Duplexes estimation

In addition, several important questions arise when one discusses large DNA fragments consisting of several base pairs. Even cases where the whole system of interest can be treated by a sufficiently accurate quantum chemical method (often this is impossible), estimates of the electronic coupling within the two-state model may lead to inaccurate results, as demonstrated for tri-mer duplexes [41]. 

Recently, the effects of static and dynamic structural fluctuations on the electron hole mobility in DNA were studied using a time-dependent self-consistent field method [33]. The motion of holes was coupled to fluctuations of two step parameters of a duplex, rise and twist (Fig. 1), namely the distances and the dihedral angles between base pairs, respectively. The hole mobility in an ideally ordered poly(G)-poly(C) duplex was found to be decreased by two orders of magnitude due to twisting of base pairs and static energy disorder. A hole mobility of 0.1 cm V s was predicted for a homogeneous system the mobility of natural duplexes is expected to be much lower [33]. In this context, one can mention several theoretical studies, based on band structure approaches, to estimate the electrical conductivity of DNA [85-87]. 

The first value is the apparent transfer distance, Da(T), which is increased by transfer between duplexes and the second is the transfer distance along one duplex, A(T)- The latter is estimated by Eq. 10, taking n as 6 and the distance between duplexes, D[Pg.121]

The transient absorption spectra of duplexes with [2AP]A4GGAs are depicted in Fig. 5. At a delay time of 100 ns, the transient absorption spectrum is attributed to the superposition of the spectra of the 2AP(-H) and G /G (-H) radical products and the hydrated electrons. The structureless tail of the eh absorption in the 350-600 nm region decays completely within At<500 ns. The formation of G VG(-H) radicals monitored by the rise of the 310-nm absorption band and associated with the decay of the 2AP V 2AP(-H) transient absorption bands at 365 and 510 nm (Fig. 5) occurs in at least three well-separated time domains (Fig. 6). The prompt (<100 ns) rise of the transient absorption at 312 nm due to guanine oxidation by 2AP was not resolved in our experiments. However, the ampHtude, A((=ioo), related to the prompt formation of the G /G(-H) radicals (Fig. 6a) can be estimated using the extinction coefficients of the radical species at 312 and 330 nm (isosbestic point) [11]. The kinetics of the G VG(-H) formation in the yits and ms time intervals were time-resolved and characterized by two well-defined components shown in Fig. 6a (0.5 /zs) and Fig. 6b (60 /zs). 

RNA-DNA double helix, estimated to be 8 bp long (Fig. 26-la). The RNA in this hybrid duplex peels off shortly after its formation, and the DNA duplex re-forms. 

From the observed rate of appearance of point mutations (one mutation per 106 gene duplications), we can estimate that one mutation occurs per 109 replications at a single nucleotide site. Point mutants tend to "back mutate," often at almost the same rate as is observed for the forward mutation. That is, one in 109 times a mutation of the same nucleotide will take place to return the code to its original form. The phenomenon is easy to understand. For example, if T should be replaced by C because the latter formed a minor tautomer and paired with A, the mutation would appear in progeny duplexes as a GC pair. When this pair was replicated, there would be a finite probability that the C of the parental DNA strand would again assume the minor tautomeric structure and pair with A instead of G, leading to a back mutation. 

The d(CGCGAATTCGCG)2 Duplex. When studied at comparable salt (NaCl) and duplex concentrations, the duplex of d(CGCGAATTCGCG) was found to have about the same Tm by DSC measurements (344 K) and by the temperature-dependent changes in the NMR chemical shifts of nonexchangeable GC and AT protons (345 K). At 0.01 M NaCl, the calorimetric enthalpy was 376 kJmol-1 of duplex, while the van t Hoff enthalpy evaluated from equation (16.28) was found to be 393 kJ-mol-1 of duplex. At a 10-fold higher salt concentration, the calorimetric enthalpy was 427 kJ-mol-1 of duplex, while the van t Hoff enthalpy was 310 kJ-mol-1 of duplex. From the ratio of the van t Hoff enthalpy to the calorimetric enthalpy at the higher salt concentration, it was estimated that 9 out of 12 base-pairs melt together in the cooperative unit, while all melt simultaneously at the low salt concentrations. 

Estimation of a Duplex Melting Enthalpy. From the average enthalpies given in Table 16.5, one can estimate the melting enthalpies of an oligonucleotide duplex based on its nucleotide sequence. For example, the oligonucleotide duplex d(ATGCAT)2 has the structure... 

The terms A/T and G/C refer to the number of A-to-T and G-to-C base pairs, respectively, in the duplex strand. The Wallace rule was designed for duplex strands of 14 to 20 base pairs. The Tm of RNA-RNA and DNA-RNA duplexes may be estimated with Equation 6.2.7... 

Calculation of As was carried out for hole transfer in finite DNA duplexes in water, in which one strand includes a G3(T) G3 sequence, n = 0-6, where G and T are, respectively, guanine and thymine nucleotide bases (in the complementary strand, of course, G and T are paired respectively, with cytosine and adenine bases) [23], The D and A sites (the solute) were taken as the middle unit of each G3 triad, or as alternative models for the n = 0 case, using one or both of the inner members of the G3 units). These structures lead to D/A sites in contact or separated by intervening bases ranging in number from 1 to 8. Using a base stacking separation of 3.4 A yields rDA = (m+ 1) (3.4 A), m = 0-8 (an estimate closely supported by detailed molecular force field calculations). 

The thermal stability of a short DNA duplex can be estimated by the simple 4 + 2 rule each GC pair contributes 4° and each AT pair contributes 2° to the duplex melting temperature in 0.9 M NaCl solution.50 Although more rigorous estimates of duplex stability are possible,51 this simple method is reasonably accurate, and, in any event, we find it useful... 

It is important to estimate the size of denatured single-copy tracer DNA. Relative to unsheared DNA, fragmented DNAs have a Tm that is lower by 500/duplex length in degrees Celsius. The size of single-stranded tracer DNA can be estimated using alkaline gel electrophoresis.8,23 A practical consideration is that the capacity of hydroxyapatite is about 100 /tg of DNA per 400 mg of hydroxyapatite. 

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