Double-stranded structures

The conformational transitions in the presented model take place accord-itig to the all-or-nothing law, i.e. they occur at the certain r.h. value. The same behaviour has been observed, for example, for the helix-coil transition of the model double-stranded structure A(pA)i7-U(pU)i7 [24]. It is worth noting that this structure is homogeneous, the same is supposed in our model. 

The double-stranded structure of DNA can be separated into two component strands (melted) in solution by increasing the temperature or decreasing the salt concentration. Not only do the two stacks of bases puU apart but the bases themselves unstack while still connected in the polymer by the phosphodiester backbone. Concomitant with this denaturation of the DNA molecule is an increase in the optical absorbance of the purine and pyrimidine bases—a phenomenon referred to as hyperchromicity of denaturation. Because of the... 

Figure 35-4. The double-stranded structure of DNA and the template function of each old strand (dark shading) on which a new (light shading) complementary strand is synthesized.

Incorporation of a flavin electron donor and a thymine dimer acceptor into DNA double strands was achieved as depicted in Scheme 5 using a complex phosphoramidite/H-phosphonate/phosphoramidite DNA synthesis protocol. For the preparation of a flavin-base, which fits well into a DNA double strand structure, riboflavin was reacted with benzaldehyde-dimethylacetale to rigidify the ribityl-chain as a part of a 1,3-dioxane substructure [49]. The benzacetal-protected flavin was finally converted into the 5 -dimethoxytri-tyl-protected-3 -H-phosphonate ready for the incorporation into DNA using machine assisted DNA synthesis (Scheme 5a). For the cyclobutane pyrimidine dimer acceptor, a formacetal-linked thymine dimer phosphoramidite was prepared, which was found to be accessible in large quantities [50]. Both the flavin base and the formacetal-linked thymidine dimer, were finally incorporated into DNA strands like 7-12 (Scheme 5c). As depicted in... 

Base pair (bp) The four nucleotides in the DNA contain the bases adenine (A), guanine (G), cytosine (C), and thymine (T). Two bases (adenine and thymine or guanine and cytosine) are held together by weak bonds to form base pairs. The two strands of human DNA are held together in the shape of a double helix by those bonds between base pairs. For example, the complementary nucleic acid base sequence to G-T-A-C that forms a double-stranded structure with the matching bases is C-A-T-G. 

While RNA molecules do not have the double stranded structure usually found in DNA, in many RNA molecules stem-loop structures are found in which the anti-parallel strands are connected by a 5-7 residue loop. Rather like the P-tum in proteins, this allows the... 

In contrast to DNA, which is quite generally found in a double-stranded structure, RNA is generally, but not always, found in nature as a single-stranded molecule. There are, as always, exceptions, one of which we note below. Double-stranded RNAs as well as hybrid DNA RNA double-stranded molecules are found. 

Although dsDNA can be adsorbed at the GC surface, it is not easily oxidized while ssDNA can be easily adsorbed and oxidized, giving higher oxidation signals, which is attributed to the oxidation of G ( 0.8 V) and A ( 1.1, vs SCE) respectively [38]. The dsDNA structure had greater difficulty transferring the electrons from the inside of the double-stranded structure to the electrode surface than the flexible ssDNA structure where the bases are in closer proximity to the GC surface. 

Polymer chains based on spiro structures have been studied as another route to heat-resistant polymers [Kurita et al., 1979]. A spiro structure is a double-strand structure (Sec. l-2c) in which the uninterrupted sequence of rings have one atom in common between adjacent rings. (Adjacent rings in ladder polymers have two or more atoms in common.) An example of a spiro polymer is the polyspiroketal synthesized from 1,4-cyclohexanedione and pentaerythri-tol (Eq. 2-249). The low solubility and intractability of spiro polymers makes it difficult to synthesize or utilize high-molecular-weight polymers. 

Fig. 1. Southern blot analysis of DNA showing (a) step 1, an agarose gel containing separated restriction fragments of DNA, denoted by (—), which is immersed in NaOH to denature the double-stranded structure of DNA, and then transferred by capillary flow to a nitrocellulose filter. In step 2, the bound DNA is allowed to hybridize to a labeled nucleic acid probe, and the unbound probe is washed off. In step 3, the filter is placed into contact with x-ray film resulting in (b) bands of exposure on the film which are detected after development and correspond to regions where the restriction fragment is...

Most plasmids are topologically closed circles of DNA. They can be separated from the bulk of the chromosomal DNA by virtue of their resistance to alkaline solution. The double-stranded structure of DNA is denatured at high pH, but because the two strands of the plasmid are topologically joined they are more readily renatured. This property is exploited in rapid procedures for the isolation of plasmid DNA from recombinant microorganisms (5,6). 

Complete denaturation of DNA leads to separation of the two complementary strands. If a solution of denatured DNA is cooled quickly, the denatured strands remain separated. However, if the temperature is held for some time just below Tm (a process known as annealing), the native double-stranded structure can be reformed. An important tool for studying DNA has been the measurement of the kinetics of reassociation of separated strands of relatively short DNA fragments.72 556 557... 

The enzyme is very sensitive to the secondary structure of the substrate. Native calf thymus DNA is quite resistant to enzymic attack by spleen exonuclease, being split at less than 4% the rate at which alkali-denatured DNA is split (11). Long deoxyribonucleotides (average chain length 20-50), which still have complementary double-stranded structure, are rather resistant to the enzyme (26). Some limited results obtained with synthetic polyribonucleotides (11) are rather puzzling since poly C was found to be completely resistant, whereas poly A, poly I, and poly U were degraded at comparable rates. In the solvent used (0.15 M acetate buffer-0.01 M EDTA, pH 5.0), poly A and poly C are believed to have... 

A recent study has shown that two different kinds of conformational changes, helix-coil transition and the folding transition, mutually interfere with each other in a drastic manner (Mikhailenko et al., 2000). As the melting of the double stranded structure, or helix-coil transition, is an essential process in the genetic activity, further studies on the biological role of the conformational change of DNA are awaited. 

Double-Stranded Helix In most cases, DNA found in the nucleus of a cell is a helical double-stranded structure. Figure 12.63 represents the double-strand structure of a short section of DNA. The double strand is rather like a ladder. The sides of the ladder are formed by the phosphate sugar backbone. The rungs of the ladder are formed by the nitrogeneous bases. 

Double-stranded DNA denatures into single strands as the temperature rises but renatures into a double-stranded structure as the temperature falls. Any two single-stranded nucleic acid molecules can form double-stranded structures (hybridize) provided that they have sufficient complementary nucleotide sequence to make the resulting hybrid stable under the reaction conditions. 

Table 5. First Platination Rate Constants. Influence of the nature of Y in cis-[PtY(NH3)2(H20)] and of the single- or double-stranded structure of the oligonucleotide...

Vardevanyan, P.O., Antonyan, A.P., Parsadanyan, M.A., Davtyan, H.G. and Karapetyan, K.T. (2003). The binding of ethidium bromide with DNA interaction with single- and double-stranded structures. Experimental and Molecular Medicine, 35, 527-533. 

Nucleic adds are well-known to play an important role in both the replicative and the transcriptive functions of the genetic codes. DNA, one of the nucleic adds, for example, has a double stranded structure consisting of two polynucleotide chains twisted about each other in a double helix, which is stabilized by spedal base-base interactions of nudeic adds. The interactions among such purine and pyrimidine families are apparently a common subject of substantial interest among chemists in the fields of organic, macromolecular, and biochemical syntheses. 

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