Structure and Replication of DNA The Double Helix

FIGURE 124-9. Structure and function of DNA. Within the cellular nucleus, tightly coiled strands of DNA are packaged in units called chromosomes. Working subunits of chromosomes are called genes. During DNA replication, the double-stranded DNA helix unwinds, exposing individual nucleotides. Complementary nucleotides are retrieved and assembled by DNA polymerases to form new strands of DNA. 

Crick when they proposed the duplex structure for DNA (fig. 26.1). First, the double helix unwinds next, mononucleotides are absorbed into complementary sites on each polynucleotide strand and finally these mononucleotides become linked to yield two identical daughter DNA duplexes. What could be simpler Subsequent biochemical investigations showed that in many respects this model for DNA replication was correct, but they also indicated a much greater complexity than was initially suspected. Part of the reason for the complications is that replication must be very fast to keep up with the cell division rate, and it must be very accurate to ensure faithful transfer of information from one cell generation to the next. 

The molecule of DNA is like a coded message. This message, the genetic information contained in and transmitted by nucleic acids, depends on the sequence of bases from which they are composed. It is somewhat like the message sent by telegraph, which consists only of dots, dashes, and spaces in between. The key aspect of DNA structure that enables storage and replication of this information is the famed double helix structure of DNA mentioned above. 

In 1953, Watson and Crick proposed a three-dimensional structure of DNA which is a cornerstone in the history of biochemistry and molecular biology. The double helix they proposed for the secondary structure of DNA gained immediate acceptance, partly because it explained all known facts about DNA, and partly because it provided a beautiful model for DNA replication. 

Most of the DNA in nature has the double helical secondary structure. The hydrogen bonds between the base pairs provide the stability of the double helix. Under certain conditions the hydrogen bonds are broken. During the replication process itself, this happens and parts of the double helix unfold. Under other conditions, the whole molecule unfolds, becomes single stranded, and assumes a random coil conformation. This can happen in denaturation processes aided by heat, extreme acidic or basic conditions, etc. Such a transformation is often referred to as helix-to-coil transition. There are a number of techniques that can monitor such a transition. One of the most sensitive is the measurement of viscosity of DNA solutions. 

At the time Pauling was working on the structure of proteins culminating eventually in his discovery of the alpha-helix. Yet this declaration sounds as if he were anticipating the mechanism of DNA replication via the double helix. It came, however, only in 1953, and it was not Pauling, but Watson and Crick, who discovered it. 

ATPase family. To accomplish the exchange, the single-stranded DNA displaces one of the strands of the double helix (Figure 28.48). The resulting three-stranded structure is called a displacement loop or D loop. This process is often referred to as strand invasion. Because a free 3 end is now bound to a contiguous strand of DNA, the 3 end can act as a primer to initiate new DNA synthesis. Strand invasion can initiate many processes, including the repair of double-stranded breaks and the reinitiation of replication after the replication apparatus has come off its template. In the repair of a break, the recombination partner is an intact DNA molecule with an overlapping sequence. 

The double helix of DNA [25] and the more complex tertiary structures of RNA [26] are linked together by hydrogen bridges between pairs of nudeobases (approx. 0.5-1.8 kcal mol per Watson-Crick base pair) [27] and by hydrophobic "stacking forces . Fluorinated carbocyclic analogs of these nudeobases have been used to study and elucidate the factors underlying base pairing, replication, and the interaction of the bases with proteins such as DNA polymerases [28]. 

The double helical structure of DNA must be disrupted during almost all biological processes in which it participates, including DNA replication and repair, as well as transcription of the DNA sequence information to RNA. Experimentally, the double helix can be separated, or denatured, by increasing the temperature to well above 50°C (122°F). If the temperature is carefully decreased, renaturation occurs when the base pairs reform. Under these conditions, hybridization can be induced by allowing the single strands... 

When we picture DNA, the image that comes immediately to mind is the iconic double helix. However, the double helix is only the storage form for genetic information, and DNA takes on very different structures when actively used during transcription, replication, and recombination. G-rich genomic regions have unusual structural potential, as they readily form G-quadruplex structures. This chapter discusses how regulated formation of G-quadruplexes contributes to key cellular processes. 

When replicative DNA polymerase encounters a thymine dimer, it cannot replicate past the site. Deoxyadenylate is incorporated opposite the first thymine base in the template, but the double helix distortion induced by the thymine dimer causes the structure to be recognized as a mismatch, and the polymerase "idles" at the damage site, converting dATP to dAMP by a continual process of insertion and exonucleolytic cleavage (due to proofreading). 

The A and B forms are relatively stable for RNA and DNA, respectively, under physiological conditions. They must not be too stable, however, because processes, such as DNA replication (see here) and transcription, cannot occur unless the double-helix structure can be opened up. Denaturation refers to the loss of secondary (or tertiary) structure over large regions of a polynucleotide. Forces favoring denaturation of polynucleotides include... 

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