Complementarity, in nucleic

Hrdlicka PJ, Babu BR, Sorensen MD, Wengel J (2004) Interstrand communication between 2- V-(pyicn-1 -yl)mcthyl-2-amino-LNA monomers in nucleic acid duplexes directional control and signalling of full complementarity. Chem Commun 1478-1479... 

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-...

The double-stranded DNA consists of two parallel chains folded into an a-helix. The chains are joined by hydrogen bonds that follow the rules of complementarity. In accordance with these rules, adenine is always bound with thymine of the other chain and guanine is always bound to cytosine (see the following scheme). The principles of molecular complementarity do not apply only to nucleic acids. Rather, they represent general rules for the formation of various supramolecular structures. If nucleotides are labeled by their first letters, the complementary pairs would be AT and GC, respectively. The structural key for complementarity is the number of hydrogen bonds. There are two such bonds in the AT pair and three in... 

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 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). 

The composition of nucleotide polymers at any locale depended upon the relative concentration of the nucleosides G, C, A or T, in the medium and may have varied as a function of time, ionic environment and other factors. The first chains that polymerized without a template produced variety whereas subsequently chains were duplicated more or less accurately by complementarity, and that process gave rise to families of nucleic acid polymers that formed the basis for similarity (clones) and diversity among organisms (Chapter 4). 

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