Secondary Structure of Nucleic Acids

A purine base always pairs with a pyrimidine base or more specifically Guanosine (G) with Cytosine (C) and Adenine (A) with Thymine (T) or Uracil (U) (Fig. 4.2). 

The G-C pair has three hydrogen bonds while the A-T pair has two hydrogen bonds. 

DNA The secondary structure of DNA consists of two polynucleotide chains wrapped around one another to form a double helix. The orientation of the helix is usually right handed witii the two chains running antiparallel to one another (Fig. 4.3). 

The sequence of bases on each strand are arranged so that all of the bases, on one strand pair with all of the bases on another strand, i.e. the number of guanosines always equals the number of cytosines and the number of adenines always equals the number of thymines. 

There are two grooves, one major and one minor, on the double helix. Proteins and drugs interact with the functional groups on the bases that are exposed in the grooves (Fig. 4.4). 

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Fig. 4.1 Nucleotides Linked Through Phosphodiester Bond Secondary Structure of Nucleic Acids...

What can we say about the secondary structure of nucleic acids The following picture of DNA fits both chemical and x-ray evidence. Two polynucleotide chains, identical but heading in opposite directions, are wound about each other to form a double helix 18 A in diameter (shown schematically in Fig. 37.7). Both helixes are right-handed and have ten nucleotide residues per turn. 

A Study of the Secondary Structure of Nucleic Acids with... 

The secondary structure of nucleic acids involves hydrogen bonding between the heterocyclic bases. A and T can form two hydrogen bonds (A — "0 as can A and U U) while G and C form three C)... 

Secondary structure of nucleic acids (Section 28.2B) The ordered arrangement of nudeic add strands. 

There is a net CD even when asymmetric molecules are randomly oriented, so the technique can be used to investigate nucleic acids in solution. The CD will depend on the particular bases involved, and the conformation of the sample. Thus changes in solution conditions that affect the secondary structure of a nucleic acid will change the base-base interactions, and result in a different CD spectrum. CD is the method of choice for monitoring the secondary structure of nucleic acids in solution. 

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. 

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

Chaperones are needed for nucleic acids as well as proteins. The concept that the proper folding of macromolecules may depend on the activities of helper proteins—molecular chaperones—has recently been extended to nucleic acids, notably RNA. As pointed out above, the formation of secondary structures in nucleic acids is an exothermic process (AH is negative), and thus favored by reductions in temperature. If temperature decreases to very low values, nucleic acids may acquire too high a stability of native secondary structure to function well. Moreover, additional regions of secondary structure may form that disrupt normal functions such as transcription and translation. 

Figure V-4 Examples of secondary structure in nucleic acids.

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... 

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. ... 

See also B-DNA, Primary, Secondary, Tertiary Structure of Nucleic Acids, Palindromes... 

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. 

Hydrogen bonding is clearly ubiquitous in stabilising protein secondary structures and nucleic acid double helices (by Watson-Crick base pairing between anti-parallel phosphodiester chains), and in the wide range of homoglycan secondary to quaternary structures. 

In Chapter 4, we identified four levels of structure—primary, secondary, tertiary, and quaternary—in proteins. Nucleic acids can be viewed in the same way. The primary structure of nucleic acids is the order of bases in the polynucleotide sequence, and the secondary structure is the three-dimensional conformation of the backbone. The tertiary structure is specifically the supercoiling of the molecule. 

The primary structure of nucleic acids is the order of bases. The secondary structure is the three-dimensional conformation of the backbone. The tertiary structure is the supercoifing of the molecule. 

Like proteins, nucleic acids have different modes of structure. Nucleotide sequence and covalent structure form the primary structure of nucleic acids. When nucleotides form regular and stable structures, it is referred as secondary structure. The ternary structure is considered as the folding of large chromosomes within the chromatin. 

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