Replication helicates

Issac, R. Ham, Y.-W. Chmielewski, J. The design of self- 65. replicating helical peptides. Curr. Opin. Struct. Biol. 2001,... 

The unmodified and complementary oligonucleotides were also synthesized, in order to detect thermodynamic and spectroscopic differences between the double helices. Circular dichroism spectra revealed that the covalently bound anthracene does not stack in the centre of the DNA double helix. Mutagenic activity by intercalative binding of the anthracene residue is thus unlikely. Only in vitro and in vivo replication experiments with site-specifically modified... 

Replication fork (Sechon 28 9) Point at which strands of double helical DNA separate... 

In most four-helix bundle structures, including those shown in Figure 3.7, the a helices are packed against each other according to the "ridges in grooves" model discussed later in this chapter. However, there are also examples where coiled-coil dimers packed by the "knobs in holes" model participate in four-helix bundle structures. A particularly simple illustrative example is the Rop protein, a small RNA-binding protein that is encoded by certain plasmids and is involved in plasmid replication. The monomeric sub unit of Rop is a polypeptide chain of 63 amino acids built up from two... 

The double helix model provides a simple explanation for cell division and reproduction. In the reproduction process, the two DNA chains unwind from each other. As this happens, a new matching chain of DNA is synthesized on each of the original ones, creating two double helices. Since the base pairs in each new double helix must match in the same way as in the original, the two new double helices must be identical to the original. Exact replication of genetic data is thereby accomplished, however complex that data may be. 

The chromosomes of Escherichia coli and other bacteria are single, double-stranded DNA molecules with a total length of more than 1,000 pm. Relaxed DNA exists as a helical molecule, with one full turn of the helix occurring approximately every 10.4 base pairs. This molecule must undergo several folding and compaction steps to fit into an E. coli cell which is only 1-3 pm long. Despite this enormous compaction, bacterial DNA must be accessible for the bacterial enzymes that catalize DNA replication and transcription... 

The ability of DNA to replicate lies in its double-helical structure. There is a precise correspondence between the bases in the two strands. Adenine in one strand always forms two hydrogen bonds to thymine in the other, and guanine always forms three hydrogen bonds to cytosine so, across the helix, the base pairs are always AT and GC (Fig. 19.29). Any other combination would not be held together as well. During replication of the DNA, the hydrogen bonds, which are... 

Helical symmetry replication of viral nucleic acid... 

The discovery of the base-paired, double-helical structure of deoxyribonucleic acid (DNA) provides the theoretic framework for determining how the information coded into DNA sequences is replicated and how these sequences direct the synthesis of ribonucleic acid (RNA) and proteins. Already clinical medicine has taken advantage of many of these discoveries, and the future promises much more. For example, the biochemistry of the nucleic acids is central to an understanding of virus-induced diseases, the immune re-sponse, the mechanism of action of drugs and antibiotics, and the spectrum of inherited diseases. 

This presented a more difficult problem How do the double-helical strands separate during DNA synthesis In a rapidly growing cell such as E. coli it has been calculated that if the strands separate by untwisting, the molecule would have to rotate at 10,000 rpm, a rate that is highly improbable. The answer to this problem lies in an understanding of the mechanism of DNA replication at the enzyme level. We will return to this subject after first considering the enzymes involved in DNA synthesis. 

In E. coli cells, DNA replication starts at a specific site called oriC. The oriC locus contains only 245 base pairs. Similar sequences are responsible for initiating the synthesis of plasmid and bacteriophage DNA. The oriC nucleotide sequence binds several units of the tetrameric form of the dnaA protein. This protein is named for the gene that encodes it. The dnaB and dnaC proteins then bind to the complex. As a result of binding these proteins, a portion of the helical DNA is unwound. This forces the rest of the DNA into a left-handed double helix that wraps around the proteins to give a structure... 

Fig. 6.7 Simplified scheme of the copying process in DNA replication via triple helices, as described by Li and Nicolaou (Ferris, 1994)...

Binds to DNA and prevents separation of the helical strands Affects neuronal transmissions Binds to opiate receptors and blocks pain pathway Acts as central nervous system depressant Inhibits Na/K/ATPase, increases intracellular calcium, and increases ventricular contractibility Blocks the actions of histamine on Hi receptor Blocks ai-adrenergic receptor, resulting in decreased blood pressure Inhibits reuptake of 5-hydroxytryptamine (serotonin) into central nervous system neurons Inhibits cyclooxygenase, inhibition of inflammatory mediators Inhibits replication of viruses or tumor cells Inhibits HIV reverse transcriptase and DNA polymerase Antagonizes histamine effects... 

Having said aU this, we need to understand how the language of DNA is translated into the language of proteins. I will get to that in the next chapter. Understanding the double helical nature of DNA first will help us understand how DNA is replicated at the time of cell division and how the translation of DNA structure into protein structure happens. 

The two major types of nucleic acids are DNA and RNA. Nucleic acids are polyphosphate esters containing the phosphate, sugar, and base moieties. Nucleic acids contain one of five purine or pyrimidine bases that are coupled within double-stranded helices. DNA, which is an essential part of the cell s chromosome, contains the information for the synthesis of protein molecules. For double-stranded nucleic acids, as the two strands separate, they act as a template for the construction of a complementary chain. The reproduction or duplication of the DNA chains is called replication. The DNA undergoes semiconservative replication where each of the two new strands contains one of the original strands. 

Figure 1. Freeze-dried gel of A. xylinum cellulose ribbons deposited during normal growth. The arrows point to triple-stranded left-hand helical microfibrils averaging 36.8 3A in diameter (1). The sample was replicated with 17.3A Pt-C and backed with 90.2A of carbon. 

Figure 4B. Freeze-dried, Pt/C replicated gel prepared from tobacco pectin. This high magnification image shows two molecules with 13A left-handed helical regions. (Bar = 100A.)...

Two independent screens have been developed to investigate the effects of fluorinated building blocks on the interactions of the dimeric peptide assembly. The impact of fluorine side chain substitutions on the stability of coiled coil folding has been studied using temperature-dependant CD spectroscopy. The second screen is based on the ability of a-helical peptides to self-replicate. Thus, peptide... 

The original system is based on peptides that contain heptad repeats, where the first and fourth positions of the repeat are hydrophobic amino acids. Such sequences form a-helices, which assemble into coiled-coil structures, as represented in Figure 7.10. The principle is then the same as that used for von Kiedrowski s self-replicating nucleotides (von Kiedrowski 1986), in the sense that a full-length peptide template (having in this case 32-35 residues) directs the condensation of the two half-length peptide substrates. 

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