Stacking, base pairing

Figure 12.16), can insert between the stacked base pairs of DNA. The bases are forced apart to accommodate these so-called intercalating agents, causing an unwinding of the helix to a more ladderlike structure. The deoxyribose-phosphate backbone is almost fully extended as successive base pairs are displaced 0.7 nm from one another, and the rotational angle about the helix axis between adjacent base pairs is reduced from 36° to 10°. 

As found for other stacked base pairs, in the stacked thymine-thymine pair changes in the interaction energy upon rotation of one thymine unit are almost completely compensated for by solvation effects [99JPC(B)884]. The adenine-thymine (A-T) base pair, which possesses a significant degree of conformational... 

The results of the various semi-empirical calculations on the reference structures contained within the JSCH-2005 database (134 complexes 31 hydrogen-bonded base-pairs, 32 interstrand base pairs, 54 stacked base pairs and 17 amino acid base pairs) are summarised in Table 5-10. The deviations of the various interaction energies from the reference values are displayed in Figure 5-5. As with the S22 training set, the AMI and PM3 methods generally underestimate the interactions whereas the dispersion corrected method (PM3-D) mostly over-estimates the interactions a little. Overall the PM3-D results are particularly impressive given that the method has only... 

The DNA-lipid cast film was stretched ca. three times in length (ca. 20 p.m thick) in the wet state, and X-ray diffraction patterns are shown in Fig. 7b. When the incident beam was irradiated parallel to the top edge of the stretched film, the circular reflection of 41 A was observed. When the beam was exposed parallel to the side edge and perpendicular to the film plane, the diffraction on the equator appeared as two spots of 41 A indicating a distance between the DNA-lipid strands and the diffraction on the meridian of 3.4 A. The distance between parallel stacked base-pairs was clearly observed [2-4]. These findings clearly show that DNA strands are ahgned... 

Another type of supramolecular interaction of DNA is the intercalation of fused aromatic compounds into the stacked base pairs in double-stranded DNA (see Figure 6). Intercalation induces not only dehydration from the polar groups in intercalator but also concomitant unwinding, lengthening, dehydration, and stiffening of the DNA double helix. 

Because both charge transport and conduction are facilitated by electron motion between stacked base pairs, one expects that single-strand DNA should conduct far less well than double strand. Measurements both of rate constants and of conduction [62] indeed show that single-strand DNA is a far less capable transfer and transport agent for charge than is the duplex. 

Our calculations with several established semiempirical schemes (INDO/S [66], MNDO [67], AMI [68], PM3 [69], and MNDO/d [70]) show that all these methods significantly underestimate the electronic coupling between r-stacked base pairs as compared with HF results. Typically, the matrix elements derived from semiempirical calculations are three to six times smaller ( ) than the corresponding HF values. 

Whereas proteins have their low energy absorption band at 280 nm, polynucleotides typically have maxima at 260 nm (38,500 cm ). A phenomenon of particular importance in the study of nucleic acids is the hypochromic effect. In a denatured polynucleotide the absorption is approximately the sum of that of the individual components. However, when a double helical structure is formed and the bases are stacked together, there is as much as a 34% depression in the absorbance at 260 nm. This provides the basis for optical measurement of DNA melting curves (Fig. 5-45).45,86 The physical basis for the hypochromic effect is found in dipole-dipole interactions between the closely stacked base pairs.7,86,87... 

Fluorescence assays are considered among the most convenient, sensitive, and versatile of all laboratory techniques. However, the purine and pyrimidine bases yield only weak fluorescence spectra. Le Pecq and Paoletti (1967) showed that the fluorescence of a dye, ethidium bromide, is enhanced about 25-fold when it interacts with DNA. Ethidium bromide, which is a relatively small planar molecule (Figure El3.4), binds to DNA by insertion between stacked base pairs (intercalation). The process of intercalation is especially significant for aromatic dyes, antibiotics, and other drugs. Some dyes, when intercalated into DNA, show an enhanced fluorescence that can be used to detect DNA molecules after gel electrophoresis measurements (see Chapter 4 and Experiments 14 and 15) and to characterize the physical structure of DNA. Two analyses of DNA will be completed in this experiment ... 

The right-handed helical structure, known as B DNA, is the most commonly occurring conformation of linear duplex DNA in nature. In this structure, the distance between stacked base pairs is 3.4 A, with approximately 10 base pairs per helical turn. The inherent flexibility of the structure, however, makes a variety of conformations possible under different conditions. In some instances, nucleotide sequence and degree of hydration dictate which conformations are favored. DNA interacts with a variety of proteins inside the cell, and these proteins can also have a significant influence on its secondary and tertiary structure. 

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]. 

Fig. 10 The three-dimensional potential energy surface describing the motion of protons between N6(A) and 04(T) and between N3(T) and N1(A) shows two critical points in the ground state. The deeper minimum corresponds to the amine/keto structure of AT and a shallow one to the imine/enol structure (A T ). Upon absorption of a UV photon the initaly delocalized excitonic states (1) undergo a rapid localization on f 10 ps timescale for single bases and 100 ps timescale for stacked base pairs to form a charge transfer (CT) states. The subsequent CT states passing through a conical intersection are carried back to the ground state.

In this article, we discussed several rigorous ab initio studies, including our own findings, which had recently put the discussion of the nature of intermolecular interactions in nucleic acid base complexes on quantitative basis. The results of computations summarized herein confirm that H-bonded and stacked base pairs are mainly stabilized by electrostatic/delocalization components and dispersion... 

P. Hobza et al., Significant structural deformation of nucleic acid bases in stacked base pairs an ab initio study beyond Hartree-Fock. Chem. Phys. Lett. 288, 7-14 (1998)... 

Co(phen) +/2+, Fe(phen)r/3+. Co(bpy) +/2+, Fe(bpy>r/3+ and Os(bpy)2+/3+ (where phen = 1,10-phenanthroline and bpy = 2,2 -bipyri-dyl). The binding was interpreted in terms of the interplay of electrostatic interactions of the metal coordination complexes with the charged sugar-phosphate backbone and the intercalative, hydrophobic, interactions within the DNA helix, i.e., the stacked base-pairs. Chronopotentiometric detection of the Co(bpy)3+ indicator was used [102] to monitor the hybridization onto a screen-printed carbon electrode of short DNA sequences from E. coli pathogen in environmental water samples. The couple Co(bpy) 5+/2+ was also used to evaluate the adsorption of DNA on gold electrodes [103-104]. 

The DNA helix is stabilized by H bonds between individual base pairs as well as by hydrophobic forces between stacked base pairs. Reagents that reduce the H bonding and decrease the polarity of the surrounding medium, such as formamide, will cause denaturation. Extremes of pH, which endow the bases with a charge, are also effective. Thus, DNA at pH 12 shows absorption at 260 nm that is 40 percent higher than that of the native form. 

Actinomycin D is a commonly used inhibitor of both DNA and RNA synthesis. Its planar structure binds noncovalently between the stacked base pairs of duplex DNA this is called intercalation. In this situation the DNA functions as a poor template. Compounds that bind in a similar way include acridine and ethidium. These affect the fidelity of DNA replication. 

Yes. Actinomycin D blocks transcription by binding to the DNA template. In doing so, it recognizes a common structural feature of all duplex DNAs, binding by intercalation between stacked base pairs (Chap. 16). 

Irrespective of its biological function, the DNA double helix may be described as a prototype 7r-stacked column and therefore a novel medium through which to examine electron-transfer reactions. The double helix is a polymer containing a relatively rigid, electronically coupled column of stacked base pairs within a water-soluble polyanion, the sugar-phosphate backbone. The electronic coupling within the column is reflected in the extensive hypochromicity of the stacked double helix compared to the random coil, and it is this stacking interaction that accounts substantially for the stabilization of the helical form (23). 

The results for covalently bound analogues of [Ru(phen)2(dppz)]2+ and [Rh(phi)2(phen)]3+ intercalated into a 15-mer oligonucleotide therefore demonstrate that photoinduced electron transfer between intercalators can occur rapidly over >40 A through a DNA helix over a pathway consisting of 7r-stacked base pairs. The DNA 7r-stack may be considered a remarkably effective medium for electronic coupling of intercalated species. 

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