Nucleic acid strand interaction

The anticodon region consists of seven nucleotides, and it recognizes the three-letter codon in mRNA (Figure 38-2). The sequence read from the 3 to 5 direction in that anticodon loop consists of a variable base-modified purine-XYZ-pyrimidine-pyrimidine-5h Note that this direction of reading the anticodon is 3 " to 5 whereas the genetic code in Table 38—1 is read 5 to 3 since the codon and the anticodon loop of the mRNA and tRNA molecules, respectively, are antipar-allel in their complementarity just like all other inter-molecular interactions between nucleic acid strands. 

The close interaction between stacked bases in a nucleic acid has the effect of decreasing its absorption of UV light relative to that of a solution with the same concentration of free nucleotides, and the absorption is decreased further when two complementary nucleic acids strands are paired. This is called the hypochromic effect. Denaturation of a double-stranded nucleic acid produces the opposite result an increase in absorption... 

Base pairing interaction between the nucleic acid strands forms the rationale for nucleic acid-based diagnostic and therapeutic technologies described in the subsequent chapters. 

An alternative to the inhibition of RNA metabolism by way of an antisense mechanism is to inhibit transcription by interacting with double-stranded DNA in chromatin. Of the two most obvious binding strategies for oligonucleotides binding to double-stranded nucleic acids, strand invasion and triple-strand formation, triple-stranding strategies, until recently, attracted essentially all of the attention. 

The loop sequence of the tpy-modified DNA strand was designed such that the strand could hybridize to a molecular beacon [Fig. 16(a)] only when in its extended, linear form [Fig. 16(h)]. Upon hybridization to the tpy-modified DNA, the molecular beacon switches from its closed, nonfluorescent form to its open, fluorescent form [Fig. 16(h)]. Both Fe and Zn form very stable [M(qjy)2] complexes and consequently, the circular structure adopted by the tpy-modified DNA strands in the presence of 1 equiv of these metal ions represented a steric barrier for its hybridization to the molecular beacon. The metal ion acted as an allosteric off switch for DNA hybridization (148). This study demonstrated that the incorporation of metal-binding ligands in nucleic acid strands can be used to create metal-dependent allosteric switches for the Watson-Crick interactions between the nucleic acid strands, a mechanism that may find applications in creating artificial systems with regulatory function. In contrast, in the presence of Cu + the DNA hybridization to the molecular beacon was energetically more favorable than the formation of circular stmctures from the tpy-containing DNA strands. Therefore, hybridization of a complementary ssDNA to the... 

Important differences between DNA and RNA appear in their secondary and tertiary structures, and so we shall describe these structural features separately for DNA and for RNA. Even though nothing in nucleic acid structure is directly analogous to the quaternary structure of proteins, the interaction of nucleic acids with other classes of macromolecules (for example, proteins) to form complexes is similar to the interactions of the subunits in an oligomeric protein. One well-known example is the association of RNA and proteins in ribosomes (the polypeptide-generating machinery of the cell) another is the self-assembly of tobacco mosaic virus, in which the nucleic acid strand winds through a cylinder of coat-protein subunits. 

The interactions of nucleic acid materials with Ln have been largely studied through their luminescent properties. The known affinity of Ln " cations for the phosphate moiety has led to many investigations of the Ln interactions with nucleotides, covered in some detail by Evans [1]. The interaction of Ln with nucleic acids has been used to probe perturbations in the integrity of nucleic acid strands and as an assay of nucleic acid hybridization. Balcarova and Brabec [45] showed that the interaction of Tb with double-stranded DNA can be used to monitor guanine bases present in distorted double-stranded regions of DNA. The enhancement of distortions in double-stranded DNA appears to be restricted to certain modifiers of nucleic acid as there is no... 

Three classes of nucleic acid triple helices have been described for oligonucleotides containing only natural units. They differ according to the base sequences and the relative orientation of the phosphate-deoxyribose backbone of the third strand. All the three classes involve Hoogsteen or reverse Hoogsteen-like hydrogen bonding interaction between the triple helix form-... 

Recently, Switzer and co-workers have further extended the multi-stranded motifs for nucleic acids with the formation of a quintet assembly with oligonucleotides containing 2,deoxy-iso-guanosine (74). To support the quintet, metal ions larger than those appropriate for quartet stabilization were required, and Cs+ ions were found to best meet this requirement. From modeling studies, a structure in which a central Cs+ interacts with ten 02 iG atoms at a distance of 3.5 A was proposed. 

---