Since Watson and Crick's historical papers on the structure and function of DNA based on Rosalind Franklin's and Maurice Wilkin's X-ray diffraction patterns tremendous scientific curiosity has been aroused by the unique and dynamic structure of the molecule of life. A-DNA and B-DNA represent different conformations of the DNA molecule, which is stabilised by hydrogen interactions between base pairs, stacking interactions between neighboring bases and long-range intra- and inter-backbone forces. This review highlights the contribution Fourier transform infrared (FTIR) spectroscopy has made to the understanding of DNA conformation in relation to hydration and its potential role in clinical diagnostics. The review will first begin by elucidating the main forms of DNA conformation found in nature and the general structures of the A, B and Z forms. This is followed by a detailed critique on infrared spectroscopy applied to DNA conformation highlighting pivotal studies on isolated DNA, polynucleotides, nucleoprotein and nucleohistone complexes. A discussion on the potential of diagnosing cancer using FTIR spectroscopy based on the detection of DNA bands in cells and tissues will ensue, highlighting the recent studies investigating the conformation of DNA in hydrated and dehydrated cells. The method of hydration as a way to facilitate DNA conformational band assignment will be discussed and the conformational change to the A-form upon dehydration will be used to explain the reason for the apparent lack of FTIR DNA signals observed in fixed or air-dried cells and tissues. The advantages of investigating B-DNA in the hydrated state, as opposed to A-DNA in the dehydrated state, are exemplified in a series of studies that show: (1) improved quantification of DNA in cells; (2) improved discrimination and reproducibility of FTIR spectra recorded of cells progressing through the cell cycle; (3) insights into the biological significance of A-DNA as evidenced by an interesting study on bacteria, which can survive desiccation and at the same time undergo the B–A–B transition. Finally, the importance of preserving the B-DNA conformation for the diagnosis of cancer is put forward as way to improve the sensitivity of this powerful technique.

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The importance of hydration and DNA conformation in interpreting infrared spectra of cells and tissues.

Previous Fourier transform infrared (FT-IR) spectroscopic studies on neoplastic and normal cells have shown different band profiles and intensity associated with absorptions of proteins and nucleic acids. In the present study, an interpretation of such differences has been attempted by comparing the spectra of DNA/RNA/protein mixtures with the spectra, particularly, obtained for lymphocytes from B-chronic lymphatic leukemia (B-CLL) patients and normal donors. FT-IR microspectroscopy analysis showed a good agreement between the intensity and the band profile of the spectra of leukemic lymphocytes and those of the binary mixture made up of 75% human serum albumin and 25% DNA. The addition of small amounts of RNA (1-5% ) modified the band shape, making it more similar to the spectrum of normal lymphocytes. An attempt was also made to estimate the relative amounts of DNA and RNA. The results demonstrated an increase in the DNA/RNA ratio value in neoplastic lymphocytes with respect to that reported in literature for normal ones.

Determination of the Relative Amount of Nucleic Acids and Proteins in Leukemic and Normal Lymphocytes by Means of Fourier Transform Infrared Microspectroscopy

Polarized Raman spectra of oriented fibers of A DNA and B DNA: anisotropic and isotropic local Raman tensors of base and backbone vibrations.

A fundamental aspect in the study of the charge–transfer (CT) organic crystals with ionic or partially ionic ground states is the investigation of the spectroscopic effect of the electron–molecular vibration coupling. 7,7,8,8‐tetracyano‐2,3,5,6‐tetrafluoroquinodimethane (TCNQF4), an electron acceptor much stronger than TCNQ, is an outstanding component of many interesting CT systems. A thorough vibrational analysis of the title compound and of its monomeric radical anion is reported. The analysis is based on the Raman depolarization ratio measurements and on infrared data of solutions of both neutral and ionic species as well as on polarized infrared spectra of oriented crystals of the neutral molecule. The vibrational assignment, completed by a normal coordinate analysis (NCA), brings to the identification of the ionization frequency shifts and to the choice of the fundamentals (b1uν19 and b2uν33) whose frequencies are diagnostic of the degree of charge transfer for a TCNQF4 moiety partner of a CT system...

Charge–transfer organic crystals: Molecular vibrations and spectroscopic effects of electron–molecular vibration coupling of the strong electron acceptor TCNQF4

Publisher Summary The chapter focuses tautomerism and electronic Structure of biological pyrimidines. The understanding of the tautomeric properties of the purine and pyrimidine bases of the nucleic acids and the determination of the electronic properties of the principal tautomers are of fundamental importance in molecular biology, in particular, in connection with the theory of mutations. The principal tautomeric properties of the fundamental biological pyrimidines-cytosine, uracil, and thymine-are due to the presence in these N-heteroaromatic compounds of electron-donor substituents, such as NH and OH, and of SH in some important analogs. The chapter discusses tautomerism of cytosine and presents the essential physicochemical properties of cytosine and some of its derivatives and to the theoretical interpretation of these properties. The chapter also discusses tautomerism and physicochemical properties of uracil and thymines and to give a theoretical interpretation of these properties. The study of the optical properties of naturally occurring pyrimidines and purines is a problem of great interest in molecular biology. The knowledge of these properties provide information important for understanding energy transfer, hypochromism, photochemistry, optical rotatory dispersion, circular dichroism, magnetic optical rotator dispersion, and magnetic circular dichroism of DNA, RNA, and related model systems. Tautomerism, electronic structures, and spectra of rare pyrimidine bases of the nucleic acids have also been discussed.

J.M. Purcell

Papers

Vibrational spectra of nucleic acid constituents—II: Planar vibrations of cytosine