The histone fold and formation of the nucleosome

We have seen how in the eubacterial chromosome, bending DNA serves to facilitate its compaction. A similar process occurs in eukaryotic cells in that DNA is bent and wrapped around a protein unit. In this case, the core unit is a protein–DNA complex termed a nucleosome. The nucleosome comprises the core histone proteins H2A, H2B, H3 and H4 arranged in a structure known as the core histone octamer, with an associated length of DNA. In order to understand how the nucleosome is a
Author(s): The Open University

The histone proteins

The genes for the histone proteins are very highly conserved across eukaryotes, reflecting their importance in DNA packaging. The histone family consists of five groups of proteins, histones H1, H2A, H2B, H3 and H4. An examination of their amino acid content gives us clues as to how the histones fulfil their role in DNA packaging. Rather like the polyamines in bacteria, these proteins are highly positively charged, with up to 20% of their amino acids being lysine or arginine, the charged side
Author(s): The Open University

The DPS protein compacts the eubacterial chromosome during stress

When an E. coli cell enters into stationary phase, transcription and cell division cease completely. In such cells, the normal chromatin components, such as those described above, are replaced by a negatively charged protein called DPS. The interaction between DPS and DNA appears to be a specialised bacterial adaptation to survive starvation. In normal conditions of growth, the DNA within the bacterial cell is distributed evenly throughout the entire cytoplasm. In stationary cells, how
Author(s): The Open University

7.2 The eubacterial chromosome

Some of the diverse roles of chromatin components can be illustrated by examining the E. coli chromosome. Like most prokaryotes, E. coli has a single chromosome consisting of a single double-stranded circular DNA molecule. There is no nucleus present, but the E. coli DNA is within a discrete entity in the cytoplasm called the nucleoid. The nucleoid contains a multitude of proteins and is in close proximity to the ribosomes, where translation occurs. In addition to
Author(s): The Open University

7.1 Introduction

Until now, we have discussed DNA primarily as a double helix, but in its natural state within the cell it is found packaged as a complex mixture with many different proteins and other components. You have already seen examples of proteins with specific roles to play, such as topoisomerases and the proteins with various DNA binding domains, but in this section we will turn our attention to the proteins that serve to pack and organise the DNA into what we call chromatin.

The packaging of
Author(s): The Open University

6.1 Introduction

The biological functions of both DNA and RNA are dependent on complex, and sometimes transient, three-dimensional nucleoprotein structures. It is in such structures that the enzymatic manipulation of DNA in the essential biological processes such as DNA replication, transcription and recombination occur, and it is important to understand the interactions that drive these processes. Whether it is the activity of enzymes associated with DNA, such as DNA topoisomerases, or the packaging of DNA o
Author(s): The Open University

The loss of a DNA base causes an abasic site

Hydrolysis of the deoxyribose Cl'–base linkage results in the complete loss of a purine or pyrimidine base, resulting in what is called an abasic site, an event with obvious genetic consequences. This hydrolysis reaction is much more likely to occur at purine bases, resulting in depurination of the DNA (Table 3a<
Author(s): The Open University

4.6 Summary

1. RNA chains play fundamentally important roles within the cell, including genetic information transfer (mRNA), components of the translation machinery (rRNA in ribosomes and tRNAs) and as regulatory small RNAs.

2. The tertiary structure of RNA is determined by interactions that maximise base pairing. Despite instability and isolation problems, the tertiary structures of several major cellular RNAs are known.

3. Transfer RNA struct
   Author(s): The Open University
   

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Aptamers

Aptamers are nucleic acid molecules that have been developed to mimic the selective and tight binding of other molecules such as antibodies. In order to identify an aptamer that is capable of binding to a target molecule, a process called Selex (systematic evolution of ligands by exponential enrichment) is utilised. The strategy relies upon a combination of a selective binding assay and amplification by PCR. A ‘library’ of short single-stranded DNA oligonucleotides is synthesised <
Author(s): The Open University

Antisense regulation of gene expression

The term antisense refers to the use of a nucleic acid that is complementary to the coding (i.e. ‘sense’) base sequence of a target gene. When nucleic acids that are antisense in nature are introduced into cells, they can hybridise to the complementary ‘sense’ mRNA through normal Watson-Crick base pairing. Synthetic antisense DNA chains as short as 15–17 nucleotides in length have been used to block specific gene expression by either physically blocking translation of the tar
Author(s): The Open University