Double-helical regions

The duplex with the normal HBB gene has one hydrogen-bonded base pair more than the duplex with the mutated HBB gene, and therefore the first duplex has more double-helical region. The single-nucleotide mismatch has a significant effect on the structure of the duplexes, which in turn strongly influences the local environment where the clusters could form. 

Transfer RNA comes in many different types that can be distinguished by details in their nucleotide sequence. Regardless of sequence differences, all tRNA molecules fold up into the same general structure with several short double-helical regions... 

The clover-leaf pattern of Figure 25-26 shows the general structure of tRNA. There are regions of the chain where the bases are complementary to one another, which causes it to fold into two double-helical regions. The chain has three bends or loops separating the helical regions. 

Pol I also has 5 — 3 -exonuclease activity that is different from the 3 — 5 -exonuclease action. It hydrolyzes DNA from the 5 end of a chain, cleaving a bond in the double-helical region at the terminal phosphodiester bond or a bond several residues distant from the 5 terminus. Either deoxy- or ribonucleotides can be removed. In fact, the main function of the 5 —> 3 exonuclease activity may be to remove ribonucleotide primers (p. 308). This activity can also excise thymine dimers formed by exposure to ultraviolet (UV) light. The three Pol I enzymatic activities are located at distinct sites (domains). 

There are a greater variety of RNA forms, with molecular weights in the range 25,000 to several million. Most RNAs contain a single polynucleotide chain, but this can fold back on itself to form double-helical regions containing A U and G C base pairs. 

Other DNA polymerases are known. DNA polymerase II and III are produced by the poZB and dnaA genes of E. coti They are similar to DNA polymerase I in most properties. They differ however, in template preferences. While DNA polymerase I acts best to fill in extended single-stranded regions near double-helical regions, DNA polymerases II and III act optimally on double-stranded DNA templates that have short gaps. 

Certain RNAs also possess substantial amounts of tertiary structure. Tertiary structure in RNA refers to the folding of secondary structural elements, such as double helical regions or hairpin stem-loops, into discrete three-dimensional structures. Forces involved in stabilizing such interactions are diverse, involving hydrogen-bonding, base... 

Fig. 20.8. Three-dimensional structure of phenylalanine specific tRNA from yeast. Watson-Crick type base pairs indicated by slabs, nonstandard base-base interactions that stabilize the tertiary structure are denoted a to h. Invariant and semi-invariant nucleotides are shaded, the four double helical regions are indicated by a a-(amino add) arm, Tarm, D arm, a.c. (anticodon arm [696]...

It is impossible for DNA to act as a direct template in the ordering of amino acids in protein synthesis, because almost all DNA is located in the nucleus and protein synthesis occurs in the cytoplasm. The genetic information in DNA is transcribed to the intermediate RNA molecule that moves to the cytoplasm, where it directs the synthesis of the gene product on the ribosomes. The RNA differs chemically from the DNA in that the sugar molecule is ribose and thymine in DNA is replaced by uracil in RNA. Structurally, RNA is predominantly a single-stranded molecule with short, double helical regions providing some three-dimensional structure. 

In RNA, the original set consisting of the Watson-Crick base pairs is complemented by the G-U wobble pair, which is admissible in RNA double helices. Other admissible bps include U-U in internal loops as well as A-A, G-A or G-G (purine-purine closing pairs) at the ends of double helical regions or in multiloops. The secondary structures, which can be drawn in two dimensions without knots or pseudoknots, are indispensable for the... 

Figure 11.13 A portion of RNA that has folded back on itself and formed a double-helical region. 

Phosphate ester Double helical region Amylosc I oToToToTo ... 

In summary, the comparison of K " and Mg samples shows the following The influence of Mg " ions on the formation of the double helical regions is not very different from that of K ions. With the backbone, Mg ions favor the secondary structure formation to a slightly larger extent than ions. But neither the Mg ... 

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