Specificity flanking sequence effect

C PCR entails enzymatic amplification of specific DNA, " sequences using two oligonucleotide primers that 1 flank the DNA segment to be amplified (fig. 27.2). The primers must complement opposite strands so that after annealing, their 3 ends in effect face each other (see fig. 21.2b). 

The three class I ADH promoters are very similar. Prominent among the ds-act-ing elements that contribute to promoter function are the TATA box, a pair of C/ EBP sites (that can also be bound by DBP) flanking the TATA box, an E-box sequence (CACGTG) just upstream at which USF can bind, and a G3T sequence (that binds Spl) one helical turn further upstream from the E-box [28, 29]. Further upstream are CTF/NF-1 and HNF-1 sites, and some elements that are specific to only some of these genes [24]. Differences among the class I genes in these and other sites affect the tissue distribution and amount of expression. Sequence differences among individuals could well affect the level and site(s) of expression, and thereby the effects of alcohol. 

A series of heptameric single-stranded (ss) DNAs and RNAs having a central 9-guanylate ion have been investigated by 31P NMR spectroscopy in order to determine its effect on each of the flanking phosphate moieties. The results showed that the ssR-NAs, but not the ssDNAs, were affected, the electronic properties and chemical reactivities of the internucleotidic phosphates being dissimilar in a sequence-specific manner... 

---