A • T base pairing

The DNA part of each control module can be divided into three main regions, the core or basal promoter elements, the promoter proximal elements and the distal enhancer elements (Figure 9.1). The best characterized core promoter element is the TATA box, a DNA sequence that is rich in A-T base pairs and located 25 base pairs upstream of the transcription start site. The TATA box is recognized by one of the basal transcription factors, the TATA box-binding protein, TBP, which is part of a multisubunit complex called TFIID. This complex in combination with RNA polymerase 11 and other basal transcription factors such as TFIIA and TFIIB form a preinitiation complex for transcription. 

Like Thr 124 and Thr 215, the Asn 69 and Asn 159 residues occupy equivalent positions in the two homologous motifs of TBP. By analogy with the symmetric binding of a dimeric repressor molecule to a palindromic sequence described in Chapter 8, the two motifs of TBP form symmetric sequence-specific hydrogen bonds to the quasi-palindromic DNA sequence at the center of the TATA box. The consensus TATA-box sequence has an A-T base pair at position 4, but either a T-A or an A-T base pair at the symmetry-related position 5, and the sequence is, therefore, not strictly palindromic. However, the hydrogen bonds in the minor groove can be formed equally well to an A-T base pair or to a T-A base pair, because 02 of thymine and N3 of adenine occupy nearly stereochemically equivalent positions, and it is sufficient, therefore, for the consensus sequence of the TATA box to be quasi-palindromic. 

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... 

Coll, M., C. A. Erederick, A. H. J. Wang, and A. Rich. A bifurcated hydrogen-bonded conformation in the D(A-T) base-pairs of the DNA dodecamer D(CGCAAATTTGCG) and its complex with distamycin. Proc. Natl. Acad. Sci. USA 1987, 84, 8385-8389. 

Fig. 4.4 Double duplex invasion of pseudo complementary PNAs. In order to obtain efficient binding, the target (and thus the PNAs) should contain at least 50% AT (no other sequence constraints), and in the PNA oligomers all A/T base pairs are substituted with...

The systems reported here are a single turn of B-DNA with G-C, A-T base pair sequence and the left handed Z-DNA with G-C base pair sequence. The B-DNA system is simulated for 4.0 psec and Z-DNA is simulated for 3.5 psec after equilibration. The simulation results are then analyzed for structural and dynamical properties. ... 

The influence of the electronic coupling on the electron transfer rate was determined by changing the length of the (A T)n bridge. As expected, the rate decreased as the number n of the A T base pairs between electron donor and electron acceptor increased [4, 7]. But, surprisingly, the exponential correlation of Eq. (1) between the rate kEr and the distance is not valid for short distances. The plots in Fig. 3 and Fig. 4 show that at 6 A the electron transfer rate /cEt is much faster than expected [4, 7]. 

Similar results are described by K. Nakatani and I. Saito in their article of this volume. The distance effect is in accord with a single step charge shift between the guanines where the A T base pairs act as bridge that are not oxidized during the reaction, as described in the articles of J. Jortner, F.D. Lewis as well as D. Beratan and M. A. Ratner in this volume. 

A T)n sequence. In double strand 21 (Scheme 5) the charge is trapped by a GGG triplet, and it turned out that the hole transport over 8 A T base pairs is nearly as efficient as the hole transport over 2 A T base pairs. 

This almost distance independent hole transfer over (A T)n sequences where adenines are charge carriers is very surprising. Maybe the transfer of a positive charge between adenines of an (A T)n sequence is extremely fast, as recent calculations of M.D. Sevilla predicted [20], One could also speculate that the positive charge is delocalized over more than one A T base pair so that polaron hopping, which is discussed in this volume by G.B. Schuster as well as E.N. Conwell, might make the hole transport in oxidized (A T)n sequences very efficient. 

Hole Transport Across a Single A T Base Pair. 51... 

Values of kcs and kcr for a family of hairpins containing a single G C base pair separated from Sa by one-to-four A T base pairs are summarized in... 

Fig. 4 Free energy dependence of the rate constants for charge separation and charge recombination for hairpins in which two A T base pairs separate the linker acceptor from the nucleobase donor. The dashed line is a fit of the charge separation data to the Marcus-Levitch-Jortner equation...

The dynamics of inter- vs intrastrand hole transport has also been the subject of several theoretical investigations. Bixon and Jortner [38] initially estimated a penalty factor of ca. 1/30 for interstrand vs intrastrand G to G hole transport via a single intervening A T base pair, based on the matrix elements computed by Voityuk et al. [56]. A more recent analysis by Jortner et al. [50] of strand cleavage results reported by Barton et al. [45] led to the proposal that the penalty factor depends on strand polarity, with a factor of 1/3 found for a 5 -GAC(G) sequence and 1/40 for a 3 -GAC(G) sequence (interstrand hole acceptor in parentheses). The origin of this penalty is the reduced electronic coupling between bases in complementary strands. 

St /G AG-0.14 V fluorescence quenching stilbene radical anion detected in transient absorption no Gs near injection site or in intervening sequence k = 1012-108 s 1 for 0-4 intervening A-T base-pairs (-3.4-17 A) exponential distance dependence of CT rate constant (3 0.6-0.7 A"1 small variations in k depending on whether G is in the A or T arm of the hairpin... 

Distance dependence of the hole transfer process from the G-region (5 -GTGTGTG-3 ) to the Py moiety was studied via pulse radiolysis of 5 -Py-conjugated ODNs with a different number of intervening A-T base pairs between the G-region and Py moiety (PyODNn (n= 1 5)) (Scheme 3). Transient absorption with a maximum peak at 470 nm assigned to Py + was observed after the electron pulse during the pulse radiolysis (Fig. 2). This initial for-... 

On the other hand, when the distance between Py and Ptz was longer (PtzPy-3) with five A-T base pairs, the formation and decay of Py + were observed in the time range of 0-100 /zs after an electron pulse. At 100 /US only Ptz + was observed (Fig. 10b). This result indicates that a hole migrates from Py + to Ptz within 100 fis. >From the time profiles of absorption peaks at 470 nm for Py + and 520 nm for Ptz +, secondary formation of Ptz + was also observed concomitant with the decay of Py + for PtzPy-3, while no secondary formation of Ptz + was observed for PtzPy-1 due to the rapid hole transfer (Fig. 10c,d). The rate constant of the hole transfer from Py + to Ptz was determined to be 2.0X104 s 1 for PtzPy-3 from the decay of Py +. 

GG8, the radical cation must traverse five A/T base pairs. Electrochemical measurements in solution have shown that the purine bases (A and G) have considerably lower Eox than the pyrimidines (C and T), with the Eox of G estimated to be about 0.25 V below that of A [20]. It is not very likely that the Eox of bases in DNA will be the same as they are in solution, but it is generally assumed that the order of Eox will remain the same. Consequently, the radical cation at Gi of AQ-DNA(l) must traverse a bridge of five A bases to reach GG8. The process whereby the radical cation crosses such bridges has been a major point of debate in consideration of long distance radical cation migration mechanisms in DNA this issue will be discussed fully below. 

Fig. 6 Structures of AQ-linked DNA oligomers used to assess the effect of converting an A/T base pair to a T/A base pair...

In contrast to the overwhelming affect of conversion of an A/T base pair in AQ-DNA(4) to a T/A base pair in AQ-DNA(5) on radical cation transport, the identical change in AQ-DNA(6) and AQ-DNA(7) has no measurable effect on the amount of strand cleavage observed at GG7 or GG2i [27]. It is apparent from consideration of these results that the effect of a change in base sequence must be considered in the context of the surrounding base pairs and not in isolation. 

The hole-resting-site and polaron-like hopping models can be distinguished by the distance and sequence behavior of radical cation migration. Analysis of the hole-resting-site model leads to the prediction that the efficiency of radical cation migration will drop ca. ten-fold for each A/T base pair that separates the G resting sites [33]. 

With the site-selective hole injection and the hole trapping device established, the efficiency of the hole transport between the hole donor and acceptor, especially with respect to the distance and sequence dependence, were examined. Our experiments showed that hole transport between two guanines was extremely inefficient when the intervening sequence consisted of more than 5 A-T base pairs [1]. Hole injection into the DNA n-stack using photoexcited dCNBPU was accompanied by the formation of dCNBPU anion radical. Therefore, hole transport would always compete with the back electron transfer (BET). To minimize the effect of BET, we opted for hole transport between G triplets, that are still lower in oxidation potential than G doublet. With this experimental system, we researched the effect of the bridging sequence between two G triplets on the efficiency of hole transport [2]. 

The cycloreversion experiments showed a clean Tf=T-DNA to T/T-DNA transformation. No by-products were detected, which supports the idea that DNA may be more stable towards reduction compared to oxidation. Even heating the irradiated DNA with piperidine furnished no other DNA strands other then the repaired strands, showing that base labile sites - indicative for DNA damage - are not formed in the reductive regime. The quantum yield of the intra-DNA repair reaction was therefore calculated based on the assumption that the irradiation of the flavin-Tf=T-DNA strands induces a clean intramolecular excess electron transfer driven cycloreversion. The quantum yield was found to be around 0=0.005, which is high for a photoreaction in DNA. A first insight into how DNA is able to mediate the excess electron transfer was gained with the double strands 11 and 12 in which an additional A T base pair compared to 7 and 8 separates the dimer and the flavin unit. 

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