Complementary regions

For this hybridization strategy to work, the two probes (the capture and the labeled probe) should be from two adjacent portions on the genome, but without having complementary regions, thus avoiding binding of probes to each other. This hybridization requires target sample to bind to both the capture and the labeled probe and, as such, is more specific than direct hybridization on a membrane filter. 

Elicitation of sweetness is explained by the AH—B—X Theory, or the Sweetness Triangle (1,23,24), wherein AH and B represent a hydrogen donor and acceptor, respectively, of sucrose. These interact with complementary regions of taste-receptor proteins. An extended hydrophobic region (X) of sucrose docks in a hydrophobic cleft of the receptor, facilitating optimal electrostatic interaction and sensory stimulation. The C2- and C3-hydroxyls of glucose (AH and B, respectively) and the back side of the fmctose ring (X) are critical to this interaction (1). 

Kinetic analysis indicates that renaturation is a two-step process. In the slow step effective contact is made between two complementary regions of DNA originated from separate strands. This rate-limiting step called nucleation is a function of the concentration of complementary strands. Nucleation is followed by a relatively rapid zippering up of adjoining base residues into a duplex structure. The steps involved in denaturation and renaturation are depicted in figure 25.14. 

Hairpin loop. A single-stranded complementary region that folds back on itself and base-pairs into a double helix. 

Unlike the double-stranded nature of DNA, RNA molecules usually occur as single strands. This does not mean they are unable to base-pair as DNA can. Complementary regions within an RNA molecule often base-pair and form complex tertiary structures, even approaching the three-dimensional nature of proteins. Some RNA molecules, such as transfer RNA (tRNA) possess several helical areas and loops as the strand interacts with itself in complementary sections. Other hybrid molecules such as the enzyme RNase P contain protein and RNA portions. The RNA part is highly complex with many circles, loops, and helical regions creating a convoluted structure. 

It must be noted that, unlike the partially folded states, the totally unfolded state lacks a complementary region. The immediate consequence of this property is that partially folded states always expose to the solvent structural regions for which there is not a corresponding configurational entropy gain (Freire and Murphy, 1991). 

RNA The secondary structure of RNA consists of a single polynucleotide. RNA can fold so that base pairing occurs between complementary regions. RNA molecules often contain both single- and double-stranded regions. The strands are antiparallel and assume a helical shape. The helices are of the A-form (see above). 

The structure of t (transfer) and r(ribosomal) RNA consists of multiple, single stranded, stem-loop structures. The stems consist of helices formed by base pairing of complementary regions within the RNA. The secondary structure of tRNA and rRNA are important for their biological functions, mRNA also assumes some degree of secondary structure but not to the same extent as tRNA and rRNA. 

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