Duplex oligonucleotides

P R E CONTENTS Preface. Stable-Isotope Assisted Protein NMR Spectroscopy in Solution, Brian J. Stockman and John L. Mar-kley. 31P and 1H Two-Dimensional NMR and NOESY-Dis-tance Restrained Molecular Dynamics Methodologies for Defining Sequence-Specific Variations in Duplex Oligonucleotides, David G. Gorenstein, Robert P. Meadows, James T. Metz, Edward Nikonowcz and Carol Beth Post. NMR Study of B- and Z-DNA Hairpins of d[(CG) 3T4(CG)3] in Solution, Sa-toshi Ikuta and Yu-Sen Wang. Molecular Dynamics Simulations of Carbohydrate Molecules, J.W. Brady. Diversity in the Structure of Hemes, Russell Timkovich and Laureano L. Bon-doc. Index. Volume 2,1991, 180 pp. 112.50/E72.50 ISBN 1-55938-396-8... 

Figure 4.18. Graphic display of macromolecular interaction with Cn3D. The display window of Cn3D illustrates the 3D structure of Zn finger peptide fragments (secondary structure features) bound to the duplex oligonucleotides (brown backbone). Zinc atoms are depicted as spheres. The alignment window shows the amino acid sequence depicting the secondary structures (blue helices and arrows for a-helical and /J-strand structures, respectively) and interacting (thin brown arrows) residues. The structure file, 1A1K.val, is derived from lAAY.pdb.

I. cntzcn O, Constant J-F, Defrancq E, et al. Photocrosslinking in ruthenium-labelled duplex oligonucleotides. ChemBioChem 2003 4 195-202. 

Figure 22.3. Separation and identification of different cleavage products at the AP site. (A) Duplex oligonucleotide containing an AP site. The damaged strand is labeled by 32P at its 5 end, as indicated by an asterisk. The AP site is designated in the DNA sequence by the X. (B) Schematic illustration of a gel showing the different mobihty of the various cleavage products at the AP site. The various products contain a different 3 end on the labeled 5 DNA fragment. These products are separated by electrophoresis on a 20% denaturing polyacrylamide gel, and the products are visualized by autoradiography.

A few of these UV resonance Raman studies have reported excitation profiles of oligonucleotides [158, 177], These studies show that the hypochromism in the resonance Raman intensities can be as large as 65% for bands enhanced by the ca. 260 nm absorption band for poly(dG-dC) and that the hypochromism can vary substantially between vibrational modes [177], In the duplex oligonucleotide poly(rA)-poly(rU) [158], similar hypochromism is seen. Although theUV resonance Raman excitation profiles of oligonucleotides have been measured, no excited-state structural dynamics have been extracted from them. 

Thus far, only one report of the UV resonance Raman excitation profiles of nucleic acids has appeared in the literature. The excitation profiles of calf thymus DNA [177] shows the same hypochromism as that observed in both single-stranded and duplex oligonucleotides. Also as expected, the excitation profiles are quite complex. Although an excitation profile is obtained for every vibrational mode, numerous bases are contributing to the Raman intensity observed in every vibration, each in its own microenvironment. Thus, the resonance Raman intensities currently are not useful for elucidating the excited-state structural dynamics of nucleic acids. 

GroessI, M., Tsybin, Y.O., Hartinger, C.G., Keppler, B.K., Dyson, P.J. Ruthenium versus platinum interactions of anticancer metallodrugs with duplex oligonucleotides characterized by electrospray ionization mass spectrometry. J. Biol. Inorg. Chem. 15, 677-688 (2010)... 

Oligonucleotides One duplex oligonucleotide is derived from Tetrahymena rDNA hexadecameric sequence (8) where the A was changed to a G at the +1 position relative to the topi cleavage site (indicated by the caret) to enhance camptothecin sensitivity (9) ... 

Remove uracil from duplex oligonucleotides containing deoxyuridine by incubation of 40 mL of end-labeled duplex (500 nM stock concentration) with 1 U of uracil DNA glycosylase for 2 h at 30°C. 

Frank Westheimer presents a thought-provoking overview of why nature chose phosphates to make the genetic tape. Even the youngest students have heard of DNA, and most have seen models of the famed double helix wherein hereditary information is encoded, but the current question. Why are phosphates in that helix , is usually passed over. The answer is in this volume. Other significant biochemical concerns, such as hydrolysis mechanisms for phosphate compounds and the NMR spectroscopy of duplex oligonucleotides and DNA complexes, are also addressed. 

Figure 16.2 Outline of the construction of a gap-lesion plasmid. A duplex oligonucleotide is prepared with a gap opposite a defined site-specific lesion, and with termini complementary of those generated by cleavage of a plasmid with two restriction enzymes. Ligation of the two forms the gap-lesion plasmid, which can be purified by gel electrophoresis. A key feature of the method is the use of restriction enzymes that cleave at non-palindromic sequences.

Alani E., Chi N.-W., Kolodner R. (1995) The Saccharomyces cerevisiae Msh2 protein specifically binds to duplex oligonucleotides containing mismatched DNA base pairs and insertions. Genes Dev. 9 234. 

Rgure 11 FLN spectra of anf/-BPDE-N -dG adducts of different stereochemistries in duplex oligonucleotides. Cunre A (-i- )-trans adduct curve B (-)-trans adduct cunre C (+)-c/s adduct curve D (-)-c/s adduct. Aex=369.4Snm. The FLN peaks are labeled with their excited-state vibrational frequencies in cm h... 

Hydrogen-Bonding Patterns Observed inthe Base Pairs of Duplex Oligonucleotides... 

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