Nucleic acids double-stranded

Nuclease SI Both a Cleaves single-stranded but not double-stranded nucleic acids... 

Finally, thermal denaturation studies of double stranded nucleic acids in the presence of the interacting species allow one also to draw conclusions on the intercalating abilities of a molecule [49] as the behaviour observed with classical intercalators and pure electrostatic binders are quite different. 

For longer double-stranded nucleic acids such as cDNA [ 200 bp (base pairs) to 1500 bp], the positively charged nylon membrane easily sequestered... 

Figure 1. Progress curves for renaturation of double-stranded nucleic acid fragments (roughly 400 bases/fragment). From Britten and Kohne with permission.

The two major types of nucleic acids are DNA and RNA. Nucleic acids are polyphosphate esters containing the phosphate, sugar, and base moieties. Nucleic acids contain one of five purine or pyrimidine bases that are coupled within double-stranded helices. DNA, which is an essential part of the cell s chromosome, contains the information for the synthesis of protein molecules. For double-stranded nucleic acids, as the two strands separate, they act as a template for the construction of a complementary chain. The reproduction or duplication of the DNA chains is called replication. The DNA undergoes semiconservative replication where each of the two new strands contains one of the original strands. 

Premstaller, A., Oberacher, H., and Huber, C. G., High-performance liquid chromatography-electrospray ionization mass spectrometry of single- and double-stranded nucleic acids using monolithic capillary columns, A a/yft ca/ Chemistry 72(18), 4386 393, 2000. 

Nucleic Acid. A nucleic acid is a natural polynucleotide. It is a sugar-phosphate chain with purine and pyrimidine bases attached to it, as shown in Chart 10. If the sugar is deoxyribose and the pyrimidine bases are cytosine and thymine, the nucleic acid is deoxyribonucleic acid, DNA if the sugar is ribose, and the pyrimidine bases are (mostly) cytosine and uracil, the nucleic acid is ribonucleic acid, RNA. The sequence of bases may appear arbitrary and random, but it constitutes a meaningful code (see Code Word). In double-stranded nucleic acids,... 

The intercalation of polycyclic aromatic compounds into duplex DNA structures was used to develop nucleic acid-based electrochemical sensors.66 For example, the bis-ferrocene-tethered naphthalene diimide (16) was used as a redox-active intercalator to probe DNA hybridization.67 The thiolated probe was assembled on a Au electrode, and the formation of the duplex DNA with the complementary analyte nucleic acid was probed by the intercalation of (16) into the double-stranded nucleic acid structure and by following the voltammetric response of the ferrocene units (Fig. 12.17a). The method enabled the analysis of the target DNA with a sensitivity that corresponded to ca. 1 x 10-20mol. 

Stereoview of the polymerase active site of HIV-1 RT [38]. The amino acid residues that compose the putative dNTP-binding site, including the three catalytically essential aspartic acids, are shown with side chains. The double-stranded nucleic acid is shown with the atomic model in the HIV-1 RT/DNA/Fab complex. The dNTP-binding site consists of structural elements from both protein and nucleic acid. The precise composition, position, and conformation of the template-primer can affect the recognition of... 

FIGURE 8-20 Rilindromes and mirror repeats Fhl indromes are sequences of double-stranded nucleic acids with twofold symmetry. In order to superimpose one repeat (shaded sequence) on the other, it must be rotated 180° about the horizontal axis then 180° about the vertical axis, as shown by the colored arrows A mirror repeat, on the other hand, has a symmetric sequence within each strand. Superimposing one repeat on the other requires only a single 180° rotation about the vertical axis. 

The close interaction between stacked bases in a nucleic acid has the effect of decreasing its absorption of UV light relative to that of a solution with the same concentration of free nucleotides, and the absorption is decreased further when two complementary nucleic acids strands are paired. This is called the hypochromic effect. Denaturation of a double-stranded nucleic acid produces the opposite result an increase in absorption... 

Chemically modified DNAs can also be used as hybridization probes, provided that the modification does not interfere with the formation of hybrid DNA molecules. A psoralen biotin label has also been developed. Psoralen is a photoactivable agent that can intercalates into single- or double-stranded nucleic acids. On irradiation at 365 nm, it will covalently bind to the probes. This labeling reaction is simple and straightforward. However, the reagents for labeling and detection are only available in a kit format. 

Yet again the conclusion can be drawn that all single-stranded RNA viruses are subject to similar restrictions with regard to information content. In nature there are no (single-stranded) RNA viruses whose replicative unit contains more than the order of 104 nucleotides. All larger viruses possess double-stranded nucleic acids or are composed of several... 

Reassociation of double-stranded nucleic acids from various sources. The genome size is indicated by arrows near the upper nomographic scale. Over a factor of lOl0, this value is proportional to the c0t (the cot ) required for half-reaction. All DNAs were sheared so that they have approximately the same fragment size (about 400 nucleotides, single-stranded). Correction has been made to give the rate that would be observed at 0.18 m sodium ion concentration. No... 

The course of a number of other photoreactions could be altered or oriented by selective binding. In particular, substances effecting single- or double-strand nucleic acid recognition and fitted with a photoreactive group may perform sequence specific photocleavage [4.56, 5.29, 5.30]. 

Especially attractive was the possibility to connect nucleosides, as has been realized, for instance, with the hexathymidine 141 and with the elongated and alternating strands 142 and 143. These compounds represent artificial oligonucleosides, which may interact with natural polynucleotides or nucleic acids. On treatment with Cu(i), 142 and 143 gave the double-helical complexes 144 and 145, respectively, inside-out analogues of double-stranded nucleic acids, which may be termed deoxy-... 

Ethidium bromide 510 595 Double-stranded nucleic acids impermeant... 

This acridine orange technique has been taken one step further by Darzynkiewicz s group. Because acridine orange fluoresces red when bound to single-stranded nucleic acid, but green with double-stranded nucleic acid, acridine orange can be used under mildly denaturing... 

Propidium iodide Propidium iodide is a probe that can be used to measure quantitatively the amount of double-stranded nucleic acid that is present in a cell. After treatment of cells with RNase, it will measure the amount of DNA present. Because it does not cross an intact cell membrane, cells need to be treated with detergent or ethanol before it can be used to determine their DNA content. It can also be used to assess the viability of cells. 

Intercalators associate with dsDNA by insertion between the stacked base pairs of DNA [52], EtBr binds to dsDNA with little to no sequence specificity, with one dye molecule inserting for every 4-5 base pairs [53]. It also binds weakly via a non-intercalative binding mechanism only after the intercalative sites have been saturated [54], Propidium iodide (PRO) is structurally similar to ethidium bromide, and both dyes show a fluorescence enhancement of approximately 20-30 fold upon binding to dsDNA [41]. As well, their excitation maxima shift 30-40 nm upon binding due to the environment change associated with intercalation into the more rigid and hydrophobic interior of the double-stranded nucleic acid structure relative to aqueous solution [41]. 

Other commonly used dyes include Hoechst 33258 and DAPI (4/,6-diamidino-2-phenylindole), both of which show selectivity towards poly A-T sequences. This selectivity limits the utility of these dyes as generic transducers in sensor applications. These dyes associate with double-stranded nucleic acids in a groove-binding motif, more specifically, via binding in the minor groove of B-DNA [41]. 

Interestingly, the emission of [Pt(tpy)(OH)]+ is quenched in water, but is restored upon intercalation with double-stranded nucleic acids [poly(dA-dT)]2 and [poly(dI-dC)]2 [73]. Although intercalation can also occur at G-C-rich sequences - and indeed it does so more strongly than for A-T - emission is then quenched by electron-transfer from guanine, the most readily oxidized of the nucleobases. The initial intercalative interactions are probably followed by covalent platination of the DNA, most likely by purine-N7 displacing the OH ligand, reminiscent of cisplatin. The absorption... 

Iqbal, A., Arslan, S., Okumus, B., Wilson, T. J., Giraud, G., Norman, D. G., Ha, T., and Lilley, D. M. J. (2008b). Orientation dependence in fluorescent energy transfer between Cy3 and Cy5 terminally-attached to double-stranded nucleic acids. Proc. Natl. Acad. Sci. USA 105, 11176-11181. 

Jehle, H. Replication of double-strand nucleic acids. Proc. Nat. Acad. Sci. U.S. 53, 1451 (1965). 

Double-stranded right-handed B-DNA has a highly repetitive, negatively charged polyphosphate surface, single-stranded nucleic acids that do not fold up to compact structures are much more flexible than the double-stranded nucleic acids and the predominantly hydrophobic bases are much more exposed. A common feature of all the A-, B- and Z-DNA conformations is that the two chains are antiparallel. 

These results indicate that RNA in a DNA-RNA hybrid is protected from cleavage Ly Eu(L1)3+ under conditions where nearly all other sites in tRNAphe are cleaved. We cannot rule out poorer binding of the metal complex to the hybrid than to RNA alone. There is ample precedence for binding of Eu(III) ions to double-stranded nucleic acids (34). Eu(III) is also known to bind well to pockets in highly structured RNAs such as tRNA (31). It is not known how the europium complex will bind to these different structures. 

Although the base triplets are of only minor importance in double-stranded nucleic acids, they have a structural role in determining and stabilizing the tertiary structure of transfer RNA, as discussed in Chapter 20. Base quadruplets where two Watson-Crick base pairs are associated as shown in Fig. 16.17 have been invoked to play a role in DNA-DNA aggregation and DNA recombination, but there is no direct evidence for their occurrence. 

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