Oligodeoxy-nucleotides

Fig. 3.12. NegativeTOF SIMS spectra obtained from oligodeoxy-nucleotides (ODN) (left) and PNA (right) [3.26].

Antisense oligodeoxy nucleotides AS-NCX1, AS-NCX2, AS-NCX3... 

Ishii, K.J. et al., Immunotherapeutic utility of stimulatory and suppressive oligodeoxy-nucleotides, Curr. Opin. Mol. Ther., 6, 166, 2004. 

CRH probably does not act alone. According to clinical neuroendocrinology, vasopressin is a prime candidate for the synergy of CRH effects at pituitary CRHj receptors, and it also has behavioral effects that are compatible with a role in depression. Chronic psychosocial stress enhances vasopressin expression and increases the number of hypothalamic neurons coexpressing CRH and vasopressin. Infusion of an antisense oligodeoxy-nucleotide, which corresponds to the mRNA of vasopressin type 1 receptor, into the septum led to reduced anxiety-related behavior that parallels decreases in vasopressin receptor binding (Landgraf et al. 1995). 

The synthesis sketched in Figure 16.12 can be used to prepare oligodeoxynucleo-tides of up to about 150 bases, and examples of the preparation of cyclic oligodeoxy-nucleotides [122] and oligoribonucleotides [131] using this technique have also been... 

Macfarlane, D.E. and Manzel, L. (1998) Antagonism of immuno stimulatory CpG-oligodeoxy-nucleotides by quinacrine, chloroquine, and structurally related compounds. J. Immunol., 160, 1122-1131. 

L. Sewell. 2003. Synovial biomarker study of ISIS 104838, an antisense oligodeoxy-nucleotide targeting TNF-alpha, in rheumatoid arthritis. In 67th Annual Meeting of the American College of Rheumatology (ACR). October 23-28, Orlando, Florida, USA. 

E. Zylber-Katz, N.M. Dean, S.D. Rabkin, R.L. Martuza, and R.I. Glazer. 1996.Treatment of glioblastoma U-87 by systemic administration of an antisense protein kinase C-a phosphorothioate oligodeoxy-nucleotide. Mol. Pharmacol. 50 ... 

In the following discussion, the VCD of a number of small oligodeoxy nucleotides will be introduced. In some of these studies, a direct comparison between observed and calculated VCD spectra was possible. As pointed out before, the observed and calculated results for the double stranded decamer d(CG)s d(CG)5, henceforth referred to simply as d(CG)s, were a major stepping stone in our efforts to interpret the observed VCD spectra of poly(dG-dC) polyfdG-dC). Thus, these results, displayed in Figure 14, will be discussed in detail. 

The existence of clathrate-like water structure adjacent to the hydrophobic surfaces of macromolecules is an attractive hypothesis. Models have been proposed which have received some support from thermodynamical arguments [808]. However, this concept has proved ineffective as a basis for the interpretation of the structure associated with the many electron density solvent peaks, separated by 2.8 A to 3.0 A, which are frequently observed on the Fourier X-ray maps close to the surface of a protein [809, 810], Recently, however, some local clathrate-like water has been observed in special cases in the high-resolution studies of the small plant protein, crambin [811], in a hydrated deoxydinucleoside-phosphate drug complex [812], in (Phe4Val6) antamanide hydrate [8131 and in an oligodeoxy-nucleotide duplex [814],... 

Immunostimula-tory Sequence (ISS) Immuno-stimulatory Sequence Oligodeoxy-nucleotide (ISS-ODN)... 

Holland, CA., Henry, A.T., Whinna, H.C., Church, F.C. (2000). Effect of oligodeoxy-nucleotide thrombin aptamer on thrombin inhibition by heparin cofactor II and antithrombin. FEBS Lett. 484, 87-91... 

Yu, R.Z., Baker, B., Chappell, A., Geary, R.S., Cheung, E., and Levin, A.A. (2002) Development of an ultrasensitive noncompetitive hybridization ligation enzyme linked immunosorbent assay for the determination of phosphorothioate oligodeoxy nucleotide in plasma. Analytical Biochemistry, 304, 19 25. 

Figure 10.9 Non-PCR random mutagenesis. Overview of a random site-directed mutagenesis method. Obtain template DNA [ssDNA (—) strand] Step 1 anneal spiked oligodeoxy nucleotide mutagenic primer (blue) with desired mutation range Step 2 extend and incorporate mutagenic primer into new (-f) strand containing dCTPaS Step 3 digest the template DNA (—) strand with Nci I and ExoIII, then reynthesize (—) strand to include mutations into (—) strand as well Step 4 transform E. coli with random mutant recombinant DNA plasmid ready for selection, DNA purification and sequence identification of mutant recombinant DNAs.

There has been a report concerning the synthesis of 2 -deoxy-P-D-xylofurano-sylpurines 47 (B=Gua, isoguanine, xanthine) and their assembly into oligodeoxy-nucleotides in this work, the sugar configuration was established by a means previously reported (Vol. 23, p. 215). ... 

There has been an extended report on the synthesis of S -epi-bicyclonucleosides of type 242 (see Vol. 29, p. 297) and their incorporation into oligodeoxy-nucleotides. ... 

Pan S, Verhoeven K, Lee JK (2005) Investigation of the initial fragmentation of oligodeoxy-nucleotides in a quadrupole ion trap eharge level-related base loss. J Am Soc Mass Spectrom 16 1853-1865. doi 10.1016/j.jasms.2005.07.009... 

Gait, M. J., Popov, S. G., Singh, M., and Titmas, R. C. (1980) Rapid synthesis of oligonucleotides Further studies in solid-phase synthesis of oligodeoxy-nucleotides through phosphotriester intermediates. Nuci Acids Res, Symp. Ser No. 7,243-257. 

Brumbaugh, J A., Middendorf, L. R., Grone, D. L, and Ruth, J. L. (1988) Continuous, on-line DNA sequencing using oligodeoxy nucleotide primers with multiple fluorophores Proc Natl Acad Sci. 85,5610-5614. 

Last, the synthesis of a-oligodeoxynucleotides requires the same reagents and the same elongation cycles as for P-oligodeoxy-nucleotide synthesis. Likewise, a-oligodeoxynucleotides are deprotected and purified by following the standard procedures. 

Ill Millican, T. A., Mock, G. A., Chauncey, M. A., Patel, T. P., Eaton, M A. W., Gunning, J., Cutbush, S. D., Neidle, S., and Mann, J. (1984) Synthesis and biophysical studies of short oligodeoxynucleotides with novel modifications. a possible approach to the problem of mixed base oligodeoxy-nucleotide synthesis, Nucl Acids Res. 12, 7435-7453... 

Schott, H. and Schrade, H (1984) Single-step elongation of oligodeoxy-nucleotides using terminal deoxynucleotidyl transferase Ear. J. Biochem 143,613-620. 

McLaughlin and colleagues have derivatized aminopropyl silica particles with alkyl and aryl residues in order to obtain hydrophobic anion-exchange supports suitable for mixed mode chromatography. These supports were successfully used for separation of sequence isomeric oligodeoxy nucleotides and tRNA fragments (15). 

The addition of a single ribonucleotide to the 3 terminus of an oligodeoxy-nucleotide increases its reactivity and, conversely, the addition of a deoxynucleo-tide to the 3 -end of an oligoribonucleotide acceptor renders it less reactive. In either case, molecules having mixed composition do not react like their pure DNA or RNA parent substrates (13). 

Yu D, Kandimalla ER, Roskey A et al (2000) Stereo-enriched phosphorothioate oligodeoxy-nucleotides synthesis, biophysical and biological properties. Bioorg Med Chem 8 275-284... 

Ziegler A, Luedke GH, Fabbro D, Altmann KH, Stahel RA, Zangemeister-Wittke U. Induction of apoptosis in small-cell lung cancer by an antisense oligodeoxy-nucleotide taigeting the Bcl-2 coding sequence. J Nad Cancer Inst 1997 89 1027-1036. 

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