Double-helical structured regions

In modern experiments one is now able to place selectively spin labels in most any region of a biomolecule. This ability is stimulating an ever increasing usage of spin label EPR spectroscopy. In addition labeling of proteins and peptides, experiments have demonstrated that DNA may be labeled without perturbation of the double-helical structure. Analysis of DNA flexibility may provide important information toward the understanding of protein-DNA and drug-DNA interactions. 

Double helical structures have been proposed for the crystalline regions of A- and B-type starches which differ from each other in the manner of the packing of the double helical chains. These chains each contain six glucose units per turn of the helix whose pitch is 21 A. Water molecules pack the spacings between the parallel chains (Figure 10.7). 

A pseudoknot is a double-hairpin structure with an extended quasi-continuous double-helical stem region (Fig. 1.15). It is formed when bases outside a hairpin structure pair with bases within the hairpin or internal loop (111,112). The pseudoknot is a potentially important tertiary structural motif of RNA and it has been identified in 16S rRNA, U2 snRNA, and some plant viral RNAs with tRNA-... 

The structures shown in Fig. 4-1 are for B-form DNA, the usual form of the molecule in solution. Different double-helical DNA structures can be formed by rotating various bonds that connect the structure. These are termed different conformations. The A and B conformations are both right-handed helices that differ in pitch (how much the helix rises per turn) and other molecular properties. Z-DNA is a left-handed helical form of DNA in which the phosphate backbones of the two antiparallel DNA strands are still arranged in a helix but with a more irregular appearance. The conformation of DNA (A, B, or Z) depends on the temperature and salt concentration as well as the base composition of the DNA. Z-DNA appears to be favored in certain regions of DNA in which the sequence is rich in G and C base pairs. 

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. 

In contrast to DNA, RNAs do not form extended double helices. In RNAs, the base pairs (see p.84) usually only extend over a few residues. For this reason, substructures often arise that have a finger shape or clover-leaf shape in two-dimensional representations. In these, the paired stem regions are linked by loops. Large RNAs such as ribosomal 16S-rRNA (center) contain numerous stem and loop regions of this type. These sections are again folded three-dimensionally—i.e., like proteins, RNAs have a tertiary structure (see p.86). However, tertiary structures are only known of small RNAs, mainly tRNAs. The diagrams in Fig. B and on p.86 show that the clover-leaf structure is not recognizable in a three-dimensional representation. 

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... 

Figure 20-3 Proposed structure of a molecule of amylopec-tin in a starch granule. The highly branched molecule lies within 9 nm thick layers, about 2 / 3 of which contains parallel double helices of the kind shown in Fig. 4-8 in a semicrystalline array. The branches are concentrated in the amorphous region.113 114 121 Some starch granules contain no amylose, hut it may constitute up to 30% by weight of the starch. It may he found in part in the amorphous bands and in part intertwined with the amylopectin.122...

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