Nucleotide sequencing and

Primary structure peptide aird/or nucleotide sequence and the relationship between the PUB sequence and that found in the sequence database(s) StQUHS... 

Figure 10.12 Response elements for heterodimers of the nuclear receptor for ds-retinoic acid (RXR) with the receptors for vitamin D (VDR), thyroid hormone (TR) and trans-retinoic acid (RAR). The half-sites of these response elements have identical nucleotide sequences and are organized as direct repeats. They differ in the number of base pairs in the spacer region between the half-sites. This difference forms the basis for the ability of the heterodimers to discriminate between the different response elements.

FIGURE 11.33 Restricdon mapping of a DNA molecule as determined by an analysis of the electrophoretic pattern obtained for different restriction endonuclease digests. (Keep in mind that a dsDNA molecule has a unique nucleotide sequence and therefore a definite polarity thus, fragments from one end are distinctly different from fragments derived from the other end.)... 

Fukumori F, CP Saint (1997) Nucleotide sequences and regulational analysis of genes involved in conversion of aniline to catechol in Pseudomonas putida UCC22 (pTDNl). J Bacterial 179 399-408. 

Bryant C, L Hubbard, WD McFlroy (1991) Cloning, nucleotide sequence, and expression of nitroreductase gene from Enterobacter cloacae. J Biol Chem 266 4126-4130. 

Noguchi N, A Emura, H Matsuyama, K O Hara, M Sasatsu, M Kono (1995) Nucleotide sequence and characterization of erythromycin resistance determinant that encodes macrolide 2 phosphotransferas I in Escherichia coli. Antimicrob Agents Chemother 39 2359-2363. 

Erickson BD, FJ Mondello (1992) Nucleotide sequencing and transcriptional mapping of the genes encoding biphenyl dioxygenase, a multicomponent polychlorinated-biphenyl-degrading enzyme in Pseudomonas strain LB400. J Bacteriol 174 2903-2912. 

Since the discovery of the double hehcal structure of deoxyribonucleic acid (DNA) by Watson and Crick in 1953 [1], there has been considerable belief that the canonical right-handed B-DNA may adopt a wide range of different conformations depending on the nucleotide sequences and environmental conditions. This speculation turned out to be a reahty [2-10]. hi hving systems, the conformational flexibility of DNA resides primarily in the polymorphs of the DNA double hehx (including right-handed and left-handed double hehcal DNA) and occurs under various environmental conditions [4j. The main family of DNA forms identified, based on circular dichroic and... 

Horinouchi, S. and Weisblum, B. (1982) Nucleotide sequence and functional map of pE194, a plasmid that specifies inducible resistance to macrolide, lincosamide, and streptogramin type B antibodies. Journal of... 

Figure 4.2 Generalized outline of a gene chip. In this example, short oligonucleotide sequences are attached to the anchoring surface (only the outer rows are shown). Each probe displays a different nucleotide sequence, and the sequences used are usually based upon genome sequence information. The sequence of one such probe is shown as AGGCA. By incubating the chip with, for example, total cellular mRNA under appropriate conditions, any mRNA with a complementary sequence (UCCGU in the case of the probe sequence shown) will hybridize with the probes. In reality, probes will have longer sequences than the one shown above...

C. Hassett, K. B. Robinson, N. B. Beck, C. J. Omiecinski, The Human Microsomal Epoxide Hydrolase Gene (EPHX1) Complete Nucleotide Sequences and Structural Characterization , Genomics 1994, 23, 433 - 442. 

Bohm, R., Sauteg M. and Bock, A. (1990) Nucleotide sequence and expression of an operon in Escherichia coli coding for formate hydrogenlyase components. Mol. Microbiol., 4, 231M3. 

Zinoni E, Birkmann A, Stadtman TC, Bock A. 1986. Nucleotide sequence and expression of the selenocysteine-containing polypeptide of formate dehydrogenase (formate-hydrogen-lyase-linked) from Escherichia coli. Proc Natl Acad Sci USA 83 4650-4. 

DNA is a structurally polymorphic macromolecule which, depending on nucleotide sequence and environmental conditions, can adopt a variety of conformations. The double helical structure of DNA (dsDNA) consists of two strands, each of them on the outside of the double helix and formed by alternating phosphate and pentose groups in which phosphodiester bridges provide the covalent continuity. The two chains of the double helix are held... 

Figure 1. Consensus nucleotide sequence and stem-loop structure of hammerhead ribozyme.

Barnett, M.J. Fisher, R.F. Jones, T. et al. Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid. Proc. Natl. Acad. Sci. USA, 98, 9883-9888 (2001)... 

Watson, R.J. Analysis of the G4-dicarboxylate transport genes of Rhizobium meliloti nucleotide sequence and deduced products of dctA, dctB, and dctD. Mol. Plant Microbe Interact., 3, 174-181 (1990)... 

Kikuchi, Y., Yasukochi, Y., Nagata, Y., Fukuda, M. Takagi, M. (1994). Nucleotide sequence and functional analysis of the meta-cleavage pathway involved in biphenyl and polychlorinated biphenyl degradation in Pseudomonas sp. strain KKS102. Journal of Bacteriology, 176, 4269-76. 

Laddaga, R. A., Chu, L., Mistra, T. K. Silver, S. 1987. Nucleotide sequence and expression of the mercurial-resistance operon from Staphylococcus aureus plasmid pI258. Proceedings of the National Academy of Science USA, 84, 5106-10. 

Two types of DNA variation commonly result in RFLPs single base changes in the nucleotide sequence, and tandem repeats of DNA sequences. 

The right-handed helical structure, known as B DNA, is the most commonly occurring conformation of linear duplex DNA in nature. In this structure, the distance between stacked base pairs is 3.4 A, with approximately 10 base pairs per helical turn. The inherent flexibility of the structure, however, makes a variety of conformations possible under different conditions. In some instances, nucleotide sequence and degree of hydration dictate which conformations are favored. DNA interacts with a variety of proteins inside the cell, and these proteins can also have a significant influence on its secondary and tertiary structure. 

Aptamers are nucleic acids which exhibit a defined structure due to their nucleotide sequence and therefore, are able to specifically bind selected targets [1] (aptus [lat.] = fitting, sticking to). Aptamers and likewise, ribozymes [2] and deoxyribozymes [3] are selected in vitro by screening nucleic acid libraries. Here we describe in detail the selection of aptamers by a process called SELEX (Systematic Evolution of Ligands by Exponential enrichment) [4]. 

Breslauer and his colleagues have been able to use this database to predict the energetics associated with the melting of a wide variety of duplexes based on the nucleotide sequence in the oligonucleotide. Conversely, from the known nucleotide sequence and the melting energetics obtained from Table 16.6, they have been able to predict the likelihood that structural features like the hairpin loop of reaction (16.25) would be observed. 

Liu, D., Kato, H. and Sugane, K. (1 997) The nucleotide sequence and predicted secondary structure of small subunit (1 8S) ribosomal RNA from Spirometra erinaceieuropaei. Cene 1 84, 221-227. 

Okamoto, P.M., Fu, Y.-H. Marzluf, G.A. (1991). Nit-3, the structural gene of nitrate reductase in Neurospora crassa nucleotide sequence and regulation of mRNA synthesis and turnover. Molecular and General Genetics 227, 213-23. 

Godoy, J.A., Pardo, J.M. Pintor-Toro, J.A. (1990). A tomato cDNA inducible by salt stress and abscisic acid nucleotide sequence and expression pattern. Plant Molecular Biology 15, 695-705. 

Leah, R. Mundy, J. (1989). The bifunctional a-amylase/subtilisin inhibitor of barley Nucleotide sequence and patterns of seed-specific expression. Plant Molecular Biology 12, 673-82. 

Kagawa, H., McLachlan, A. D., Brenner, S., Karn, J., and Gengyo-Ando, K. (1989). Paramyosin gene (unc-15) of Caenorhabditis elegans Molecular cloning, nucleotide sequence and models for thick filament structure./. Mol. Biol. 207, 311-333. 

Agrawal, S. (1999) Importance of nucleotide sequence and chemical modifications of anti-sense oligocnucleotides. Biochim. Biophys. Acta., 1489, 53-68. 

Buzayan, J.M., Hampel, A. and Bruening, G. (1986) Nucleotide sequence and newly formed phosphodiester bond of spontaneously ligated satellite tobacco ringspot virus RNA. Nucleic Acids Res., 14, 9729-9743. 

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