Biochemistry nucleic acid structure

Cimino, C.P., Camper, H.B., Isaacs, S.T., and Hearst, J.E. (1985) Psoralens as photoactive probes of nucleic acid structure and function Organic chemistry, photochemistry, and biochemistry. Annu. Rev. Biochem. 54, 1151-1193. 

Figure 2.16 Orientations found in DNA helices. (Adapted with permission from Figure 2.11 of Saenger, W. Principles of Nucleic Acid Structure, Springer-Verlag, New York, 1984 copyright 1984, Springer-Verlag, New York and Figure 1.22 A, B, C of Cowan, J. A. Inorganic Biochemistry, An Introduction, 2nd ed., Wiley-VCH, New York, 1997. Copyright 1997, Wiley-VCH.)...

Anne-Ctcile Declais (12), Department of Biochemistry, CRC Nucleic Acid Structure Research Group, University of Dundee, Dundee DDl 5EH, United Kingdom... 

This chapter describes practical aspects of the application of UV absorbance temperature profiles to determine the thermodynamics of nucleic acid structural transitions. Protocols and practical advice are presented for issues not normally addressed in the primary literature but that are crucial for the determination of reliable thermodynamics, such as sequence design, sample preparation, choice of buffer, protocols for determining strand concentrations and mixing strands, design of microvolume cuvettes and cell holder, instrumental requirements, data analysis methods, and sources of error. References to the primaiy literature and reviews are also provided where appropriate. Sections of this chapter have been adapted from previous reviews and are reprinted with permission from the Annual Review of Biochemistry, Volume 62 1993, by Annual Reviews wwwAnnualReviews.org (6) and with permission from Biopolymers 1997, by John Wiley Sons, Inc. (4). 

G. D. Cimino, H. B. Gamper, S. T. Isaacs, and J. E. Hearst, Psoralens as photoactive probes of nucleic acid structure and function organic chemistry, photochemistry and biochemistry Annual Review of Biochemistry, vol. 54, pp. 1151-1193, 1985. 

In Chapter 1 we saw that a major achievement of the first half of the twentieth cen tury was the picture of atomic and molecular structure revealed by quantum mechan ICS In this the last chapter we examine the major achievement of the second half of that century—a molecular view of genetics based on the structure and biochemistry of nucleic acids... 

One of the most important and exciting advances in modern biochemistry has been the application of spectroscopic methods, which measure the absorption and emission of energy of different frequencies by molecules and atoms. Spectroscopic studies of proteins, nucleic acids, and other biomolecules are providing many new insights into the structure and dynamic processes in these molecules. 

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. 

In the version of evolutionary theory popularised by Dawkins (1976), the fundamental unit of life is a gene, a conceptual abstraction clothed in the biochemistry of the nucleic acid DNA. The purpose, or telos, of this gene is replication - to make copies of itself - copies which because of random chemical and physical processes maybe more or less accurate. The particular chemical structure of DNA provides a mechanism whereby such faithful copying can readily occur - as James Watson and Francis Crick pointed out... 

Metz, D.H., and Brown, G.L. (1969) The investigation of nucleic acid secondary structure by means of chemical modification with a carbodiimide reagent. I. The reaction between N-cyclohexyl-N -b-(4-methylmorpholinium)ethyl carbodiimide and model nucleotides. Biochemistry 8, 2312-2328. 

Equation 4.9 has been extensively applied to study the mechanisms of electrophilic (e.g., protonation) reactions, drug-nucleic acid interactions, receptor-site selectivities of pain blockers as well as various other kinds of biological activities of molecules in relation to their structure. Indeed, the ESP has been hailed as the most significant discovery in quantum biochemistry in the last three decades. The ESP also occurs in density-based theories of electronic structure and dynamics of atoms, molecules, and solids. Note, however, that Equation 4.9 appears to imply that p(r) of the system remains unchanged due to the approach of a unit positive charge in this sense, the interaction energy calculated from V(r) is correct only to first order in perturbation theory. However, this is not a serious limitation since using the correct p(r) in Equation 4.9 will improve the results. 

Simon RH, Eelsenfeld G (1979) A new procedure for purifying histone pairs H2A + H2B and H3 + H4 from chromatin using hydroxylapatite. Nucleic Acids Res 6 689-696 Simpson RT (1978) Structure of the chromatosome, a chromatin particle containing 160 base pairs of DNA and all the histones. Biochemistry 17 5524-5531 Simpson RT, Stafford DW (1983) Structural features of a phased nucleosome core particle. Proc Natl Acad Sci U S A 80 51-55... 

X-ray analysis of proteins and nucleic acids is especially important as the absolute structure is needed for many advances in the field of medicine and biochemistry. 

A. Sreedhara and J. A. Cowan, Structural and catalytic roles for divalent magnesium in nucleic acid biochemistry. Biometals, 2002,15,211-223. 

A number of microorganisms produce free nucleosides which, although structurally similar to the nucleosides of primary biosynthesis, are not normally utilized for nucleic acid synthesis. These have emerged as useful probes for the elucidation of the biochemistry of RNA, DNA... 

Practice with the software introduced in the Experimental Procedure until you are familiar with it. Use proteins and nucleic acids discussed in your biochemistry class as exercises for bibliographic searches and structure/sc-quence studies. Several more examples are provided in the Study Problems. Continue to use the Web resources described in this experiment as you proceed through this laboratory course. 

The nucleic acids are among the most complex molecules that you will encounter in your biochemical studies. When the dynamic role that is played by DNA in the life of a cell is realized, the complexity is understandable. It is difficult to comprehend all the structural characteristics that are inherent in the DNA molecules, but most biochemistry students are familiar with the double-helix model of Watson and Crick. The discovery of the double-helical structure of DNA is one of the most significant breakthroughs in our understanding of the chemistry of life. This experiment will introduce you to the basic structural characteristics of the DNA molecule and to the forces that help establish the complementary interactions between the two polynucleotide strands. 

G Blackburn and M Gait, Nucleic Acids m Chemistry andBiology (1991), Oxford University Press (New York) An excellent book on general aspects of nucleic acids R Boyer, Concepts m Biochemistry (1999), Brooks/Cole (Pacific Grove, CA), pp 30-44, 280-310 Structure and function of DNA... 

A Lehmnger, D Nelson, and M Cox, Principles of Biochemistry, 3rd ed (1999), Worth Publishers (New York), pp 907-930 DNA structure and function J Le Pecq and C Paoletti,/ Mol. Biol. 27, 87 (1967) A Fluorescent Complex Be tween Ethidium Bromide and Nucleic Acids ... 

---