Complexity: of DNA

The renaturation rate of DNA is an excellent indicator of the sequence complexity of DNA. For example, bacteriophage T4 DNA contains about 2 X 10 nucleotide pairs, whereas Escherichia coli DNA possesses 4.64 X 10 . E. coli DNA is considerably more complex in that it encodes more information. Expressed another way, for any given amount of DNA (in grams), the sequences represented in an E. coli sample are more heterogeneous, that is, more dissimilar from one another, than those in an equal weight of phage T4 DNA. Therefore, it will take the E. coli DNA strands longer to find their complementary partners and reanneal. This situation can be analyzed quantitatively. 

Chemical approach to the study of supramolecular biological structure of chromatin, nucleoproteide complex of DNA 99UK365. 

Emi, N., Kidoaki, S., Yoshikawa, K., and Saito, H. Gene transfer mediated by polyarginine requires a formation of big carrier-complex of DNA aggregate. Bio-chem. Biophys. Res. Commun. 1997, 231, 421-424. 

Complexes of DNA with cationic detergents were found to behave similarly to the DNA/CL They also are soluble in nonpolar organic solvents and form condensed DNA structures, with one notable exception. The morphology of some of the DNA/detergent... 

Plasmid DNA can be complexed electrostatically with cationic polymers. These complexes can be used for gene transfer [241]. Like the complexes of DNA with cationic lipids these complexes adhere to the cell surface with their cationic surface charges. Thereafter, they are internalized, presumably by adsorptive endocytosis. 

Oupicky D, Parker AL, Seymour LW (2002) Laterally stabilized complexes of DNA with linear reducible polycations strategy for triggered intracellular activation of DNA delivery vectors. J Am Chem Soc 124 8-9... 

Fig. 2 (a) Schematic of the formation of silver clusters using DNA oligonucleotide as scaffold. After complexation of DNA with silver cations, the mixture is reduced with NaBtL, and the fluorescent cluster is formed, (b) Absorption spectra of silver clusters acquired every 30 min using [5 -AGGTCGCCGCCC-3 ] = 10 uM. [Ag+] = 60 uM. and [BfLj-] = 60 pM. The foremost spectrum was acquired 9 min after adding the BH4, and it has at 426 nm. The inset spectrum shows the last spectmm in the series (692 min), with peaks at 424 and 520 nm. (c) Induced circular dichroism spectra. The cell path length was 5 cm. The spectra were collected 2 min (A, dashed-dotted line), 20 min (B, dotted line), 40 min (C,fine dashed line), 60 min (D, coarse dotted line), and 150 min (E, solid line) after adding the BH [32]... 

Chromatin The material of chromosomes. It is a complex of DNA, histones, and nonhistone proteins (chromosomal proteins, non-histone) found within the nucleus of a cell. [NIH]... 

Simoes S, Slepushkin V, Gaspar R, et al. Gene delivery by negatively charged ternary complexes of DNA, cationic liposomes and transferrin or fusigenic peptides. J Biol Chem 1998 5(7) 955-964. 

Analysis of noncovalent complexes of DNA and RNA by mass spectrometry. Chem Rev 2001, 101, 377-390. 

Fig. 10 Schematic illustrations of the formation of a DNA-oriented LB film by using a polyion complex of DNA/intercalator and cationic lipid monolayers...

As we begin to appreciate that there is much information about drug targets that genomics cannot provide, the focus has shifted from genomics to proteomics. The shift in focus parallels the appreciation of the complexity of proteins, which exceeds the complexity of DNA sequences. While a DNA sequence may allow one to predict the amino-acid sequence of a protein—in cases where an open reading frame sequence (with a start and stop codon) is apparent—it can neither assure expression nor provide information about protein function. 

It is common practice to include under the umbrella of quaternary structure other kinds of complexes between biopolymers. For example, the complex of DNA with histones to form nucleosomes may be said to have quaternary structure, the DNA also being regarded as a component subunit. 

The asialoglycoprotein receptor has been widely used because it is a part of the surveillance system in the circulation and it removes proteins as they age by the spontaneous loss of sialic acid (212, 213). This hepatic receptor has been widely used (214) to deliver reporter genes to the rat liver in vivo. In a study, a ligand for the asialoglycoprotein receptor (ASOR) was covalently linked to poly(L-lysine). After hepatic uptake of the complex of DNA and the ASOR-poly (L-lysine) conjugate, the reporter gene product is found in the liver (214). Other examples of receptor-mediated... 

With this overview of the complexity of DNA structure, we are now ready to turn, in the next chapter, to a discussion of DNA metabolism. 

DNA in eukaryotic chromosomes exists in a highly compacted form known as chromatin, a complex of DNA with a great variety of proteins. Five proteins called histones are present in large amounts (see table 25.2) and are believed to form a regularly repeating structural motif. The remaining proteins are present in smaller amounts and are irregularly distributed. 

Nucleosome. A complex of DNA and an octamer of histone proteins in which a small stretch of the duplex is wrapped around a molecular bead of histone. 

As the LET of the ionizing radiation increases, the RBE increases as do clustered lesions such as DSBs. The presence of O2 has then no longer such a dominating effect on increasing the complexity of DNA lesions and thus the OER drops. This is exemplified for ultrasoft X-rays in Table 12.24. 

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