Polypurine-polypyrimidine

Similar intramolecular processes are known for homop-urine-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. 

For heterogeneous polypurine polypyrimidine tracts, the effect of various divalent metal ions on the transition to and stability of the H-DNA triplexes can be very different depending on the seqnence of snch For... 

Rusche, J.J., and Hurley, L.H., Facilitation of a structural transition in the polypurine/polypyrimidine tract within the proximal promoter region in the human VEGF gene by the presence of potassium and G-quadruplex-interactive agents, Nucleic Acids Res. 33, 6070-6080, 2005. 

The widespread occurrence of polypurine polypyrimidine tracts in eukaryotic DNA suggests that these sequences may have a biological function. Analysis of eukaryotic sequence databases reveals thousands of polypurine polypyrimidine tracts, many with the potential for triplex formation. These polypurine regions of DNA can potentially influence biology in several ways. They could provide binding sites for regulatory proteins, influ-... 

Attention should be given to the selection of primers. Typically, primers used are between 15 and 30 bases in length, with guanine-cytosine composition between 40 and 60%. The primer should not have within its sequence any unusual composition such as stretches of polypurines or polypyrimidines. The primer pair should not be complementary at the 3 ends, since otherwise the DNA synthesizing enzyme can extend one primer over the other primer, creating a double-stranded product whose length approximates the sum of the two primers. This artifact is called primer dimer, which could very well become the predominant and undesirable PCR product when primer pairs complementary at the 3 ends are used (B4, N3). 

A particularly exotic DNA structure, known as H-DNA, is found in polypyrimidine or polypurine tracts that also incorporate a mirror repeat. A simple example is a long stretch of alternating T and C residues (Fig. 8-23). The H-DNA structure features the triple-stranded form illustrated in Figure 8-22 (a, b). Two of the three strands in the H-DNA triple helix contain pyrimidines and the third contains purines. 

Triple-stranded DNA can be generated intermolecularly or intramolecu-larly and can only be formed if one strand of the original B-helix is all purines (A and G) and the corresponding region of the other strand is all pyrimidines. It is more stable at low pH and has a second polypyrimidine strand wound in the major grove of B-DNA where it forms Hoogsteen base-triples with a complementary polypurine strand. Fig. 3.2. Triple-... 

Putative Shine-Dalgamo polypurine sequences can be discerned just upstream from the start codons of the ORFs in all the archaea except the sulfothermophiles the 3 ends of all of the 16S rRNAs exhibit a conserved polypyrimidine sequence. 

DNA-RNA hybrid duplexes are substrates for RNase H and reverse transcriptase. The crystal structure of a hybrid deoxy-polypyrimidine with polypurine RNA has been solved. The structure showed an A-form duplex, and the terminal base pair abuts the minor groove of another duplex creating a bend. RNase H is believed to interact through the minor groove but of an intermediate width between an A- and B-form duplex. The present structure did not exhibit an intermediate width of minor groove. A crystal structure of the chimeric ODN d(CCACTAGTG)rG shows that the presence of the 3 -ribonucleotide induces a... 

H-DNA (triple helix) segments can form when a polypurine sequence is hydrogen bonded to a polypyrimidine sequence. H-DNA, which has been observed to form under low pH conditions, is made possible by nonconventional, Hoogsteen base pairing. H-DNA may play a role in recombination. 

H-DNA a DNA sequence consisting of a polypurine segment hydrogen bonded to a polypyrimidine strand that forms a triple helix involves the formation of nonconven-tional base pairing... 

The set of primers has to be designed specifically for the sample DNA. The primer length is usually 10-30 base pairs (bp) and their complementary sequence must be unique in the template. Additionally, there should be no intra or inter primer complementarity in order to avoid the formation of primer-dimers. Ideally, the number of each base in the primer is relatively equal. Unusual sequences such as long stretches of polypurines or polypyrimidines and repetitive sequences must be avoided. The melting temperature for both primers should be similar and lie between 55 and 80 °C. 

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