DNA : RNA hybridization

Although relatively dehydrated DNA fibers can be shown to adopt the A-conformation under physiological conditions, it is unclear whether DNA ever assumes this form in vivo. However, double-helical DNA RNA hybrids probably have an A-like conformation. The 2 -OH in RNA sterically prevents dou-... 

This estimation (and the distribution of repetitive-sequence DNA) is based on a variety of DNA-RNA hybridization techniques and, more recently, on direct DNA sequencing. Similar techniques are used to estimate the number of active genes in a population of unique-sequence DNA. In brewers yeast Saccha-romyces cerevisiae, a lower eukaryote), about two thirds of its 6200 genes are expressed. In typical tissues in a higher eukaryote (eg, mammalian liver and kidney), between 10,000 and 15,000 genes are expressed. Different combinations of genes are expressed in each tissue,... 

In the Hybrid-Capture assay (Digene), a full-length RNA probe is hybridized to denatured HBV DNA in solution and the hybrids are captured on the surface of a tube coated with anti DNA RNA hybrid antibody. The bound hybrids are reacted with antihybrid antibody labeled with alkaline phosphatase. A chemiluminescent substrate is converted to a luminescent compound by the bound alkaline phosphatase. Light emission is measured in a luminometer and the concentration of HBV DNA, in pg/ml, is determined from a standard curve. The concentrations of the standards are determined spectrometrically (A260nm/A280nm). 

Studies of base-base CT in B-form DNA duplexes versus A-form DNA R-NA hybrids also confirmed our fundamental tenet that the pathway of efficient charge transfer will be the well-stacked pathway. In A-form duplexes considerable intra- and interstrand stacking exists. Not surprisingly then, in DNA RNA hybrids we observed a similar distance dependence for the yields of intra- and interstrand CT [105]. So, the distinction between intra- and interstrand CT observed in B-DNA duplexes truly correlates with differences in base stacking. 

In DNA RNA hybrids, where intrastrand base stacking is comparable to B-DNA, we observed efficient long range guanine oxidation when using ethidium as an intercalating photooxidant [130]. Conversely, a Rh(III) com-... 

Fig. 10 Charge transport is observed in a variety of nucleic acid assemblies over a wide distance regime (3.4-200 A). Shown are examples of nucleic acid structures through which charge transport has been examined a B-form DNA b DNA-RNA hybrids c cross-over junctions and d nucleosome core particles. In all assemblies, the charge transport chemistry is extremely sensitive to the structure of the -stacked nucleic acid bases...

F ig U re 1 3.1 A schematic view of RNA chain elongation catalyzed by an RNApolymerase. In the region being transcribed, the DNA double helix is unwound by about a turn to permit the DNAs sense strand to form a short segment of DNA-RNA hybrid double helix. That forms the transcription bubble. Note that the DNA bases in the bubble on the antisense strand are now exposed to the enzyme and are useable as a template for chain elongation. The RNApolymerase works its way down the DNA molecule until it encounters a stop signal. (Reproduced from D. Voet and J. G. Voet, Biochemistry, 3rd, edn, 2004 Donald and Judith G Voet. Reprinted with permission of John Wiley and Sons, Inc.)... 

Previous work has suggested that aminoglycoside specificity may occur in nucleic acid forms that display features characteristic of an A-type conformation (RNA triplex, DNA-RNA hybrid duplex,RNA duplex, DNA triplex, A-form DNA duplex, and DNA tetraplex ), rather than in naturally occurring RNA. However, conflicting results have been reported regarding the conformation of the triplex and of the Watson-Crick duplex within these triplexes. Both... 

Of those small molecules best able to bind DNA-RNA hybrids, very few have been found. At last count, the number was less than ten. For comparison, the nnmber of molecules known to target duplex DNA is perhaps in the thousands. Few reported attempts have been made to target the unique structure of the DNA-RNA hybrids, and consequently only a handful of molecules have been identified. " " A few years ago, we identified aminoglycosides as the antibiotics most likely to stimnlate groove-based recognition of A-form nucleic acid... 

CD and UV melting profiles in the presence of the ligands were carried ont to confirm the presence of a DNA-RNA hybrid duplex in the presence of the ligands. The addition of 2.2 tiM of neomycin and ethidium bromide results in a increase of 12°C, whereas the addition of 6 resnlts in a increase of 20°C. Increased concentration of 6 caused a gradual increase in the hybrid melting temperature. As the concentration of NM was increased from 0 p.M to 3 p.M, the melting temperature of the hybrid increases from 48.9°C to 70.1°C, a 21.2°C increase overall. 

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