of the {beta}-clamp on DNA satisfies D {le} 10{sup -14} cm{sup 2}/s, much slower than the frictionless limit of D = 10{sup -10} cm{sup 2}/s. We find that the {beta} clamp remains at the 3-foot end in the presence of E. coli single-stranded binding protein (SSB), which would allow for a sliding clamp to wait for binding of the DNA polymerase. Replacement of SSB with Human RP-A eliminates this interaction; free movement of sliding clamp and poor binding of clamp loader to the junction allows sliding clamp to accumulate on DNA. This result implies that the clamp not only acts as a tether, but also a placeholder.
Date: July 5, 2007
Creator: Laurence, T A; Kwon, Y; Johnson, A; Hollars, C; O?Donnell, M; Camarero, J A et al.
Partner: UNT Libraries Government Documents Department

Rapid emergence of hepatitis C virus protease inhibitor resistance is expected

Description: Approximately 170 million people worldwide are infected with hepatitis C virus (HCV). Current therapy, consisting of pegylated interferon (PEG-IFN) and ribavirin (RBV), leads to sustained viral elimination in only about 45% of patients treated. Telaprevir (VX-950), a novel HCV NS3-4A serine protease inhibitor, has demonstrated substantial antiviral activity in patients with chronic hepatitis C genotype 1 infection. However, some patients experience viral breakthrough during dosing, with drug resistant variants being 5%-20% of the virus population as early as day 2 after treatment initiation. Why viral variants appear such a short time after the start of dosing is unclear, especially since this has not been seen with monotherapy for either human immunodeficiency virus or hepatitis B virus. Here, using a viral dynamic model, we explain why such rapid emergence of drug resistant variants is expected when potent HCV protease inhibitors are used as monotherapy. Surprisingly, our model also shows that such rapid emergence need not be the case with some potent HCV NS5B polymerase inhibitors. Examining the case of telaprevir therapy in detail, we show the model fits observed dynamics of both wild-type and drug-resistant variants during treatment, and supports combination therapy of direct antiviral drugs with PEG-IFN and/or RBV for hepatitis C.
Date: January 1, 2009
Creator: Rong, Libin; Perelson, Alan S & Ribeiro, Ruy M
Partner: UNT Libraries Government Documents Department

The Korarchaeota: Archaeal orphans representing an ancestral lineage of life

Description: Based on conserved cellular properties, all life on Earth can be grouped into different phyla which belong to the primary domains Bacteria, Archaea, and Eukarya. However, tracing back their evolutionary relationships has been impeded by horizontal gene transfer and gene loss. Within the Archaea, the kingdoms Crenarchaeota and Euryarchaeota exhibit a profound divergence. In order to elucidate the evolution of these two major kingdoms, representatives of more deeply diverged lineages would be required. Based on their environmental small subunit ribosomal (ss RNA) sequences, the Korarchaeota had been originally suggested to have an ancestral relationship to all known Archaea although this assessment has been refuted. Here we describe the cultivation and initial characterization of the first member of the Korarchaeota, highly unusual, ultrathin filamentous cells about 0.16 {micro}m in diameter. A complete genome sequence obtained from enrichment cultures revealed an unprecedented combination of signature genes which were thought to be characteristic of either the Crenarchaeota, Euryarchaeota, or Eukarya. Cell division appears to be mediated through a FtsZ-dependent mechanism which is highly conserved throughout the Bacteria and Euryarchaeota. An rpb8 subunit of the DNA-dependent RNA polymerase was identified which is absent from other Archaea and has been described as a eukaryotic signature gene. In addition, the representative organism possesses a ribosome structure typical for members of the Crenarchaeota. Based on its gene complement, this lineage likely diverged near the separation of the two major kingdoms of Archaea. Further investigations of these unique organisms may shed additional light onto the evolution of extant life.
Date: May 1, 2007
Creator: Elkins, James G.; Kunin, Victor; Anderson, Iain; Barry, Kerrie; Goltsman, Eugene; Lapidus, Alla et al.
Partner: UNT Libraries Government Documents Department

Model of transcriptional activation by MarA in escherichia coli

Description: The AraC family transcription factor MarA activates approximately 40 genes (the marA/soxS/rob regulon) of the Escherichia coli chromosome resulting in different levels of resistance to a wide array of antibiotics and to superoxides. Activation of marA/soxS/rob regulon promoters occurs in a well-defined order with respect to the level of MarA; however, the order of activation does not parallel the strength of MarA binding to promoter sequences. To understand this lack of correspondence, we developed a computational model of transcriptional activation in which a transcription factor either increases or decreases RNA polymerase binding, and either accelerates or retards post-binding events associated with transcription initiation. We used the model to analyze data characterizing MarA regulation of promoter activity. The model clearly explains the lack of correspondence between the order of activation and the MarA-DNA affinity and indicates that the order of activation can only be predicted using information about the strength of the full MarA-polymerase-DNA interaction. The analysis further suggests that MarA can activate without increasing polymerase binding and that activation can even involve a decrease in polymerase binding, which is opposite to the textbook model of activation by recruitment. These findings are consistent with published chromatin immunoprecipitation assays of interactions between polymerase and the E. coli chromosome. We find that activation involving decreased polymerase binding yields lower latency in gene regulation and therefore might confer a competitive advantage to cells. Our model yields insights into requirements for predicting the order of activation of a regulon and enables us to suggest that activation might involve a decrease in polymerase binding which we expect to be an important theme of gene regulation in E. coli and beyond.
Date: January 1, 2009
Creator: Wall, Michael E; Rosner, Judah L & Martin, Robert G
Partner: UNT Libraries Government Documents Department


Description: The proteolytic removal of about 60 amino acids from the COOH terminus of the bacteriophage T4 helix-destabilizing protein (gene 32 protein) produces 32*I, a 27,000-dalton fragment which still binds tightly and cooperatively to single-stranded DNA. The substitution of 32*I protein for intact 32 protein in the seven-protein T4 replication complex results in dramatic changes in some of the reactions catalyzed by this in vitro DNA replication system, while leaving others largely unperturbed. (1) Like intact 32 protein, the 32*I protein promotes DNA synthesis by the DNA polymerase when the T4 polymerase accessory proteins (gene 44/62 and 45 proteins) are also present. The host helix-destabilizing protein (Escherichia coli ssb protein) cannot replace the 32*I protein for this synthesis. (2) Unlike intact 32 protein, 32*I protein strongly inhibits DNA synthesis catalyzed by the T4 DNA polymerase alone on a primed single-stranded DNA template. (3) Unlike intact 32 protein, the 32*I protein strongly inhibits RNA primer synthesis catalyzed by the T4 gene 41 and 61 proteins and also reduces the efficiency of RNA primer utilization. As a result, de novo DNA chain starts are blocked completely in the complete T4 replication system, and no lagging strand DNA synthesis occurs. (4) The 32*I protein does not bind to either the T4 DNA polymerase or to the T4 gene 61 protein in the absence of DNA; these associations (detected with intact 32 protein) would therefore appear to be essential for the normal control of 32 protein activity, and to account at least in part for observations 2 and 3, above. We propose that the COOH-terminal domain of intact 32 protein functions to guide its interactions with the T4 DNA polymerase and the T4 gene 61 RNA-priming protein. When this domain is removed, as in 32*I protein, the helix destabilization induced by the protein is controlled ...
Date: July 1, 1980
Creator: Burke, R.L.; Alberts, B.M. & Hosoda, J.
Partner: UNT Libraries Government Documents Department


Description: Because this DOE grant was abruptly terminated without warning, this group was not able to accomplish the insertion of the biosensor genes into the mouse lines. They have been able to generate some of the mouse lines but have not been able to complete the ones that would give them the model systems that would allow them to investigate metastasis real-time in living tumors at the cellular level. Nonetheless, until the loss of funding, they have made progress in applications of the equipment to biological problems involving RNA and protein movement in living cells. The following products were delivered: (1) Imaging of gene expression in living cells and tissues, Singer RH, Lawrence DS, Ovryn B, Condeelis J, J Biomed Optics 10:0514061-0514069, 2005. This paper describes the method for activating single genes within cells and tissues. (2) Single Cell Gene Expression Profiling: Multiplexed Expression Fluorescence in situ Hybridization (FISH): Application to the Analysis of Cultured Cells. Levsky JM, Braut SA, Singer RH, Cell Biology: A Laboratory Handbook Volume 4, eds Celis JE, et al, 121-130. Academic Press, 2005. This paper describes the methodology for single cell expression profiling in tissues. (3) Spatial regulation of beta-actin translation by Src-dependent phosphorylation of ZBP1, Huttelmaier S, Zenklusen D, Lederer M, Dictenberg J, Lorenz M, Meng X, Bassell GJ, Condeelis J, Singer RH, Nature 438:512-515, 2005. This paper describes the mechanism by which the translational repressor of actin mRNA ZBP1 can effect regulation of cell motility and metastasis. (4) Visualization of mRNA translation in living cells, Rodriguez AJ, Shenoy SM, Singer RH, Condeelis J, J Cell Biol 175:67-76, 2006. This work describes a method to visualize mRNA translation in single cells. (5) Imaging mRNA movement from transcription sites to translation sites, Rodriguez AJ, Condeelis J, Singer RH, Dictenberg JB, Semin Cell Dev Biol 18:202-208, 2007. ...
Date: October 11, 2007
Partner: UNT Libraries Government Documents Department


Description: We have previously reported the chemotherapeutic effect of rifamycin derivatives on an ascites tumor, using increased life span as a criterion. These derivatives inhibit (1) RNA-instructed DNA polymerase in crude viral extracts; (2) virus-induced transformation in tissue cultures; and (3) the growth of tumors in vivo. One rifamycin derivative, rifazone-8{sub 2} (R-8{sub 2}), not only inhibits transformation in chick fibroblasts but affects the growth of transformed cells. The present study demonstrates that rifampicin and R-8{sub 2} act as cytocidal (rather than cytostatic) agents against some ascites cell lines.
Date: August 1, 1978
Creator: Hughes, Ann M. & Calvin, Melvin
Partner: UNT Libraries Government Documents Department

Coordinateendonucleolytic 5' and 3' trimming of terminally blocked blunt DNA double-strand break ends by Artemis nuclease and DNA-dependent protein kinase

Description: Previous work showed that, in the presence of DNA-PK, Artemis slowly trims 3'-phosphoglycolate-terminated blunt ends. To examine the trimming reaction in more detail, long internally labeled DNA substrates were treated with Artemis. In the absence of DNA-PK, Artemis catalyzed extensive 5' {yields} 3' exonucleolytic resection of double-stranded DNA. This resection required a 5'-phosphate but did not require ATP, and was accompanied by endonucleolytic cleavage of the resulting 3' overhang. In the presence of DNA-PK, Artemis-mediated trimming was more limited, was ATP-dependent, and did not require a 5'-phosphate. For a blunt end with either a 3'-phosphoglycolate or 3'-hydroxyl terminus, endonucleolytic trimming of 2-4 nucleotides from the 3'-terminal strand was accompanied by trimming of 6 nucleotides from the 5'-terminal strand. The results suggest that autophosphorylated DNA-PK suppresses the exonuclease activity of Artemis toward blunt-ended DNA, and promotes slow and limited endonucleolytic trimming of the 5'-terminal strand, resulting in short 3' overhangs that are trimmed endonucleolytically. Thus, Artemis and DNA-PK can convert terminally blocked DNA ends of diverse geometry and chemical structure to a form suitable for polymerase mediated patching and ligation, with minimal loss of terminal sequence. Such processing could account for the very small deletions often found at DNA double-strand break repair sites.
Date: February 18, 2008
Creator: Povirk, Lawrence; Yannone, Steven M.; Khan, Imran S.; Zhou, Rui-Zhe; Zhou, Tong; Valerie, Kristoffer et al.
Partner: UNT Libraries Government Documents Department


Description: It is shown that rifampicin, and especially its relative dimethyl-N-benzyl-N-desmethyl rifampicin, can inhibit focus formation by Moloney sarcoma virus on BALB/3T3 tissue cultures. At a dose level of 10 {micro}g/ml DMB appears to totally inhibit focus formation while reducing virus replication by at least a factor of fifty and cell proliferation by only a factor of three. These observations, taken together with those of others, suggest a role for the hybrid RNA-DNA dependent DNA polymerase and the gene for its synthesis both in normal cell processes and in the transformation process.
Date: March 1, 1971
Creator: Calvin, Melvin.; Joss, Urs R.; Hackett, Adeline J. & Owens, RobertB.
Partner: UNT Libraries Government Documents Department


Description: UmuD{sub 2} cleaves and removes its N-terminal 24 amino acids to form UmuD'{sub 2}, which activates UmuC for its role in UV-induced mutagenesis in E. coli. Cells with a non-cleavable UmuD exhibit essentially no UV-induced mutagenesis and are hypersensitive to killing by UV light. UmuD has been shown to bind to the beta processivity clamp (''beta'') of the replicative DNA polymerase, pol III. A possible beta-binding motif has been predicted in the same region of UmuD shown to be important for its interaction with beta. We performed alanine-scanning mutagenesis of this motif (14-TFPLF-18) in UmuD and showed that it has a moderate influence on UV-induced mutagenesis but is required for the cold sensitive phenotype caused by elevated levels of wild-type UmuD and UmuC. Surprisingly, the wild-type and the beta-binding motif variant bind to beta with similar K{sub d} values as determined by changes in tryptophan fluorescence. However, this data also implies that the single tryptophan in beta is in strikingly different environments in the presence of the wild-type versus the variant UmuD proteins, suggesting a distinct change in some aspect of the interaction with little change in its strength. Despite the fact that this novel UmuD variant is noncleavable, we find that cells harboring it exhibit phenotypes more consistent with the cleaved form UmuD', such as resistance to killing by UV light and failure to exhibit the cold sensitive phenotype. Cross-linking and chemical modification experiments indicate that the N-terminal arms of the UmuD variant are less likely to be bound to the globular domain than those of the wild-type, which may be the mechanism by which this UmuD variant acts as a UmuD' mimic.
Date: October 26, 2005
Creator: Beuning, P J; Simon, S M; Zemla, A; Barsky, D & Walker, G C
Partner: UNT Libraries Government Documents Department

SATB1 packages densely-looped, transciptionally-active chromatinfor coordinated expression of cytokine genes

Description: SATB1 is an important regulator of nuclear architecture that anchors specialized DNA sequences onto its cage-like network and recruits chromatin remodeling/modifying factors to control gene transcription. We studied the role of SATB1 in regulating the coordinated expression of Il5, Il4, and Il13 from the 200kb cytokine gene cluster region of mouse chromosome 11 during T-helper 2 (Th2)-cell activation. We show that upon cell activation, SATB1 is rapidly induced to form a unique transcriptionally-active chromatin structure that includes the cytokine gene region. Chromatin is folded into numerous small loops all anchored by SATB1, is histone H3 acetylated at lysine 9/14, and associated with Th2-specific factors, GATA3, STAT6, c-Maf, the chromatin-remodeling enzyme Brg-1, and RNA polymerase II across the 200kb region. Before activation, the chromatin displays some of these features, such as association with GATA3 and STAT6, but these were insufficient for cytokine gene expression. Using RNA interference (RNAi), we show that upon cell activation, SATB1 is not only required for chromatin folding into dense loops, but also for c-Maf induction and subsequently for Il4, Il5, and Il13 transcription. Our results show that SATB1 is an important determinant for chromatin architecture that constitutes a novel higher-order, transcriptionally-active chromatin structure upon Th2-cell activation.
Date: May 23, 2006
Creator: Cai, Shutao; Lee, Charles C. & Kohwi-Shigematsu, Terumi
Partner: UNT Libraries Government Documents Department

Comparison of multiple ecogenomics methods for determining ecosystem function in uranium-contaminated environments

Description: Background: Bioremediation may offer the only feasiblestrategy for the nearly intractable problem of metal and radionuclidecontamination of soil and groundwater. To understand bioremediation incontaminated environments, it is critical to determine the organismspresent in these environments, analyze their responses to stressconditions, and elucidate functional position in the environment.Methods: We used multiple molecular techniques on both sediment andgroundwater to develop a better understanding of the functionalcapability and stress level within the microbial community inrelationship to over one hundred geochemical parameters. Due to the lowpH (3.5-4.5) and high contaminant levels (e.g., uranium) microbialdensities and activities were low. We used a phage polymeraseamplification system to construct large and small insert DNA libraries,performed metagenome sequencing, constructed clonal libraries of selectfunctional genes (SSU rRNA gene, nirK, nirS, amoA, pmoA, and dsrAB), useda SSU rDNA Phylochip microarray (9,000 taxa), and a functional gene array(23K genes). A complete comparison for community differences andsimilarities between the different techniques was assessed using severalbioinformatics techniques. Results: SSU rDNA analysis revealed thepresence of distinct bacterial phyla, including proteobacteria,acidobacteria, and planctomycetes along the contaminant gradient.Metagenome analysis identified many of the same organisms, and diversitywas lower in water than sediment. Analysis with functional gene arrays,phylochip, and specific probes for genes and organisms involved inbiogeochemical cycling of C, N, and S, metal resistance, stress response,and contaminant degradation suggested that the dominant species could bebiostimulated during in situ uranium reduction. Several other findings ofdifference and similarities between methods are presented. Conclusion:These systems biology field studies could be enabling for strategies toattenuate nletal and radionuclide contamination.
Date: January 10, 2007
Creator: Hazen, T.C.; Dehal, P.; Arkin, A.P.; Fields, M.W.; Keller, M.; Zhou, J. et al.
Partner: UNT Libraries Government Documents Department

A neural network system for prediction of RNA polymerase II promoters

Description: One of the most difficult problems in the analysis of eucaryotic genes is the detection of RNA polymerase II promoter regions. Although promoter regions vary in the primary DNA sequence, a basic group of core promoter elements has been suggested in the literature. Many human promoter sequences contain a TATAA sequence element at approximately 30 bases upstream of the cap site (transcription start site). Other elements are the GC box which binds SPA and upregulates transcription, the CAAT box, and the ATG initiator codon. To characterize promoters, we constructed frequency matrices for each element using experimentally mapped human promoter regions. Additionally, we constructed histograms for the distances separating the various elements. We then used a neural network to combine these informational elements. The output of the neural network is then processed using a set of expert rules which depend on GRAIL`s ability to find exons in anonymous DNA. This improves the selectivity of promoter detection and reduces the false positive rate.
Date: December 31, 1994
Creator: Matis, S.; Shah, M.; Mural, R. & Uberbacher, E.
Partner: UNT Libraries Government Documents Department

Characterization of the mammalian DNA polymerase gene(s) and enzyme(s). Annual progress report

Description: Two Genes for DNA polymerase delta were identified from the wild type Chinese hamster ovary cells. These genes were cloned via RT-PCR from mRNA prepared the Chinese hamster ovary cells using primers specific to conserved sequences of the DNA polymerase {delta} gene. The first gene encodes a PCNA dependent DNA polymerase {delta} gene whereas the second gene encodes a PCNA independent DNA polymerase {delta} gene. Methods were developed to clone these genes in expression vector and host systems. The role of the two genes in DNA replication and repair was determined.
Date: January 1, 1995
Creator: Mishra, N.C.
Partner: UNT Libraries Government Documents Department

Rapid detection of biothreat agents based on cellular machinery.

Description: This research addresses rapid and sensitive identification of biological agents in a complex background. We attempted to devise a method by which the specificity of the cellular transcriptional machinery could be used to detect and identify bacterial bio-terror agents in a background of other organisms. Bacterial cells contain RNA polymerases and transcription factors that transcribe genes into mRNA for translation into proteins. RNA polymerases in conjunction with transcription factors recognize regulatory elements (promoters) upstream of the gene. These promoters are, in many cases, recognized by the polymerase and transcription factor combinations of one species only. We have engineered a plasmid, for Escherichia coli, containing the virA promoter from the target species Shigella flexneri. This promoter was fused to a reporter gene Green Fluorescent Protein (GFP). In theory the indicator strain (carrying the plasmid) is mixed with the target strain and the two are lysed. The cellular machinery from both cells mixes and the GFP is produced. This report details the results of testing this system.
Date: December 1, 2004
Creator: Lane, Todd W. & Gantt, Richard W.
Partner: UNT Libraries Government Documents Department

Selection for Unequal Densities of Sigma70 Promoter-like Signalsin Different Regions of Large Bacterial Genomes

Description: The evolutionary processes operating in the DNA regions that participate in the regulation of gene expression are poorly understood. In Escherichia coli, we have established a sequence pattern that distinguishes regulatory from nonregulatory regions. The density of promoter-like sequences, that are recognizable by RNA polymerase and may function as potential promoters, is high within regulatory regions, in contrast to coding regions and regions located between convergently-transcribed genes. Moreover, functional promoter sites identified experimentally are often found in the subregions of highest density of promoter-like signals, even when individual sites with higher binding affinity for RNA polymerase exist elsewhere within the regulatory region. In order to investigate the generality of this pattern, we have used position weight matrices describing the -35 and -10 promoter boxes of E. coli to search for these motifs in 43 additional genomes belonging to most established bacterial phyla, after specific calibration of the matrices according to the base composition of the noncoding regions of each genome. We have found that all bacterial species analyzed contain similar promoter-like motifs, and that, in most cases, these motifs follow the same genomic distribution observed in E. coli. Differential densities between regulatory and nonregulatory regions are detectable in most bacterial genomes, with the exception of those that have experienced evolutionary extreme genome reduction. Thus, the phylogenetic distribution of this pattern mirrors that of genes and other genomic features that require weak selection to be effective in order to persist. On this basis, we suggest that the loss of differential densities in the reduced genomes of host-restricted pathogens and symbionts is the outcome of a process of genome degradation resulting from the decreased efficiency of purifying selection in highly structured small populations. This implies that the differential distribution of promoter-like signals between regulatory and nonregulatory regions detected in large bacterial genomes ...
Date: March 1, 2006
Creator: Huerta, Araceli M.; Francino, M. Pilar; Morett, Enrique & Collado-Vides, Julio
Partner: UNT Libraries Government Documents Department

Regulation of chloroplast number and DNA synthesis in higher plants. Final report, August 1995--August 1996

Description: The long term objective of this research is to understand the process of chloroplast development and its coordination with leaf development in higher plants. This is important because the photosynthetic capacity of plants is directly related to leaf and chloroplast development. This research focused on obtaining a detailed description of leaf development and the early steps in chloroplast development including activation of plastid DNA synthesis, changes in plastid DNA copy number, activation of chloroplast transcription and increases in plastid number per cell. The research focused on the isolation of the plastid DNA polymerase, and identification of genetic mutants which are altered in their accumulation of plastid DNA and plastid number per cell.
Date: June 17, 1997
Creator: Mullet, J.E.
Partner: UNT Libraries Government Documents Department

Characterization and modification of phage T7 DNA polymerase for use in DNA sequencing. Final report, June 1, 1988--January 31, 1996

Description: This project has focused on the DNA polymerase of phage T7 for use in DNA sequencing. A complex of T7 DNA polymerase and E. coli thioredoxin form a highly processive DNA polymerase. The exonuclease activity of the enzyme can be reduced by chemical or genetic modifications resulting in an enzyme that has several properties useful in sequencing including high processivity and lack of discrimination against dideoxynucleotides. Manganese ion eliminates all discrimination against ddNTPs allowing sequence determination based on band intensity. A single tyrosine residue in the active site of T7 DNA polymerase is responsible for the efficient incorporation of ddNMPs. Replacement of the phenylalanine at this position in Klenow or Taq DNA polymerase with tyrosine eliminates discrimination against ddNTPs, a property that has advantages for cycle sequencing. Pyrophosphorolysis catalyzed by a polymerase results in the hydrolysis of specific fragments in DNA sequencing reactions, a problem that is eliminated by the addition of pyrophosphatase. The thioredoxin domain of gene 5 protein has been identified and transferred to Klenow DNA polymerase to make it processive. We have crystallized a complex of T7 DNA polymerase/thioredoxin bound to a primer-template in the presence of a dNTP.
Date: August 1, 1996
Creator: Richardson, C.C.
Partner: UNT Libraries Government Documents Department

PCR detection of groundwater bacteria associated with colloidal transport

Description: Colloidal transport may increase the amount of contaminant material than that which could be transported by water flow alone. The role of colloids in groundwater contaminant transport is complicated and may involve many different processes, including sorption of elements onto colloidal particles, coagulation/dissolution, adsorption onto solid surfaces, filtration, and migration. Bacteria are known to concentrate minerals and influence the transport of compounds in aqueous environments and may also serve as organic colloids, thereby influencing subsurface transport of radionuclides and other contaminants. The initial phase of the project consisted of assembling a list of bacteria capable of sequestering or facilitating mineral transport. The development and optimization of the PCR amplification assay for the detection of the organisms of interest, and the examination of regional groundwaters for those organisms, are presented for subsequent research.
Date: February 29, 1996
Creator: Cruz-Perez, P.; Stetzenbach, L. D. & Alvarez, A. J.
Partner: UNT Libraries Government Documents Department

Characterization of the mammalian DNA polymerase gene and protein. Annual progress report

Description: Methods were developed to purify the DNA polymerases of the {alpha}-family from Chinese hamster cells and their mutants selected as resistant to aphidicolin or specific inhibitor of DNA polymerases of the {alpha}-family. The wild type and mutant DNA polymerases were characterized with respect to their biochemical properties. A methodology was also developed to identify the replication intermediates and aphidicolin was found to inhibit a replication intermediate of the 24Kb size indicating the fact that aphidicolin inhibits the elongation process during DNA replication. This is the first demonstration of such role of aphidicolin in the eukaryotic DNA replication.
Date: January 1, 1993
Creator: Mishra, N.C.
Partner: UNT Libraries Government Documents Department

One-Step PCR Sequencing. Final Technical Progress Report for February 15, 1997 - November 30, 2001

Description: We investigated new chemistries and alternate approaches for direct gene sequencing and detection based on the properties of boron-substituted nucleotides as chain delimiters in lieu of conventional chain terminators. Chain terminators, such as the widely used Sanger dideoxynucleotide truncators, stop DNA synthesis during replication and hence are incompatible with further PCR amplification. Chain delimiters, on the other hand, are chemically-modified, ''stealth'' nucleotides that act like normal nucleotides in DNA synthesis and PCR amplification, but can be unmasked following chain extension and exponential amplification. Specifically, chain delimiters give rise to an alternative sequencing strategy based on selective degradation of DNA chains generated by PCR amplification with modified nucleotides. The method as originally devised employed template-directed enzymatic, random incorporation of small amounts of boron-modified nucleotides (e.g., 2'-deoxynucleoside 5'-alpha-[P-borano]- triphosphates) during PCR amplification. Rather than incorporation of dideoxy chain terminators, which are less efficiently incorporated in PCR-based amplification than natural deoxynucleotides, our method is based on selective incorporation and exonuclease degradation of DNA chains generated by efficient PCR amplification of chemically-modified ''stealth'' nucleotides. The stealth nucleotides have a boranophosphate group instead of a normal phosphate, yet behave like normal nucleotides during PCR-amplification. The unique feature of our method is that the position of the stealth nucleotide, and hence DNA sequencing fragments, are revealed at the desired, appropriate moment following PCR amplification. During the current grant period, a variety of new boron-modified nucleotides were synthesized, and new chemistries and enzymatic methods and combinations thereof were explored to improve the method and study the effects of borane modified nucleotides on polymerase and unmasking mechanisms. This approach takes advantage of differences in reactivity of the normal and modified nucleotidic linkages to generate PCR sequencing fragments that terminate at the site of incorporation of the modified nucleotide. In principle, the position of the modified nucleotide in each ...
Date: April 16, 2004
Creator: Shaw, B. R.
Partner: UNT Libraries Government Documents Department