Self-complementary sequences

We still need to clear up one or two points of nomenclature in normal replication of nucleic acids, the matrix (the + strand) and the newly formed daughter strand (- strand) are held together by Watson-Crick hydrogen bonding. This process is also referred to as cross-catalytic . Normal autocatalysis is different it leads to a product which corresponds in structure to the matrix, so that there is no difference between the + and - strands. Such self-complementary sequences are called palindromes. 

Most p-independent terminators have two distinguishing features. The first is a region that produces an RNA transcript with self-complementary sequences, permitting the formation of a hairpin structure (see Fig. 8-2la) centered 15 to 20 nucleotides before the projected end of the RNA strand. The second feature is a highly conserved string of three A residues in the template strand that are transcribed into U residues near the 3 end of the hairpin. When a polymerase arrives at a termination site with this structure, it pauses (Fig. 26-7). Formation of the hairpin structure in the RNA disrupts several A=U base pairs in the RNA-DNA hybrid segment and may disrupt important interactions... 

The most common type of oligonucleotides studied in the early work of the Breslauer research group involved self-complementary sequences. For example, the sequence d(GCGCGC) can form a duplex in a process according to... 

Tetranucleotides containing dG dC base pairs form stable duplexes at low temperature so that the self-complementary sequences dC-dC-dG-dG [contains dC(3 -5 )dG but no dG(3 -5 )dC binding sites] and dG-dG-dC-dC [contains dG(3 -5 )dC but no dC(3 -5 )dG binding sites] serve as excellent oligonucleotide duplexes for differentiating pyrimidine(3 -5 )purine specificity from purine(3 -5 )pyrimidine specificity associated with drug complexation (66, 67). ... 

Primer dimer formation can be a potential problem in PCR amplifications. Although we generally avoided the use of self-complementary sequences when designing primers, we found that dimer formation was not a problem at an annealing temperature of 35° even when 6 bases of a 10-bp primer could potentially hybridize. 

DNA sequence located roughly 20 bases on the 5 side of the termination site. The RNA produced on transcription of this region is able to form a hairpin structure that causes the RNA polymerase to stall and eventually dissociate from the DNA template. A stretch of uridyl nucleotides at the 3 end of the RNA hairpin is part of the rho-inde-pendent terminator sequence that is also believed to help destabilize the enzyme-DNA complex. A rho-dependent terminator also contains a self-complementary sequence capable of forming a hairpin structure. In an unknown mechanism, the rho protein hydrolyzes ATP and destabilizes the RNA polymerase-DNA complex as it stalls at the hairpin, eventually leading to the termination of transcription. 

RNA polymerase proceeds along the DNA template, transcribing one of its strands until it reaches a terminator sequence. This sequence encodes a termination signal, which in E. coli is a base-paired hairpin on the newly synthesized RNA molecule (Figure 5.28). This hairpin is formed by base pairing of self-complementary sequences that are rich in G and C. Nascent RNA spontaneously dissociates from RNA polymerase when this hairpin is followed by a string of U residues. 

Most p-independent terminators have two distinguishing features. The first is a region that produces an RNA transcript with self-complementary sequences, permitting the formation of a hairpin structure (see Fig. 

The presence of self-complementary sequences (called palindromes) within a single strand of polynucleotide can cause the palindromic portion of it to form intramolecular base pairs (Figure 4.27 and Figure 4.28). tRNAs and rRNAs have extensive base pairing of this type, although it can happen in DNA too. 

The hexose rings in these analogues have a different regiochemistry of attachment to the backbone - C-6, C-4 in h-DNA and C-4, C-2 in p-RNA - and the base stacking is different. For example, studies of self-complementary sequences, such as 5 -TTTTAAAA-3 and 5 -AAAATTTT-3, which show equivalent energies with native duplexes, are quite different with the modified backbones. In p-RNA, the for the duplex of the first sequence is much higher than that of the second. In h-DNA, the situation is reversed and the duplex of the second sequence is more stable than the first. The different backbones have been proposed to alter the inclination between the backbone... 

For bimolecular structures (duplexes), it is generally recommended that self-complementary sequences be avoided, since they have high propensity to form competing hairpin structures. Even non-self-complementary duplexes can some-... 

Note the fourfold difference in equations 17 and 20 which is ultimately reflected in the different concentration dependence of the for self-complementary versus non-self-complementary sequences (equation 3). 

Self-complementary sequences. For self-complementary duplexes, 7, (in Q is given by ... 

Non-self-complementary sequences. If the strands are present in equal concentrations ... 

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