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2.2What Kind of Molecule is DNA?

2.2.1

Nucleic Acids as a Unit

Fig. 2-2. Nucleotides

DNA is a type of nucleic acid. A nucleic acid is a compound consisting of a base, a pentose and a phosphate (Fig. 2-2A). As shown in Figure. 2-2B, bases are aromatic ring (heterocyclic) compounds containing nitrogen, and are roughly divided into purines and pyrimidines. There are five main bases in nucleic acids (Fig. 2-2B). Their names and one-letter abbreviations are frequently referred to throughout this book, and should therefore be remembered. There are two types of pentose: ribose and 2-deoxyribose (Fig. 2-2C). Compounds consisting of a base and a pentose are collectively called nucleosides (Fig. 2-3). In nucleosides, the carbon numbers of a sugar are expressed as "number'." Compounds in which a phosphate or phosphates are linked to the hydroxyl group of their sugar in nucleosides are called nucleotides or nucleic acids (Fig. 2-4). The number of phosphates added is not necessarily one, and in fact many nucleotides have three phosphates (Fig. 2-5). The position of a phosphate is not limited to 5', but many of the phosphates found in living bodies are 5'-phosphates. There are many types of functional nucleotides. Typical examples include ATP (adenosine 5'-triphosphate), which supplies energy to enzymatic reactions that require it, and cAMP (adenosine 3', 5'-cyclic monophosphate), which works in the signal transduction pathway. When bases are not specified, they are called NMP (ribonucleoside monophosphate) or dNTP (deoxyribonucleoside triphosphate).
Nucleic acids are roughly classified into DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). The difference between the two lies in whether the pentose is 2-deoxyribose (in this case, DNA) or ribose (in this case, RNA). There is also a base-level difference between DNA and RNA: A, C and G are common, but T is found only in DNA and U is found only in RNA (Fig. 2-5).

Fig. 2-3. Nucleosides

Fig. 2-4. Nucleotides

Fig. 2-5. Nucleotide types

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2.2.2

High-molecular Nucleic Acids

Fig. 2-6. Structure of high-molecular nucleic acids

DNA is polydeoxyribonucleotide in which nucleotides are polymerized. 5' and 3' of 2-deoxyribose are joined by phosphodiester linkage (Fig. 2-6). High-molecular RNA is required when genes are expressed, and as shown in Figure. 2-6, high-molecular DNA and high-molecular RNA have very similar structures. Both are long strings of molecules with the linkage of pentoses in a certain direction (in Fig. 2-6, the upward part is the 5' direction or the 5' end, and the downward part is the 3' direction or the 3' end).
From the specification of whether a high-molecular nucleic acid is DNA or RNA, its structure can be simply expressed as a sequence of single letters (a base sequence). By convention, the 5' end is written on the left-hand side and the 3' end on the right-hand side, unless otherwise specified.

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2.2.3

DNA - a Double Strand

All high-molecular DNA found in nature (excluding that of viruses) is double-stranded (Fig. 2-7). DNA takes a shape called B-form, and as shown in Figure 2-8, two bases - A and T - are linked by two hydrogen bonds while C and G are linked by three hydrogen bonds. These respectively form base pairs, and create a right-handed helix with a diameter of approximately 2 nm (Fig. 2-7). Since a particular pairing rule exists, once the base sequence of one DNA strand is known, that of the other strand is automatically determined; these two are called complementary strands. The length of DNA is often expressed as the number of base pairs (bp).
The directions of the two strands (5' → 3') run opposite to each other in an orientation referred to as antiparallel. The "spiral stairs" formed by the bases are not situated in the center of the helix structure; rather, they are slightly deviated from the center, creating wider grooves (major grooves) and narrower grooves (minor grooves) (Fig. 2-7). These grooves play important roles when proteins that control the expression of genes recognize base sequences and attach to them.

Fig. 2-7. Double-stranded structure of DNA (B-form)

Fig. 2-8. Hydrogen bonds forming
Watson-Crick base pairs

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2.2.4

RNA - a Single Strand

All high-molecular RNA found in nature (except that of viruses) is single-stranded. In many cases, however, RNA is partially double-stranded due to the pairing of bases within the strand. This structure is called A-form, and is characterized by a minimal difference between wider and narrower grooves. Like DNA-DNA and RNA-RNA pairings, DNA and RNA form pairs by creating antiparallel double strands.

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2.2.5

Circular Strands for Prokaryotes and Linear Double Strands for Eukaryotes

Fig. 2-9. Circular and straight-chain structures of DNA

Many prokaryotes have closed-circular double-stranded DNA. In other words, their DNA has no ends. Its structure forms a twisted shape (Type I) (Fig. 2-9). Type II is a form in which the twist of Type I is uncoiled as a result of nicking in the DNA strands, but this form is rare in nature. On the other hand, all nuclear DNA in eukaryotes is linear double-stranded (Type III) and has ends. This difference in form between prokaryotes and eukaryotes is a key characteristic of DNA.

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Denaturation and Renaturation of DNA

Double strands of DNA are separated into single strands in an alkali environment with a pH value of 12 or more or by heating to 90˚C or higher. This is called the denaturation of DNA. The phenomenon of proteins losing their higher-order structure is also called denaturation; however, organic media and acids that denature proteins precipitate but do not denature DNA. The transformation of single-stranded DNA back to double strands is called renaturation or annealing. During this process, base pairs are formed between two single strands. Annealing between heterogeneous DNA, or between DNA and RNA, is called hybridization. These techniques are frequently used in genetic engineering.

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DNA - a Long, Thin Thread

DNA is the thread of life. E. coli has circular double-stranded DNA with an approximate length of 2 mm. A human somatic cell contains linear double-stranded DNA of approximately 2 m, consisting of 6 x 109 base pairs. To help visualize this, if they were magnified to 500,000 times, the diameter of the DNA would be 1 mm and its length would be 1,000 km. Since DNA in human somatic cells is distributed to 46 threads, the length per thread would be approximately 22 km. This 1,000-km DNA would be housed in a nucleus with a diameter of 5 m. The number of DNA threads is doubled to 96 before cell division, and these are distributed equally to the two daughter cells without fail.

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