Secondary and Tertiary Structure of Nucleic Acids

An enormous kick-start to modern molecular biology was given by the seminal 1953 Nature paper of Francis Crick and Jim Watson on the double helical structure of DNA. It was based on two important observations. 

Sir Alexander Todd, who won the 1957 Chemistry Nobel Fh-ize was a former pupil of Allan Glen s school in Glasgow, where I also got my secondary education. He not only established the chemical structure of nucleic acids, but we owe to him our knowledge of the structures of FAD, ADP and ATP. 

FIGURE 3.18 The B-form of the DNA double helix viewed along the helix axis in a ball and stick representation (left) and in a space-filling representation (right). The major and minor grooves are indicated. 

Rosalind Fanklin took the X-ray photographs of DNA which were used by Watson and Crick in their prediction of the structure of DNA. She died of ovarian cancer in 1958. 

FIGURE 3.19 The classic Watson—Crick base pairing between A and T, and between G and C in DNA. 

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Due to base pairing and base stacking the H NMR chemical shifts of purines are changed if they are incorporated in double-stranded dNA or RNA. As a consequence, high-resolution NMR spectroscopy is an important tool for determining the secondary and tertiary structure of nucleic acids. ... 

Primary, Secondary, Tertiary, and Quaternary Structure of Proteins Secondary and Tertiary Structures of Nucleic Acids... 

Jack A (1979) Secondary and Tertiary Structure of Nucleic acids. In Offord RE, ed. International Review of Biochemistry, Chemistry and Macromolecules II A, Vol. 2.24, pp. 211-256. University Park Press, Baltimore. 

Stacking usually involves molecules with a sufficiently large aromatic moiety. In water these parts tend to stack. This interaction may provide a significant contribution to the stability of secondary and tertiary structure of nucleic acids. Ultrasonic studies of stacked systems were undertaken in hope of gaining information on the kinetics of stacking processes as well as on the nature of stacking interactions. 

The influence of cobalt(III)—amine cations on native and denatured calf thymus DNA was first reported in 1972—3 [87, 88]. Subsequent studies on tRNA [89] and DNA [90] confirmed that such complex cations are very effective in stabilizing secondary and tertiary structures of nucleic acids. Karpel et al have extended the studies on cobalt to a series of platinum metal derivatives and the results are summarized in Table l.III 91]. 

ENERGETICS THAT CONTROL THE STABILITY AND DYNAMICS OF SECONDARY AND TERTIARY STRUCTURE OF NUCLEIC ACIDS. 

In contrast, RNA occurs in multiple copies and various forms (Table 11.2). Cells contain up to eight times as much RNA as DNA. RNA has a number of important biological functions, and on this basis, RNA molecules are categorized into several major types messenger RNA, ribosomal RNA, and transfer RNA. Eukaryotic cells contain an additional type, small nuclear RNA (snRNA). With these basic definitions in mind, let s now briefly consider the chemical and structural nature of DNA and the various RNAs. Chapter 12 elaborates on methods to determine the primary structure of nucleic acids by sequencing methods and discusses the secondary and tertiary structures of DNA and RNA. Part rV, Information Transfer, includes a detailed treatment of the dynamic role of nucleic acids in the molecular biology of the cell. 

Abstract Now an incisive probe of biomolecular structure, Raman optical activity (ROA) measures a small difference in Raman scattering from chiral molecules in right- and left-circularly polarized light. As ROA spectra measure vibrational optical activity, they contain highly informative band structures sensitive to the secondary and tertiary structures of proteins, nucleic acids, viruses and carbohydrates as well as the absolute configurations of small molecules. In this review we present a survey of recent studies on biomolecular structure and dynamics using ROA and also a discussion of future applications of this powerful new technique in biomedical research. 

Metal ions are usually required to promote and stabilize functionally active or native conformations of nucleic acids, as well as to mediate nucleic acid-protein interactions. However, metal ions can also cause structural transformation of nncleic acids, or denature their native structures. In addition to structural roles, some metal compounds can indnce cleavage (i.e. scission, fragmentation, or depolymerization) and modification (withont cleavage) of nucleic acids. Metal-nucleic acid interactions can be either nonspecific or dependent on the chemical nature of nucleotide residues, nucleic acid sequence, or secondary and/or tertiary structure of nucleic acids. The specificity of these interactions is dependent... 

Assignments based on a comparison of chemical and spectroscopic information generally require prior knowledge of the polymer sequence, or primary structure, but not of the secondary and tertiary structure of a protein or nucleic acid. The most noteworthy of this class of procedures are ... 

Denaturation The process by which the secondary and tertiary structure of proteins and nucleic acids is broken down to form random chains. In the case of DNA, it specifically refers to the separation of double-stranded DNA into single strands by the breaking of the hydrogen bonds that form the complementary base pairing, usually by increasing the temperature. 

It is reasonable to expect that secondary and tertiary structures of polymeric and rather complex molecules of nucleic acids may be altered as a consequence of their fixation at the surface. A different adsorbabil-ity of the groups through which molecules of the nucleic acid are anchored at the surface and the existence of the strong electric field next to the electrode undoubtedly play an important role in inducing these interfacial alterations. 

The complex folded structures adopted by tRNAs illustrates the fact that nucleic acids with a properly adjusted primary sequence can adopt complex secondary and tertiary structures. Apropos of this, Francis Crick once said that transfer RNA is an RNA molecule trying to look like a protein. 

Nucleic acids have a primary, secondary, and tertiary structure analogous to the classification of protein structure. The sequence of bases in the nucleic acid chain gives the primary structure of DNA or RNA. The sequence of bases is read in a 5 -> 3 direction, so that you would read the structure in the next figure as ACGT. See Figure 8-1. 

While this notion may conjure up visions of plastic materials it is important to remember that proteins and nucleic acids are also polymers. Many proteins form globular structures and, indeed, may interlock to encapsulate a large volume of space as exemplified by the coatings of capsid viruses. In a prebiotic world, polypeptides could have formed in aqueous solution through the sequential reaction of amino acids. The individual amino acids hydrogen bond donor and acceptor groups, amines, carbonyls and carboxylic acids, would all have helped to keep the molecules in solution. Once a polypeptide had formed, however, many of these would be unavailable as they became incorporated in the hydrogen bond network that formed the secondary and tertiary structure. This would result in a more hydrophobic surface for the protein capsule which would make an effective cell. 

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