Secondary structure, polynucleotides

Fig. 5. Nonduplex polynucleotide secondary structures hairpin (A), cruciform (B), bulge (C), bubble (D), three-way junction (E), and four-way junction (F).

By analogy to the levels of structure of proteins the primary structure of DNA IS the sequence of bases along the polynucleotide chain and the A DNA B DNA and Z DNA helices are varieties of secondary structures... 

In 1953, James Watson and Francis Crick made their classic proposal for the secondary structure of DNA. According to the Watson-Crick model, DNA under physiological conditions consists of two polynucleotide strands, running in opposite directions and coiled around each other in a double helix like the handrails on a spiral staircase. The two strands are complementary rather than identical and are held together by hydrogen bonds between specific pairs of... 

TABLE 11.1. Association Constants of Various Nucleic Acids with Neomycin. From top to bottom, various polynucleotides with their conformational preference (B- to A-form) are listed in 10 mM sodium cacodylate, 100 mM NaCl, 0.1 mM EDTA, pH 6.8. RNA targets that have previously been shown to bind neomycin are also listed. These targets are examples of RNA secondary structures that show high-affinity binding to aminoglycosides. Solution conditions for RNA targets vary as shown... 

Secondary structure of DNA consists of two strands of polynucleotides coiled around each there in the form of double helix. The backbone of each strand is sugar-phosphate unit and the base unit of each strand are pointed into the interior of the helix and are linked through H-bonds. G and C are held by three H-bonds, A and T are held by two bonds. Unlike DNA, RNA has a single strand. 

The absorption coefficients of polynucleotides are different from those calculated from the sum of the mononucleotides in part this reflects the secondary structure. The abrupt increase in the absorption of DNA at the melting point, where the secondary structure changes from the double helix to a random coil, is well known. It is therefore... 

Our objective is to understand how the noncovalent interactions responsible for nucleic acid secondary structure (i.e. base stacking and base pairing) affect the photophysics of these multichromophoric systems. Here we describe initial experimental results that demonstrate dramatic differences in excited-state dynamics of nucleic acid polymers compared to their constituent monomers. Although ultrafast internal conversion is the dominant relaxation pathway for single bases, electronic energy relaxation in single-stranded polynucleotides... 

The first scientific articles from the IKhPS were submitted for publication in the early 1960s, among them being Nikolay s reports on his work in the new field. His major project in nucleotide chemistry was specific chemical modifications of heterocyclic bases. Reactions of hydroxylamine with cytidine and uridine were studied in detail and a new reagent, O-methylhydroxylamine, was proposed for modification of cytidine. These investigations aimed at the development of efficient methods for sequencing and analysis of the secondary structure of polynucleotides. Later, a reaction of chloroacetaldehyde with adenosine and cytidine was discovered and used for preparation of fluorescent polynucleotide derivatives. 

RNA molecules form secondary structure by folding their polynucleotide chains via hydrogen bond formations between AU pairs and GC pairs. The thermochemical stability of forming such hydrogen bonds provides useful criterion for deducing the cloverleaf secondary structure of tRNAs that is, tRNA molecules are folded into DFI... 

Just as main-chain NH 0=C hydrogen bonds are important for the stabilization of the a-helix and / -pleated sheet secondary structures of the proteins, the Watson-Crick hydrogen bonds between the bases, which are the side-chains of the nucleic acids, are fundamental to the stabilization of the double helix secondary structure. In the tertiary structure of tRNA and of the much larger ribosomal RNA s, both Watson-Crick and non-Watson-Crick base pairs and base triplets play a role. These are also found in the two-, three-, and four-stranded helices of synthetic polynucleotides (Sect. 20.5, see Part II, Chap. 16). 

Arnott S (1981) The secondary structures of polynucleotide chains as revealed by X-ray diffraction analysis of fibers. In Neidle S (ed) Tbpics in nucleic acid structure. MacMillan, London, pp 65-82... 

Further potential polynucleotide-ligand interactions involve the negative surface charges (that can electrostatically interact with positively charged non-protein and protein ligands) and surface structural elements such as minor and major grooves and secondary structure loops. Thus, for example, polynucleotides can have palindromic complementary sequences, for example,... 

An interaction of metal ions with phosphates usually leads to stabilization of polynucleotide secondary and tertiary stmctures, depending on the metal ions and their concentrations, whereas base binding or chelating base and phosphate by the same metal ion may result in destabilization, conformational change, or denaturation of the polynucleotide structures (see also Sections 3.3.1 and 3.3.2). However, phosphate-specific binding can also induce significant conformational changes in DNA structure. The mechanisms of the latter structural interconversions are... 

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). 

RNA The secondary structure of RNA consists of a single polynucleotide. RNA can fold so that base pairing occurs between complementary regions. RNA molecules often contain both single- and double-stranded regions. The strands are antiparallel and assume a helical shape. The helices are of the A-form (see above). 

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. 

Structure Probes.—The introduction of fluorescing labels into nucleic acids can yield valuable structural information, and both organic compounds and metal ions [Tb (ref. 136) and Eu (ref. 137)] have been used as fluorescent probes for tRNA and other polynucleotides. The degree of secondary structure in RNA has been estimated from Raman scattering by the phosphate group vibrations. A number of n.m.r. studies have appeared, but discussion of these is more suited to a review on n.m.r. spectroscopy. Lanthanide ions have been used as contact shift reagents to probe tRNA structure. ... 

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