Nucleic acids and chromatin

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	Time: 12 hours Level: Advanced

	Introduction Introduction Resource This unit helps you understand the properties of nucleotides and how they contribute to secondary and tertiary structures of nucleic acids at the molecular level. You will learn about the different composition...

	1 The biological role of nucleic acids 1.1 Early observations Resource Some of the earliest observations of macromolecules within living cells were of nucleic acids in the form of chromosomes. These long dark-staining objects, which became visible in the nucleus of cells... 1.2 Nucleic acids: genetic, functional and structural roles in the cell Resource The first role that one immediately thinks about for nucleic acids is that of an inherited genetic material, principally in the form of DNA. In some cases, the inherited genetic material is RNA instead... 1.3 Nucleic acids and the flow of genetic information Resource The ‘flow’ of information from an organism's genome to the synthesis of its encoded proteins is referred to as the central dogma and emphasises the crucial roles that nucleic acids play within the cell...

	2 The molecular structure of nucleic acids 2.1 The primary structure of nucleic acids Resource We now know the detail of the order of individual bases, i.e. the genome sequence, of many of the organisms listed in Table 1. In Section 2 we will focus on the structures of nucleic acids within the cell,... 2.2 General features of higher-order nucleic acid structure Resource Polynucleotide chains are intrinsically flexible molecules and have the potential to form many different higher-order structures. Their flexibility derives from rotation around bonds in the sugar-phosphate... 2.3 Analysing nucleic acid structures Resource In studying nucleic acid structures, many different experimental approaches can be adopted. In many cases, nucleic acid structures are examined in vitro, under non-physiological conditions, such as after... 2.4 Analysis of nucleic acids by electrophoresis and hybridization Resource Nucleic acids can be separated according to size by gel electrophoresis, most commonly performed using a horizontal gel (Figure 7a). This is in contrast to the vertical gel electrophoresis set-up, which... Summary of Section 2 Resource Nucleic acids are intrinsically highly flexible molecules.

	3 Structural aspects of DNA 3.1 The helical structure of DNA Resource Having outlined the general principles of nucleic acid structures, we will now focus on how these principles influence the formation of specific structures found in DNA. 3.2 Higher-order DNA structures: DNA twisting and torsional effects Resource As discussed earlier, the helical nature of DNA results for the most part from the properties of the bases, their interactions and the geometry of the helix itself. There is, however, another important... 3.2 Higher-order DNA structures: DNA twisting and torsional effects (continued) Resource The energy introduced into DNA by twisting has great potential as a regulatory mechanism, since the free energy can be stored in a variety of different high-energy conformations along the chain. 3.3 Other structures in DNA Resource We will finish our discussion of DNA structure by examining two cases of unusual structures that can arise. Summary of Section 3 Resource Watson–Crick base pairing arises due to hydrogen bonding between A and T and G and C and spatial limitations within the hydrophobic core of the helix.

	4 RNA structure and function 4.1 The varied structures of RNA Resource RNA is a versatile cellular molecule with the ability to adopt a number of complex structural conformations. Although RNA is often thought of as a single-stranded molecule it is actually highly structured.... 4.2 The structure of tRNA Resource Transfer RNAs are small and compact molecules. Comparisons of the base sequences of many tRNAs led to the predicted four-leaf clover structure shown in Figure 18a, which follows the rule of maximising... 4.3 Hairpin formation and micro-RNAs Resource A class of small RNA molecules called micro-RNAs (miRNAs) has been identified in recent years. The roles of these small RNAs are only just beginning to be understood, but many are expressed only at specific... 4.4 Ribozymes Resource Several types of RNA have been shown to have catalytic activity directed towards strand cleavage. They were originally observed in the case of ‘self-splicing’ introns, i.e. segments of the immature non-protein-coding... 4.5 The use of nucleic acids as targeting agents Resource We have already described how catalytic functions such as backbone cleavage found in ribozymes can be harnessed to target destruction of specific RNAs and how hybridization techniques are used to identify... 4.6 Summary Resource 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...

	5 DNA damage 5.1 Introduction Resource The integrity of DNA as a genetic material is of paramount importance to an organism, and a multitude of proteins exist that serve to prevent or reverse damage to the DNA. However, like all biological... 5.2 The chemical stability of DNA Resource There are two main features of DNA that make it susceptible to damage. The first is the linkage between the deoxyribose Cl’ atom and the base (Figure 3b), a bond that is highly susceptible to hydrolysis.... Summary of Section 5 Resource The stability of DNA makes it suitable as a store of genetic information.

	6 Protein–nucleic acid interactions 6.1 Introduction Resource 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... 6.2 Non-covalent bonding in site-specific binding Resource The affinity of a protein for DNA is determined in thermodynamic terms by the free energies of the individual components compared to the free energy of the DNA-protein complex. DNA binding proteins, which... 6.3 The recognition of specific DNA sequences by proteins Resource Transcription factors act by binding to specific DNA regions, dependent upon the recognition of particular sequences of bases, usually through direct interactions in the major groove. They are known to... 6.4 Non-specific DNA-protein interactions Resource As we saw above, most sequence-specific DNA binding proteins recognise and bind to their target DNA sequence with a high affinity by utilising structural domains that make sequence-specific contacts with... 6.5 Conformational changes upon protein–DNA interactions Resource During binding, both the protein and the DNA can alter their conformation. In the case of proteins, this conformational change can involve small changes in side-chain location, but can also involve local... Summary of Section 6 Resource Sequence-specific protein–DNA interactions are achieved through the formation of non-covalent bonds between amino acid side-chains in the protein and bases in the major groove of the DNA.

	7 DNA packaging and chromatin 7.1 Introduction Resource 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... 7.2 The eubacterial chromosome Resource 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... 7.3 The eukaryotic chromosome Resource Whilst the bulk of eukaryotic DNA is packaged by proteins different from those in the eubacterial chromosome, the principles of bending DNA and neutralising the negative charges in its backbone are shared.... 7.3 The eukaryotic chromosome (continued) Resource When chromatin is isolated from the nucleus and examined under the electron microscope, it can be seen as a 30 nm fibre. This fibre is formed through the action of the histone H1 on the nucleosomal DNA... Summary of Section 7 Resource Packaging of DNA serves to protect against damage, to compact the DNA helix into a suitable size within the cell, and to act as both a platform for and an intrinsic part of the structural and regulatory...

	8 Chromosomal organisation in the eukaryotic nucleus 8.1 Introduction Resource The average human cell has around two metres of DNA within its nucleus. In the interphase nucleus, in which transcription and replication are going on, this DNA is packaged into nucleosomes that are variably... 8.2 Chromosome scaffolds Resource Most of the chromosomal DNA chains within the interphase nucleus are believed to be held on a scaffold or backbone structure made from various proteins, with loops of between 20 and 200 kb extruding from... 8.3 Chromosome distribution within the nucleus Resource DNA from any one particular chromosome is a single chain, many millions of bases long, and this chain is attached to a scaffold structure. It is not surprising then, that if we examine the interphase nucleus,... 8.4 The organisation of the mitotic chromosome Resource In order to prepare the chromosome for mitosis, a process in which DNA molecules become physically separated, an additional stage of compaction occurs to reach the highest level. The processes involved... Summary of Section 8 Resource Eukaryotic DNA is compacted through a hierarchical series of events, from nucleosomes to 10nm and 30 nm fibres, then through further stages to the chromomena fibres, which are attached to scaffolds to...

	End of of unit questions End of of unit questions Resource What effect does ethidium bromide intercalation have on supercoiled DNA?

	References and Acknowledgements References Resource Acknowledgements Resource

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Topic outline

Introduction

1 The biological role of nucleic acids

2 The molecular structure of nucleic acids

3 Structural aspects of DNA

4 RNA structure and function

5 DNA damage

6 Protein–nucleic acid interactions

7 DNA packaging and chromatin

8 Chromosomal organisation in the eukaryotic nucleus

End of of unit questions

References and Acknowledgements

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