Double-helical secondary regions

The left-handed Z-DNA structure of poly[d(A-T)] poly[d(A-T)] as well as poly[d(A-C)] poly[d(G-T)] in the presence of Ni ions leads to characteristic IR and Raman spectra. Markers for these particular double-helical secondary structures are Raman frequency (phos-phodiester chain vibration at 746 and 815 cm syn geometry of the purines evidenced by a breathing mode coupled to the deoxyribose vibration at 622 cm a characteristic profile in the 1300-1400 cm region with a shift of the 1374 cm purine line lo lower wavenumbers correlated with the antijsyn reorientation of the nucleosides under the B - Z transition. " ... 

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... 

The secondary clover-leaf structure of tRNA is stabilized by Watson-Crick base pairs. The tRNA s are a large family of molecules consisting of 71 to 76 nucleotides, with about 10% of rare bases (Fig. 15.2). The known nucleotide sequences of over 200 tRNA s [695J can be arranged in a characteristic clover-leaf model with four double helical stems and three loop regions. In some of the positions, the same nucleotide occurs, called invariant, in others only the type is conserved, i.e.,... 

Base pairing between nucleic acid bases can occur in RNA with adenine pairing with uracil, and cytosine pairing with guanine. However, the pairing is between bases within the same chain, and it does not occur for the whole length of the molecule (e.g. Fig. 6.18). Therefore, RNA is not a double helix, but it does have regions of helical secondary 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... 

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 ... 

In contrast to Mg + and Mn +, which stabilize secondary structures in DNA and RNA, Cu + destabilizes DNA and RNA double helices, and this is attributed to the ability of copper to bind to the nucleic acid bases. Chao and Kearns have recently explored the possibility that this binding, as detected by electron and nuclear magnetic resonance spectroscopy, might be used to probe certain structural features of nucleic acid molecules, such as the looped out regions of tRNAs. The nature of the Cu complexes formed with nucleosides and nucleotides varies with the specific nucleic acid derivatives used and also the pH. Thus, in the pH range 8.5—10.0, copper forms a water-soluble complex with the ribose OH groups of the ribonu-cleosides and 5 -ribonucleotides, but these complexes cannot form with any of the deoxynucleosides or the 2 - and 3 -ribonucleotides. It is suggested that copper(ii) could stabilize unusual polynucleotide structures or interactions in certain enzymatic systems the latter could, for example, be responsible for translational errors in the RNA,DNA polymerase system which are known to be induced by transition metals. 

The structure of tRNA has been estabUshed in greater detail. These naturally occurring nucleic acids are the smallest so far isolated and in many cases the sequence has been determined. The clover leaf model, first proposed by Holley et al. (1965) is now generally accepted as a description of secondary structure in these biologically important nucleic acids. The tertiary structure has not been completely elucidated but it is clear that the molecule is extremely compact and is composed of double-helical regions with hairpin loops containing five to seven nucleotides. The structure is quite stable and is probably more compact than that of rRNA. 

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). 

RNA chains are usually single-stranded and lack the continuous helical structure of double-stranded DNA. However, RNA still has considerable secondary and tertiary structure because base pairs can form in regions where the strand loops back on itself. As in DNA, pairing between the bases is complementary and antiparallel. But in RNA, adenine pairs with uracil rather than thymine (Fig. 12.18). Basepairing in RNA can be extensive, and the irregular looped structures generated are... 

The reactive -NHj, -OH and -NH groups of purine and pyrimidine bases are responsible for certain properties of N.a., e.g. formation of specific hydrogen bonds between purines and pyrimidines, leading to secondary structures. Thus complementary linear chains can form a double helix (see DNA), or a linear strand can fold on itself, forming alternate linear and helical regions (RNA). Other forces involved in the... 

Knowledge of the secondary structure also allowed correlation of the CD spectra and the type of helicity. For example, in the case of poly-(/ )-2/Ba , a positive Cotton effect at the vinylic region corresponds to a clockwise sense at the conjugated double bonds. 

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