Triplex Watson-Crick structure

The formation of three-stranded nucleic acid complexes was first demonstrated over five decades ago [56] but the possible biological role of an extended triplex was expanded by the discovery of the H-DNA structure in natural DNA samples [57-59]. H-DNA is an intermolecular triplex that is generally of the pyrimidine-purine x pyrimidine type ( dot -Watson-Crick pairing and cross Hoogsteen base paring) and can be formed at mirror repeat sequences in supercoiled plasmids [59]. 

DNA can exist in several structural forms. Two variations of the Watson-Crick form, or B-DNA, are A- and Z-DNA. Some sequence-dependent structural variations cause bends in the DNA molecule. DNA strands with appropriate sequences can form hairpin/cruciform structures or triplex or tetraplex DNA... 

Figure 5-34 (A) Two conformations of a segment of the yeast phenylalanine tRNA gene. The segment shown codes for the 3 end of the tRNA molecule shown in Fig. 5-30, including the T /C loop. (B) Formation of H-DNA (Fig. 5-24) proposed for a sequence in plasmid pGG32. The major element of the structure is the triplex, which is formed from the Watson-Crick duplex ( ) associated with the homopyrimidine loop through Hoogsteen base pairing (o, +). One of the two possible "isomeric" forms is shown. See Mirkin et al.378...

Triple-helix formation by G-rich oligonncleotides is supported by Mg + but strongly inhibited by physiological concentrations of certain monovalent cations, especially K+, most likely dne to oligonncleotide self-association in competitive structures such as guanine-quadruplexes. " Variation of the cation enviromnent can differentially promote the assembly of multistranded nncleic acid structural alternatives. For example, by specifically counteracting the induction/stabilization of quadruplex structures by potassium ions, certain divalent ions (i.e. Mn +, Co +, and Ni + but not Mg +) at low millimolar concentrations allow triplex formation in the presence of 150mMK+. In contrast, certain mono- and divalent metal ions can promote the transition from Watson-Crick duplexes to G4 quadruplex structures relatively efficiently K" " > Ca + >... 

Figure 2 Most common DNA/RNA binding modes. Left Strand invasion of homopyrimidine PNA into duplex DNA yields a PNA2-DNA triplex. Right Hybridization of mixed sequence PNA with complementary DNA or RNA produces Watson-Crick base-paired duplex structures.

Polynucleotides were reported to form triple helices as early as 1957. Triple strands can form by non-Watson-Crick hydrogen bonds between the third strand and purines involved in Watson-Crick hydrogen bonding with the complementary strand of the duplex (for review, see Ref 34). Thus, triple-stranded structures can be formed between a third strand composed of pyrimidines or purines that interact with a homopurine strand in a homopurine-homopyrimidine strand in a duplex DNA. With the demonstration that homopyrimidine oligonucleotides could indeed form triplex structures (35-37), interest in triple-strand approaches to inhibit transcription heightened. 

This table takes only structures into account for which atomic coordinates have been deposited at the Protein Data Bank. Given polyads occur in several chain this indicated before the polyad. If polyads include bases from different chains the chain identifier is indicated in parenthesis. The numbering of bases involved in polyads is not given for regular triplex/tetr lex structures. The topology corresponds to the classification presented in Table 1. H-bonds between bases are indicated by dots. No difference is made between Watson-Crick and non-canonical base-base interactions. The base sequence follows the H-bond interaction pattern. For example, in the non-cyclic triad C.G.A C is bound to G and G to A. In more complex cases parentheses have been used. The H-bond analysis of nucleic acid structures has been performed with HBexplore. 

Abstract The physical aspects of DNA structure and function are overviewed. Major DNA structures are described, which include the canonical Watson-Crick double helix (B form), B , A, Z duplex forms, parallel-stranded DNA, triplexes and quadruplexes. Theoretical models, which are used to treat DNA, are considered with special emphasis on the elastic-rod model. DNA topology, supercoiling and their biological significance are extensively discussed. Recent developments in the understanding of molecular interactions responsible for the stability of the DNA double helix are presented. 

The regular double-helix structure of DNA, typically called B-DNA, in which two complementary strands are held together by Watson-Crick base pairs, is well recognized. Recently it has been found that under certain conditions DNA can form non-canonical structures, such as Z-DNA, A-motif, G-quadru-plex, i-motif, triplex, hairpin, and erueiform. These structures are particularly seen in the human genome with repeat DNA sequences, which account for more than 50% of the total genomie DNA, while simple sequence repeats account for approximately 3% of the total DNA. Although some of these unusual DNA structures have not been directly detected in vivo, they have been... 

Fig. 2. Hydrogen-bonding patterns in polynucleotides, including Watson-Crick pairing characteristic of duplex DNA and RNA (top) Hoogsteen pairing formed in triplex structures (bottom left) and wobble pairing often found in RNA (bottom right).

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