Aaaaaannnnaaaaaannnna

Figure 5.6 A plot of expected roll angles for the repeating-sequence, curved DNA studied by electron microscopy in Fig. 5.5. The curvature k may be calculated as 10.7 over any A6N4 repeat by taking a Fourier transform of these roll angles, as indicated by the broken line. Roll angles are most positive in the Fourier transform at step 7, where the minor groove of the DNA lies along the outside of the curve. which step you assign to be step 0, or which step you assign as step 9, so long as all 10...

H1

Which increase their bulk but do not alter the electric charge see Fig. 7.10(c). And arginine amino acids can also be modified by the addition of one methyl group. The most important kinds of histone modification, in the context of chromosome dynamics, are listed in Table 7.1. These modifications are usually highly specific, and restricted mainly to the two exposed and flexible ends of each polypeptide histone chain. For example, acetylation, by reducing the net positive charge, reduces the...

Info

Figure 11.5 A summary of protein-to-protein contacts between DNA methylases and other cellular enzymes. In (a) we see that the major methyl-cytosine-binding-protein 'methyl-CG-2' (or MeCP2) will bind to both methylases Dnmtl or Dnmt3L, thereby linking methylation with maintenance or imprinting activities. In (b) we see that the major histone de-acetylase that removes acetyl groups from lysine on histone proteins, will bind to all of Dnmtl, 3a, 3b and 3L, thereby linking histone deacetylation...

Nn

Figure 8.7 Examples of how protein-to-protein interactions are used to recognize the spatial pattern of DNA recognition sites. The steroid receptors, as represented by the estrogen receptor, bind to 'inverted' repeats, but other receptors bind to 'tandem' repeats. Receptor proteins for (a) estrogen, (b) thyroid, (c) vitamin D3, (d) retinoic acid, (e) 9-cis-retinoic acid all bind to repeats of the same hexameric sequence, 'AGGTCA'. However, they do not confuse these sites, as each requires a...

Preface

We also now appreciate that molecular biology is not a trivial aspect of biological systems. It is at the heart of the matter. Almost all aspects of life are engineered at the molecular level, and without understanding molecules we can only have a very sketchy understanding of life itself. All approaches at a higher level are suspect until confirmed at the molecular level. Francis Crick, What Mad Pursuit, 1988 This is a book about DNA, the most central substance in the workings of all life on...

Into J Chromosomes

In Chapter 1 we gave a general description of the biology of a typical cell, and we explained how DNA plays a central role in that biology, by specifying the construction of protein molecules. Since then, we have considered DNA mainly as a simple, double-helical thread which undergoes transcription and replication, and which wraps itself around protein spools. Our task in the present chapter will be to describe the assembly of DNA into chromosomes. How does DNA fold into the highly compact...

Further Reading

Abrescia, N.G., Thompson, A., Huynh-Dinh, T., and Subirana, J.A. (2002) Crystal structure of an antiparallel DNA fragment with Hoogsteen base pairing. Proceedings of the National Academy of Sciences, USA 99, 2806-11. A short d(ATATAT) double helix which contains Hoogsteen A-T base pairs throughout. Arnott, S. (1970) The geometry of nucleic acids. Progress in Biophysics and Molecular Biology 21, 265-319. A summary of early X-ray studies on fibrous samples of DNA. Chaires, J.B. and Waring, M.J.,...

Bibliography

Allfrey, V., Faulkner, R.M., and Mirsky, A.E. (1964) The acetylation and methylation of histones and their possible role in the regulation of RNA synthesis. Proceedings of the National Academy of Sciences, USA 51, 786-94. First inference that the acetylation of histones might be correlated with transcription. Arents, G., Burlingame, R.W., Wang, B.-C., Love, W.E., and Moudrianakis, E.N. (1991) The nucleosomal core histone octamer at 3.1 A resolution a tripartite protein assembly and a...

T G C T

Figure 10.9 (a) During normal replication, a DNA polymerase enzyme can make new strands in a 5' to 3'direction hence it can copy one strand continuously, but has to copy the other strand in small pieces of size around 300 base-pairs, which will be joined together subsequently by a ligase enzyme. (b) DNA of repeated sequence (CAG)n may expand in size during replication, if the new CTG strand slips backward, so that some CAG are copied twice. (c) DNA of repeated sequence (CTG)n may contract in...

C

Figure 3.2 Four possible base-pairs of the Watson-Crick type, each of which joins a large purine (A, G) to a small pyrimidine (T, C), and in the same perspective as Fig. 3.1. Figure 3.2 Four possible base-pairs of the Watson-Crick type, each of which joins a large purine (A, G) to a small pyrimidine (T, C), and in the same perspective as Fig. 3.1. subtle motions of the base pairs can accumulate over a series of such base pairs, to make different kinds of double helix. We said in the last...

DNA Supercoiling

In Chapter 4 we explained how a DNA molecule must twist - or untwist - and curve, in order to carry out its various functions in biology. For example, DNA has to untwist near the start-sites of all genes, often at or near TATA sequences, so that RNA polymerase can unwind or separate the strands and construct new RNA strands according to the rules of Watson-Crick base-pairing. Similarly, DNA must untwist at all origins of replication, so that DNA polymerase can construct a new DNA strand in...

Grm

C-G pairs, 29, 30,31, 32-4, 51-2 'C' helix, X-ray diffraction studies, 204 CA TG steps, 49, 52, 53, 59, 307, 309 CAG repeat sequence, 252-7 Cancer anticancer drugs, 67-8 bisulfite-PCR diagnosis, 277 dinucleotide repeats link, 255 DNA methylation, 284-7 GLI protein, 86 see also mutations Capillary electrophoresis, 214, 244 Carbon atoms in A-T pair, X-ray diffraction studies, 207 Carrier plasmids, 239-40 Catalysts, 316 CC GG steps, 51, 53, 305-6, 307 Centromere, 152 CG CG steps, 49, 51, 307...

Exercises

6.1 For this exercise you will need a substantial length (say about 1.5 m) of flexible rod or cord. An electric extension cord, with circular cross-section about 6 mm diameter, is ideal or else you may use rubber tubing (provided it is not curved when relaxed) or even a plaited rope of the kind which is sold at boat shops. For the sake of convenience, we shall refer to all of these models as 'cords'. a Use the cord to reproduce the transformation shown in going from Fig. 6.1(b) to (c). For each...

Structure of DNA

Our goal in this book has been to explain, as simply as possible, how DNA works in biology. For that reason, we have tried not to dwell too much on the methods which are used by scientists to study DNA instead we have tried to give an integrated picture of DNA as obtained by many different methods of analysis. We have emphasized on many occasions that DNA is a very tiny object yet our pictures of DNA have been drawn in terms of images which may be perceived by the reader on a 'household' scale....

DNA sequencing and array technologies

Cantor, C.R. and Smith, C.L. (1999) Genomics the science and technology behind the human genome project. John Wiley and Sons, New York. A summary of methods used for the sequence analysis of entire genomes. Elkin, C.J., Richardson, P.M., Fourcade, H.M., Hammon, N.M. et al. (2001) High-throughput plasmid purification for capillary sequencing. Genome Research 11, 1269-74. Methods for sequencing 18 million bases of DNA per day at one facility in the USA. Gupta, V., Cherkassky, A., Chatis, P.,...

Biology 1 for Non Scientists

One day two of us were having lunch together at a Cambridge College. We got into a conversation with one of our neighbors at the table, who was a senior historian. After a while he asked us what we did, and we explained that we were scientists, working with the very tiny molecules of biology. Then he said, 'I don't see how you do it'. 'Work all the time with things that you can't see'. You see, even people of great intelligence and learning, who spend their lives gathering evidence and...

The Molecule And How It Works

Chris R Calladine Horace R Drew Ben F Luisi Andrew A Travers A systematic and comprehensive analysis of the structure of DNA from a wonderfully fresh perspective. The book is a systematic effort to understand this fascinating molecule from the inside out, building from the first, and simplest, principles____I recommend it very highly. We see DNA structures so often that it is often taken for granted that the molecule should not be anything but an aesthetically appealing, spiraling helix. But...

Curving j

In the last two chapters we have learned some rudimentary things about DNA. We have learned (a) why DNA forms a helix, (b) how the bases make ordered pairs at the center of the helix, (c) how the bases twist like a propeller within any base-pair, and (d) how the overall shape of a helix depends on the local parameters roll, slide, and twist over a series of base-pair steps. This is the stuff of chemistry, not biology. When are we going to start talking about DNA in biology That is exactly what...

G G C T

Figure 1.11 Part of the gene codes for part of the protein chain. Each set of three nucleotides (or bases) in the DNA specifies one amino acid, according to the scheme of Table 1.1. Figure 1.12 From DNA to RNA to protein. The DNA is copied into 'messenger-RNA', which then travels outside the nucleus to the ribosome, where it specifies the assembly of some particular protein, according to the series of nucleotides in its chain as in Table 1.1. For simplicity, we have not mentioned here that many...

Protein Interacti

In the previous chapter we explained how the vast majority of chromosomal DNA is associated with packaging proteins, such as histones. Those abundant proteins bind to most parts of the lengthy chromosomal DNA with only a slight preference for base sequence and in organisms whose cells have nuclei, they serve mainly to compact the long DNA by a factor of about 10 000, into the minute volume of a cell nucleus. Chromosome compaction can control the access of RNA polymerase enzyme to the start site...

Triplet expansions and microsafellifes

Chang, Y.C., Ho, C.L., Chen, H.H., Chang, T.T. et al. (2002) Molecular diagnosis of primary liver cancer by microsatellite DNA analysis in the serum. British Journal of Cancer 87, 1449-53. Over 100 different microsatellites were screened to diagnose liver cancer from tumor DNA in blood. Girardet, A., Hamamah, S., Anahory, T., Dechaud, H. et al. (2003) First preimplantation genetic diagnosis of hereditary retinoblastoma using informative microsatellite markers. Molecular and Human Reproduction...

Cytosine methylation in cancer embryonic development and cloning

Cezar, G.G., Bartolomei, M.S., Forsberg, E.J., First, N.L. et al. (2003) Genome-wide epigenetic alterations in cloned bovine fetuses. Biology of Reproduction 68, 1009-14. Cattle embryos which are prepared by nuclear transfer show reduced levels of cytosine methylation, so as to cause abortion. Clark, S.J. and Melki, J.M. (2002) DNA methylation and gene silencing in cancer which is the guilty party Oncogene 21, 5380-7. Gene silencing prior to cytosine methylation may be the cause of human...

Transgenic mice animals and plants

Jimenez-Bermudez, S., Redondo-Nevado, J., Munoz-Blanco, J., Caballer, J.L. et al. (2002) Manipulation of strawberry fruit softening by antisense expression of a pectate lyase gene. Plant Physiology 128, 751-9. The genetic design of strawberries which ripen more slowly than normal. Marquet-Blouin, E., Bouche, F.B., Steinmetz, A., and Muller, C.P. (2003) Neutralizing immunogenicity of transgenic carrot-derived measles virus hemagglutinin. Plant Molecular Biology 51, 459-69. Genetic modification...

Helix cck

It is crucially important, not only in biology but in all fields of science, to understand the inner workings of Nature as well as its external form. For example, consider the funny-looking object shown from two perspectives in Fig. 2.1. It has five different colors, but what is it How would you go about making such an object A poor scientist would study the object superficially, and give a name to each particular feature, such as the intersection of five edges he or she would be deeply...

The Chemical Theory of Basestacking Interactions in DNA

In Chapter 2 we explained how the water-repelling hydrophobic quality of the bases could push a 'ladder' of DNA into a twisted, double-helical shape and we called that a first-order effect on the structure of DNA. Then in Chapter 3 we invoked the same hydrophobic property in order to account for the 'propeller twist' which is usually found in the Watson-Crick base-pairs and we described that as a weaker, 'second-order' effect. Propeller twist makes the stacking of base-pairs onto one another...

RNA ribozymes and DNAzymes

Ribozymes were discovered in the 1980s, with the surprising finding that certain RNA molecules could cleave either themselves or other RNA molecules. Subsequently it was found that ribozymes can also catalyze other chemical reactions, in addition to cutting. We can learn something about the catalytic potential of RNA from the X-ray crystal structure of the ribosome, because it appears that the active site, where peptide units are linked, is constructed mostly or entirely from RNA and that the...

Gg Ga

Figure 9.9 Investigation of hairpin-loops by means of cleavage with single-strand specific S1 nuclease, followed by gel electrophoresis of the cleavage products. cutting of the strand within its loop of eight unpaired bases, halfway up the gel. This result shows conclusively that S1 nuclease recognizes the structure of the DNA rather than its sequence, for the same sequence TTCCTCTT is not cut when it is part of a double helix on the right. In summary, one can cut the DNA by using a wide...

N

Figure 8.7 Examples of how protein-to-protein interactions are used to recognize the spatial pattern of DNA recognition sites. The steroid receptors, as represented by the estrogen receptor, bind to 'inverted' repeats, but other receptors bind to 'tandem' repeats. Receptor proteins for a estrogen, b thyroid, c vitamin D3, d retinoic acid, e 9-cis-retinoic acid all bind to repeats of the same hexameric sequence, 'AGGTCA'. However, they do not confuse these sites, as each requires a unique...

O

Figure 1.9 The phosphate group as part of a sugar-phosphate chain. Each atom is 1-2 A wide atom types are phosphorus P and oxygen O . bases form pairwise interactions that join the two strands of DNA together weakly see Chapter 2 . The three parts of a nucleotide can also be studied in isolation, as collections of just a few atoms. For example, a phosphate contains one phosphorus and four oxygen atoms, as shown in Fig. 1.9. The atoms themselves are made of protons, neutrons, and electrons. They...

Q

So far in this book we have said a lot about the structure of DNA as a double helix, and the way in which different kinds of double helix can result from the different geometries with which base-pairs stack on one another. But in most chapters our DNA, seen as a long rod or thread, has been straight. Only in Chapter 4 did we consider a molecule of DNA which follows a curved path and the curve there was in a plane, like a garden path. We have now reached the stage where we must explain the...

Cytosine Methylation and DNA Epigenetics

In Chapter 10 we discussed many aspects of 'normal genetics' and its relation to modern medicine. Normal genetics comes about mainly from the pairing of two bases across any double helix, as A with T or G with C in a Watson-Crick fashion. We also pointed out that those same DNA bases may become modified reversibly to different chemical forms by cellular enzymes known as 'methylases'. Once we add DNA methylation to our list of unexpected phenomena which have been observed in biology, we enter...