The primary structure of DNA

The primary structure of DNA is the way in which the DNA building blocks are linked together. Whereas proteins have over twenty building blocks to choose from, DNA has only four—the nucleosides deoxyadenosine, deoxyguanosine, deoxycytidine, and deoxythymidine (Fig. 6.1). 

Each nucleoside is constructed from two components—a deoxyribose sugar and a base. The sugar is the same in all four nucleosides and only the base is different. The four possible bases are two bicyclic purines (adenine and guanine), and two smaller pyrimidine structures (cytosine and thymine) (Fig. 6.2). 

The nucleoside building blocks are joined together through phosphate groups which link the 5 -hydroxyl group of one nucleoside unit to the 3 -hydroxyl group of the next (Fig. 6.3). 

With only four types of building block available, the primary structure of DNA is far less varied than the primary structure of proteins. As a result, it was long thought that DNA only had a minor role to play in cell biochemistry, since it was hard to see how such an apparently simple molecule could have anything to do with the mysteries of the genetic code. 

The solution to this mystery lies in the secondary structure of DNA. 

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The problem of sequencing nucleic acids is in principle similar to that of sequencing proteins. At first, the job might appear to be easier because there are only four bases compared to 20 common amino acids. In fact, it is much more difficult. Even the smallest DNA molecule contains at least 5,000 nucleotide units, and some DNA molecules contain 1 million or more nucleotide units. To determine the exact base sequence in such a molecule is a task of considerable magnitude. 

Enzymes called restriction endonucleases are used to spilt the DNA chain at known four-base sequences. 

A small quantity of DNA is obtained from some source associated with a crime—semen, blood, or hair roots, perhaps associated with a rape, murder, or other 

There are two main uses of DNA profiling in dealing with a crime. One is to compare a suspect s profile with a sample from the scene of the crime. Some years ago. 

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By analogy to the levels of structure of proteins the primary structure of DNA IS the sequence of bases along the polynucleotide chain and the A DNA B DNA and Z DNA helices are varieties of secondary structures... 

A structural gene is a linear sequence of codons which codes for a functional polypeptide, that is, a linear sequence of amino acids. Individual polypeptides may have a structural, enzymatic or regulatory role in the cell. Although the primary structure of DNA is the same in prokaryotes and eukaryotes, there are differences between the genes of these two types of organism, in internal structure, numbers and... 

The primary structure of DNA is a one-dimensional system similar to four-letter text and can be subjected to the simplest combinatory rules. The particular motifs can be combined with one or several other motifs in away similar to using building blocks. For instance, G-rich motif can be added to one or both ODN flanks. A certain sequence, e.g., a sequence containing unmethylated deoxyribodi-nucleotide CpG motifs that mimic prokaryotic DNA (I), can be placed between similar or different motifs, like GC-rich palindrome and/or G-rich motifs (Fig. I). Various motif combinations will yield a number of putative DNA sequence variants that can be used for further tests and selection of perspective ODN compounds (see Notes 1-4). 

The primary structure of DNA is based on repealing nucleotide units, where each nucleotide is made up of the sugar, i.e., 2 -deoxyribose, a phosphate, and a heterocyclic base, N The most common DNA bases are the purines, adenine (A) and guanine (G), and the pyrimidines, thymine (T) and cytosine (C) (see Fig. I). The base, N, is bound at the l -position of the ribose unit through a heterocyclic nitrogen. 

The primary structure of DNA consists of nucleotides linked by a phosphodiester bond between the 5 -OH of one unit and the 3 -OH of the next unit. To fully describe a DNA molecule, the base sequence must be known. Methods for sequencing have been developed, and, at present, over 150 bases can be sequenced per day. The counterpart of sequencing, the synthesis of oligonucleotides having known base sequences, is also highly developed. 

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. 

Having discussed the primary structure of DNA and RNA, we now consider how the nucleotide sequence is reproduced or transcribed into another molecule. This information transfer takes place by an interesting hydrogen-bonding interaction between specific pairs of bases. 

The genetic information of living organisms is coded in DNA in the form of base pair sequences. There are four types of nucleotides, which are linked to a polynucleotide with a sugar-phosphate backbone. The arrangement of nucleotides along the one-dimensional chain is called the primary structure of DNA, which directly encodes the primary structure of proteins by means of... 

Lindahl T. instability and decay of the primary structure of DNA. Nature 1993 362 709-715. 

The sequence or order of the nucleotides defines the primary structure of DNA and RNA. The nucleotides of the polymer are linked by phosphodiester bonds... 

The presence of site-specific endodeoxyribonucleases (restrictases) is essential for construction of recombinant DNA molecules, determination of the primary structure of DNA, and some other studies of genetic material.. The producers of the following restriction endonucleases BanI, Haelll, Mbol, Aflll, Asu I, Pst I, are found among the strains CC IBSO. Other strains can utilize aspartic and glutamic acids, valine, glycine, histidine, proline, and other amino acids. ... 

To study in more detail this effect of the primary structure of DNA on platiniim binding, our group (30) as well as that of Haseltine (3I) developed a method for detecting platinum binding at specific sequences in DNA. 

The linear sequence of nucleotides linked by phosphodiester bonds constitutes the primary structure of nucleic acids. Like polypeptides, polynucleotides can twist and fold Into three-dimensional conformations stabilized by noncovalent bonds. Although the primary structures of DNA and RNA are generally similar, their three-dimensional conformations are quite different. These structural differences are critical to the different functions of the two types of nucleic acids. 

Like all polymers, proteins and DNA are composed of a sequence of repeating units that interact at various levels to produce the active structure. Although the primary structure of DNA does largely determine its physical and biological properties, that of proteins is of minimal use in determining the desired active structure. This section is not intended to replace a biochemistry textbook, but it provides the basic information necessary to understand how the molecular structure of proteins and plasmid DNA differ, and how this impacts macromolecular stability in a general sense. 

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