Homopurine-homopyrimidine

DNA is prone to structural polymorphism its sttucture can differ markedly from the classical donble hehx. For example, under snperhehcal stress, circnlar closed DNA can adopt an unnsnal structure, denoted H-DNA, in which homopurine-homopyrimidine tracts unwind and ntUize the pyrimidine-rich strand to form an intramolecnlar triplex with another homopnrine homopyrimidine tract the remaining purine single strand is left unpaired. The formation of H-DNA reqnires the presence of metal ions such as Mg + or... 

Frangois et al. (1989) designed a 17-mer homopyrimidine oligomer to recognize, via Hoogsteen pairing, a 17-bp homopurine-homopyrimidine sequence. Inhibition of restriction in this sequence could be obtained in the micromolar range (Fig. 12.4 (III)). 

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. 

Similar intramolecular processes are known for homopurine-homopyrimidine tracts in circular covalently closed DNA. Under the superhelical stress in such circular DNA, half the pyrimidine strand is unpaired and forms Hoogsteen base pairs with the remaining polypurine-polypyrimidine duplex. 

Some sequences in DNA have a marked propensity to adopt altered conformations within the double helix. Homopurine-homopyrimidine sequences,... 

Base triads do, of course, occur in nucleic acid triplexes. However, tetraplex structures may also contain triads and in RNA structures triads often play a crucial role. Triplexes are formed by the interaction of a third strand in the major groove of a double helix. The duplex has to be composed of a homopurine-homopyrimidine sequence (piuine - R, pyrimidine - Y). The third strand can bind in a parallel or antiparallel orientation to one of the duplex strands. In parallel orientation, a homopyrimidine third strand binds to the homopurine strand of the duplex (YRY). This leads to the two canonical triads TAT and C+GC. Protonation of C (C+) at N3 is required for the formation of two H-bonds between C and G. Therefore, parallel triplexes are pH dependent. These structures have two canonical base triads TAT and C+GC. For an antiparallel orientation of the third strand relative to the binding duplex strand, a homopruine sequence is required that binds to the homopurine strand of the duplex (RRY). This results in the canonical triads GGC, AAT and TAT, where however the TAT triad is different to the corresponding triad in parallel triplexes. In addition to these standard triads, triplexes can also accommodate non-canonical base triads. Fig. 3 shows the two canonical triads C+GC and TAT in an intra-molecular triplex consisting of a DNA duplex and... 

Lyamichev, V.I., Mirkin, S.M., Frank-Kamenetskii, M.D., 1985. A pH-dependent structural transition in the homopurine-homopyrimidine tract in superhelical DNA. J. Biomol. Struct. Dyn. 3 327-338. 

The central strand of the triplex must be purine rich since a pyrimidine does not have two hydrogen bonding surfaces with more than one hydrogen bond. Thus triple-stranded DNA requires a homopurine homopyrimidine region of DNA. If the third strand is purine rich, it forms reverse Hoogsteen hydrogen bonds in an antiparallel orientation with the purine strand of the Watson-Crick helix. If the third strand is pyrimidine rich, it forms Hoogsteen bonds in a parallel orientation with the Watson-Crick paired purine strand. 

The urocanamide derivative (96) has been assessed for stabilising triple-helices, and was shown to have specific recognition of a CG inversion of a homopurine-homopyrimidine duplex.The pteridone (97) has been used as a fluorescent sensor for melting transitions in A-tract DNA, where it was found to be more sensitive than in UV melting spectroscopy. ... 

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