Double complementarity

FIGURE 1.5 The DNA double helix. Two complementary polynucleotide chains running in opposite directions can pair through hydrogen bonding between their nitrogenous bases. Their complementary nucleotide sequences give rise to structural complementarity. 

RNA is often depicted as a single-stranded molecule. However, in many RNA s, internal complementarity may result in secondary (and tertiary) structure in which one part of the RNA molecule forms a double-stranded region with another part of the same molecule. There are usually a number of mismatches in these structures. Names have been given to some of these structural features (Fig. 4-3). 

Double-stranded DNA exhibits complementarity in forming the double helix. The complementary sequences have opposite polarity that is, the two chains run in opposite directions as in the following illustration ... 

The last section of this chapter includes in brief a procedure of McF adden (9) for in situ hybridization. In situ hybridization relies on the complementarity of the bases contained within DNA and RNA. In addition to the hybridization (reassociation) of complementary DNA strands, hybridization is possible between DNA and RNA strands that are complementary. Also, hybridization is possible between a synthetic sequence and a sequence of biological origin. In situ hybridization may be used to determine the location of a specific nucleic acid sequence within a cell. The procedure requires the use of a probe for the sequence of interest. The probe, in turn, must be complementary to the sequence of interest. The probe may be either single stranded or double stranded, DNA or RNA. There must exist a method by which to detect the probe. 

The tertiary structure of DNA is the structural level that is most relevant to 3-D reality. Traditionally, ODNs in a physiologically relevant aqueous solution are considered to be in a random-coiled ssDNA state or in the form of dsDNA helix in the presence of a complementary DNA, including the case of self-complementarity. The double helix is the dominant tertiary structure for biological DNA that can be in one of the three DNA conformations found in nature, A-DNA, B-DNA, and Z-DNA. The B-conformation described by Watson and Crick (11) is believed to predominate in cells (12). However other types of nucleic acid tertiary structures different from random or classical double-stranded helix forms can also be observed. Among them are triplexes, quadruplexes, and several other nucleic acid structures (13, 14). 

Other researchers are employing DNA to promote nanoparticle assemblies. As mentioned in the sidebar on pages 42-44, hydrogen bonds knit the strands of the DNA s double helix. DNA consists of strings of four bases adenine (A), thymine (T), cytosine (C), and guanine (G). The structures of the bases and the helix permit only the binding of A with T, and C with G. This is called complementarity, for if the base at one location is an A, the base on the opposite strand will be its complement, T, not a C or a G. If it is a G, then the other base will be a C. 

Figure 20. Two-dimensional arrays constructed from DAE and DAE+J motifs. Two arrays are shown, one containing two components, A and B, and a second containing four components, A, B, C, and D. Each of die starred components contains one or two hairpins perpendicular to the plane of the array. The double-crossover molecules are represented as two closed figures connected by two short lines. The helix axis of each domain is represented by a dotted line. The sticky ends are drawn schematically as complementary geometrical shapes, representing Watson-Crick complementarity. The horizontal repeat is two units in the top array and four in the bottom array the vertical repeat is a single unit in both arrays. The perpendicular hairpins are visible as stripes when this array is examined in the atomic force microscope.

To reduce the hybridization stringency, researchers choose conditions that stabilize double-stranded DNA, allowing sequences that share only partial complementarity to form base pairs. Examples of such conditions include reducing the hybridization temperature and increasing the salt concentration in solution. 

Figure 1. Catalysis and template action of RNA and proteins. Catalytic action of one RNA molecule on another one is shown in the simplest case, the "hammerhead ribozyme." The substrate is a tridecanucleotide forming two double-helical stacks together with the ribozyme (n = 34) in the confolded complex. Tertiary interactions determine the detailed structure of the hammerhead ribozyme complex and are important for the enzymatic reaction cleaving one of the two linkages between the two stacks. Substrate specificity of ribozyme catalysis is caused by secondary structure in the cofolded complex between substrate and catalyst. Autocatalytic replication of oligonucleotide and nucleic acid is based on G = C and A = U complementarity in the hydrogen bonded complexes of nucleotides forming a Watson-Crick type double helix. Gunter von Kiedrowski s experi-...

Figure 2. The logic of complementary replication and mutation. Template-induced synthesis of RNA is based on nucleotide complementarity (G h C and A = U) in the double helix. The synthesis starts at the 5 -end of the template and adds nucleotide after nucleotide to the growing chain. In this way a negative copy is obtained, being the minus- or plus-strand when a plus- or a minus-strand was the template, respectively. Dissociation of the double-helical plus-minus-duplex completes complementary replication. Three classes of...

The Crick-Watson base pairing with the complementarity C-G and A-T (for DNA) or A-U (for RNA) is a consequence of the delicate balance between aromatic resonance energies and bond energies for CC, CO and CN single and double bonds. 

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