Double-stranded oligonucleotide

Fluorescence studies and the binding interaction of Quartz/APES/RB with single- and double-stranded oligonucleotides (ssDNA and dsDNA) in Tris-HCl buffer solution of pH 7.4 were carried out. Quartz/APES/RB exhibited emission at 576 nm, whereas Quartz/APES without BB where nonfluorescent, suggesting that RB successfully assembled on the surface of quartz wafers. By comparison with Aem of 5 x 10 5 M RB solution, which was 588 nm, a hypsochromic shift was found. Considering the fluorescence microscopical image of Quartz/APES/RB, it... 

Ying Z, Xiang-Ying S, Bin L (2009) Fluorescent recognition for single- and double-stranded oligonucleotides based on rhodamine B-modified self-assembled bilayers. Chin J Anal Chem 37 665-670... 

Figure 2 Double-stranded oligonucleotide photoprobes that simulate modified DNA and intended to cross-link to DNA-binding proteins. (A) Probe modeling interstrand cross-linking by cisplatin Source From Ref. [63], with permission from the American Chemical Society via the Rightslink service (license number 2458870278307 granted June 30, 2010). The benzophenone probe prior to reaction with DNA is shown in the lower part of the panel. (B) Photoaffinity probe for bacterial DNA repair proteins. TT is a simulated thymine dimer intended to be recognized as a site of damage in DNA, and T (two instances) is the diazirine thymine derivative T Source From Ref. [64], with permission from Wiley.

A completely different mode of interaction has been reported for Pt(en)2, which binds to double-stranded oligonucleotides in a noncova-lent manner. NMR studies have indicated that in the duplexes d(TCGGGATCCCGA)2 and d(CAATCCGGATTG)2 this square planar Pt(II) species selectively binds to the AT sequence in the minor groove [101]. It was suggested that the binding is stabilized by close van der Waals interactions as well as hydrogen bonds [101]. 

It is generally believed that Pt(IV) complexes are prodrugs which are transformed to Pt(II) species before binding to DNA. However, the direct reaction of Pt(IV) complexes such as cis,trans,cis-[Pt(NH3)2(OH)2Cl2] with double-stranded oligonucleotides is reported to give Pt(IV) intra- and interstrand cross-links (119). 

An EMSAs is a simple assay to determine if a DNA sequence is able to bind a specific protein. Purified, cellular, or nuclear protein extract is incubated with labeled double-stranded oligonucleotide DNA probes, usually 20-25 nucleotides long. Each probe contains the SNP nucleotide (one per probe) and the identical sequence corresponding to the sequence around the SNP. The mixture is then run on a nondenaturing gel. If the DNA sequence binds the protein, there is a shift in the mobility of the complex (e.g., lane 2, Fig. 12.3). Specific and nonspecific competitors are often added to demonstrate specificity of the shift (lanes 5-7, Fig. 12.3). If an antibody... 

Fig. 4 The prompt (At=100 ns) yields of the G /G(-H) radicals, 4>g. as a function of the number of T bridging bases in the double-stranded oligonucleotides (adapted from...

A few recent NMR investigations of polynucleotides include studies of triple-helical DNA,689 Holliday junctions,290 double-stranded oligonucleotides containing adducts of carcinogens,690 691 of hairpin loops with sheared A A and G G pairs,692 and of proton exchange in both imino and amino groups.693... 

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