The tertiary structure of DNA

The tertiary structure of DNA is often neglected or ignored, but it is important to the action of the quinolone group of antibacterial agents (Chapter 10). The double helix is 

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A single helix is a coil a double helix is two nested coils The tertiary structure of DNA in a nucleosome is a coiled coil Coiled coils are referred to as supercoils and are quite common... 

The distortion of the tertiary structure of DNA induced by cisplatin depends on which type of adduct is formed. Only two types of structures have been determined, either by means of X-ray crystallography or NMR - the GG intrastrand and interstrand adducts [42-44]. There is, however, good reason to believe that 5 -AG intrastrand adduct is structurally very similar to the GG counterpart. 

The tertiary structure of DNA is the structural level that is most relevant to 3-D reality. Traditionally, ODNs in a physiologically relevant aqueous solution are considered to be in a random-coiled ssDNA state or in the form of dsDNA helix in the presence of a complementary DNA, including the case of self-complementarity. The double helix is the dominant tertiary structure for biological DNA that can be in one of the three DNA conformations found in nature, A-DNA, B-DNA, and Z-DNA. The B-conformation described by Watson and Crick (11) is believed to predominate in cells (12). However other types of nucleic acid tertiary structures different from random or classical double-stranded helix forms can also be observed. Among them are triplexes, quadruplexes, and several other nucleic acid structures (13, 14). 

The tertiary structure of DNA is complex. DNA does not normally exist as a straight linear polymer, but as a supercoiled structure. Supercoiiing is associated with special proteins in eukaryotic organisms. Prokaryotic organisms have one continuous molecule white eukaryotes have many (e.g. humans have 46). Viruses also contain nucleic acids and their genetic material can be either DNA or RNA. 

The tertiary structure of DNA depends on supercoihng. In prokaryotes, the circular DNA is twisted before the circle is sealed, giving rise to super-coiling. In eukaryotes, the supercoiled DNA is complexed with proteins known as histones. 

Similar to the three-dimensional structure of proteins, three levels of organisation can be distinguished for DNA. The primary structure is determined by the sequence of nucleotides, usually written as the sequence of bases they contain. The secondary structure is given by the shape of the double stranded helix. This helical chain does not exist as a straight, long molecule. It forms turns and twists and folds. This coiling is referred to as the tertiary structure of DNA. 

Of this sub-class of reactions, one is most Interesting. This is the formation of a closed ring chelate of clsplatln with the N-7 and 0-6 nucleophilic sites of guanine. It had been shown previously that the clsplatln reacted primarily with the GC rich regions of DNA. It has also been suggested that the tertiary structure of DNA is probably too plastic to exhibit the necessary stereoselectivity. It is also known that the clsplatln does not... 

This scheme of semiconservative replication, based on the classical DNA model of Watson and Crick (1953), with subsequent refinements (Pauling and Corey, 1956), corresponds to recent experimental findings, and its chemical and biochemical principles are well known and have been incorporated in all the textbooks of organic chemistry, biochemistry, and genetics. There is no need, therefore, to describe here the nature of the internucleotide (intermonomer) bonds, models of the tertiary structure of DNA, the results of its physical and physico-chemical study, and other material relevant to DNA structure. 

For a 3-cm-long molecule of DNA to fit inside a cell so tiny that we can only see it with a microscope, the polynucleotide chain must be folded into a more compact form. Not only must the DNA be compacted, it must be folded in a way that allows it to cany out its main functions. The way the chain is folded defines the tertiary structure of a nucleic acid. 

In contrast, RNA occurs in multiple copies and various forms (Table 11.2). Cells contain up to eight times as much RNA as DNA. RNA has a number of important biological functions, and on this basis, RNA molecules are categorized into several major types messenger RNA, ribosomal RNA, and transfer RNA. Eukaryotic cells contain an additional type, small nuclear RNA (snRNA). With these basic definitions in mind, let s now briefly consider the chemical and structural nature of DNA and the various RNAs. Chapter 12 elaborates on methods to determine the primary structure of nucleic acids by sequencing methods and discusses the secondary and tertiary structures of DNA and RNA. Part rV, Information Transfer, includes a detailed treatment of the dynamic role of nucleic acids in the molecular biology of the cell. 

The C-terminal domain (85 amino acid residues, not completely denatured at 90 °C) of the so-called a subunit of the RNAP from the extremely thermophilic eubacterium T. thermophilus (Tt) has been expressed uniformly N/ C-labelled and structurally characterized by the NMR spectroscopy. The tertiary structure of the domain, comprising a helical turn and four helices, was found to be almost identical to that of the corresponding domain from the mesophilic E. coli, despite 32% sequence homology. The interaction of the Tt domain with a variety of DNAs at 37 °C and 50 °C was investigated by chemical shift perturbation of the NMR signals and the DNA binding site was localized. ... 

The base sequence and the tertiary structure of the yeast tRNA specific for phenylalanine (tRNA " ) is typical of all tRNAs. The molecule (see also p.86) contains a high proportion of unusual and modified components (shaded in dark green in Fig. 1). These include pseudouridine (T), dihydrouridine (D), thymidine (T), which otherwise only occurs in DNA, and many methylated nucleotides such as 7-methylguanidine (m G) and—in the anticodon—2 -0-methylguanidine (m G). Numerous base pairs, sometimes deviating from the usual pattern, stabilize the molecule s conformation (2). 

On average, d-G residues in double-stranded DNA do not efficiently trap DNA. The d-G residues within pUC19 do not have identical chemical environments, and there must be a range of reactivities toward 75h, but most of the d-G residues within pUC19 have very little reactivity with 75h. The tertiary structure of double-helical DNA inhibits the formation of the C-8 adduct. This inhibition of C-8 adduct formation may explain why native DNA reacts with 76h and related compounds to generate ca. 5-20% of the minor N-2 adduct 115 in addition to the C-8 adduct, while the N-2 adduct is undetectable in studies involving monomeric (j.Q 4 -4s. 04,io6.io7... 

DNA-binding proteins contact their recognition sequences via defined structural elements, termed DNA-binding motifs (overview Pabo Sauer, 1992 Burley, 1994). DNA-binding motifs are often found in structural elements of the protein which can fold independently from the rest of the protein and therefore represent separate DNA-binding domains. They can, however, also occur within sequence elements which can not independently fold, but whose folding depends on the tertiary structure of the rest of the protein. 

Unpaired bases may bulge at various points in double-stranded stems of longer palindromes. These imperfect palindromes in the DNA are responsible for much of the tertiary structure of the various kinds of RNA. The tertiary structure, in turn, often determines the interaction of the RNA with enzymes and other proteins. 

All types of nucleic acids interact with proteins. Chromosomal DNA forms stable nonspecific complexes with structural proteins that stabilize their tertiary structure it also forms transient complexes with enzymes and regulatory proteins that modulate DNA and RNA metabolism. The gross tertiary structure of DNA in E. coli and a typical eukaryotic chromosome is described in the next section. 

Sequence analysis is a core area of bioinformatics research. There are four basic levels of biological structure (Table 1), termed primary, secondary, tertiary, and quaternary structure. Primary structure refers to the representation of a linear, hetero-polymeric macromolecule as a string of monomeric units. For example, the primary structure of DNA is represented as a string of nucleotides (G, C, A, T). Secondary structure refers to the local three-dimensional shape in subsections of macromolecules. For example, the alpha- and beta-sheets in protein structures are examples of secondary structure. Tertiary structure refers to the overall three-dimensional shape of a macromolecule, as in the crystal structure of an entire protein. Finally, quaternary structure represents macromolecule interactions, such as the way different peptide chains dimerize into a single functional protein. 

Nucleic acids have a primary, secondary, and tertiary structure analogous to the classification of protein structure. The sequence of bases in the nucleic acid chain gives the primary structure of DNA or RNA. The sequence of bases is read in a 5 -> 3 direction, so that you would read the structure in the next figure as ACGT. See Figure 8-1. 

The tertiary structure of recombinant DNA-derived pig GH has been reported [137], The conformation includes a large proportion of a-helix (about 54%), 4 antiparallel a-helices being arranged in a left-twisted helical bundle. Several unrelated proteins also contain 4 a-helices arranged in this way, but the connections in GH are unusual and unlike those found elsewhere. In view of the marked homology between the amino acid sequences of members of the GH-prolactin protein family, it seems likely that a similar tertiary structure will be found in other GHs and in prolactins and placental lactogen. 

Although the base triplets are of only minor importance in double-stranded nucleic acids, they have a structural role in determining and stabilizing the tertiary structure of transfer RNA, as discussed in Chapter 20. Base quadruplets where two Watson-Crick base pairs are associated as shown in Fig. 16.17 have been invoked to play a role in DNA-DNA aggregation and DNA recombination, but there is no direct evidence for their occurrence. 

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