Page 119 - Academic Press Encyclopedia of Physical Science and Technology 3rd BioChemistry

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Encyclopedia of Physical Science and Technology en010k-502 July 16, 2001 16:56

Nucleic Acid Synthesis 857

Various processes have evolved to maintain the genomic equimolar amounts of A and T and of G and C (Chargaff’s
integrity, as discussed later. rule), unlike in RNA, which is single stranded (except in
Finally, two other critical differences between DNA and some viruses). X-ray diffraction studies also showed that
RNA are in the length and structure of the polymer chains. DNA in double helix exists in the B-form, which is right
DNA polymers, as elaborated later, usually exist as a he- handed and has a wide major groove and a narrow minor
lix consisting of two intertwining chains, while RNA is groove. Most of the reactive sites in the bases, including
present mostly as a single chain. Furthermore, DNA could C O and NH groups, are exposed in the major groove
contain up to several billion deoxynucleotide monomeric (Figs. 1C and 1D). One turn of the helix has10 base pairs
◦
◦
units in the genomes of higher organisms, although the (bp) with a rise of 34 . Thus, each pair is rotated 36 rel-
genomes of smaller self-replicating units such as viruses ative to its neighbor. Elucidation of the structure of DNA
contain only a few thousand deoxynucleotides. In con- bound to proteins show that one turn of the helix contain-
trast, RNA chains are never more than a few thousand ing 10.5 bp could be significantly bent or distorted. For
nucleotides long. example, some DNA binding proteins bind to the minor
groove, causing its widening accompanied by compres-
sion of the major groove. In some special regions of the
B. Base Pairing in Nucleic Acids: Double
genomes, e.g., in telomeres and segments with unusual
Helical Structure of DNA
repeated sequences, alternative forms such as triple he-
The most important discovery in molecular biology was lical structure and Z-DNA may exist. The Z-DNA has a
the identification of the right-handed double helical struc- left-handed, double-helical structure. In these or in tor-
ture of DNA, where two linear chains are held together sionally stressed DNA, the bases can be held together
by base pair complementarity. This discovery by Watson by different type of H-bonding called Hoogsteen base
and Crick in 1953 heralded the era of molecular biol- pairing.
ogy, which was preceded by the rapid accumulation of
genetic evidence indicating that DNA, as the genetic ma-
C. Size, Structure, Organization,
terial of all organisms, is the primary storehouse of all
and Complexity of Genomes
their information. Exceptions to this fundamental prin-
ciple were found in certain bacterial, plant, and mam- Except for certain viruses, DNA is the genetic mate-
malian viruses, in which RNA constitutes the genome. rial for all organisms and self-replicating units, including
However, the viruses are obligate parasites and are not virusesandsuchintracellularorganellesaschloroplasts(in
able to self-propagate as independent species; thus, they plants), kinetoplasts (in protozoa), and mitochondria (in
have to depend on their hosts, which have DNA as their most eukaryotes). Genomic DNA is double helical (except
genetic material. Thus, DNA in all genomes (except some for the genomes of certain bacterial viruses), and its size
single-stranded DNA viruses) consists of two strands of is related to the complexity of the organism (Table I). In
polydeoxynucleotides which are anti-parallel in respect subcellular organelles, viruses, and plasmids, the genome

to the orientation of the 5 -3 phosphodiester bond in the often exists as a circular molecule consisting of up to sev-
polymers (Fig. 1D). The two strands are held together by eral thousand base pairs. The genome of bacteria, such as
H-bonding between a purine in one strand and a pyrimi- that of the widely studied enteric strain E. coli, is present
dine in the complementary strand. Normally, adenine (A) as a single, circular, double-stranded molecule containing
pairs with T and G pairs with C; A and T are held to- about 4.7 million base pairs. By and large, the genome
gether by two H-bonds, and G and C are held together of many small self-replicating entities is circular DNA,
by three H-bonds involving both exocyclic C O and ring without any terminus in the unbranched polymeric chain.
NH (Fig. 1C). As a result, G•C pairs are more stable than In contrast, the large nuclear genomes of more com-
A•T pairs. Because U is structurally nearly identical to T, plex organisms (from lower eukaryotes such as unicel-
except for the C-5 methyl group, U also pairs with A in the lular yeast with a genome size only an order of magni-
common configuration. Although H-bonds are inherently tude larger than that of E. coli, to mammals with genomes
weak, the stacking of bases in two polynucleotide chains larger by three orders of magnitude) consist of multiple,
makes the duplex structure of DNA quite stable and in- distinct, linear subunits organized in chromosomes. De-
duces a fibrillar nature in the DNA polymer. X-ray diffrac- pendingonthestageofthecellcycle,thestructureof chro-
tion studies of the DNA fiber, and subsequent crystallo- mosomes (collectively called chromatin) varies from the
graphic studies of small (oligonucleotide) DNA pieces, highly extended and amorphous state occurring in much
led to the detailed structural elucidation. This was ini- of the (interphase) nucleus to highly compacted, linear,
tially aided by chemical analysis showing equivalence of organized chromosomes (metaphase) after completion of
purines and pyrimidines in all double-stranded DNA and DNA duplication followed by cell division (mitosis). This