Base sequence, effect

Keywords Long-distance charge transport DNA damage Polaron hopping Ion gated base sequence effects... 

Base Sequence Effects on Radical Cation Migration in DNA -... 

Fig. 7 Structures of AQ-linked DNA oligomers containing a regularly repeating sequence of base pairs that were used to assess the effect of base sequence effects on long-distance radical cation migration...

Base Sequence Effects on the Rates of Guanine Oxidation. 144... 

The [2AP]A GGAi2- and [2AP]T GGTi2- oligonucleotides containing a single 2AP residue and a single GG doublet separated only by adenine (n=0, 2, 4, 6, 8) or thymine (n=0, 1, 2, 3, 4) bases were used to study base sequence effects on electron transfer at a distance. The [2AP]Ai4 and [2AP]Ti4 oligonucleotides were used as controls. All of the duplexes exhibit well-defined... 

Base Sequence Effects on Excess Electron Transfer. Cai et al.69 investigated low temperature electron and hole transfer to intercalator trapping sites in various polynucleotide duplexes and compared them with previous results found for salmon sperm DNA. Electron and hole transfer in DNA was found to be base sequence dependent. In glassy aqueous systems (7 M LiBr, D20 glasses at 77 K), excess electron-transfer rates increase in the order polydldC-polydldC < DNA... 

Liu C-S, Schuster GB (2003) Base sequence effects in radical cation migration in duplex DNA support for the polaron-like hopping model. J Am Chem Soc 125 6098-6102 Llano J, Eriksson LA (2004) First principles electrochemical study of redox events in DNA bases and chemical repair in aqueous solution. Phys Chem Chem Phys 6 2426-2433... 

We first consider why base sequence effects can affect the thermodynamic stabilities of double-stranded DNA. The neighboring base-base stacking energies have been analyzed in detail (e.g., see [116, 117]). These interactions are base sequence dependent because of potential steric clashes and electrostatic effects between the... 

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 primary conclusion that follows from the effect of base sequence on the efficiency of radical cation migration through duplex DNA is that base pairs cannot be considered in isolation. For example, the effect of placing a T in a sequence of purines depends critically on the nature and number of purines. In this regard, the effect of base sequence on radical cation transport emerges from examination of collective properties of the DNA. This is a clear indication that the charge is delocalized over several base pairs, a conclusion that is supported by extensive quantum calculations. 

Mutations are often classified according to the effect they have on the structure of the gene s protein product. This change in protein structure can be predicted using the genetic code table in conjunction with the base sequence of DNA or mRNA. A variety of such mutations is listed in Table 1-4-1. Point mutations and frameshifts are illustrated in more detail in Figure 1-4-2. 

At Oak Ridge, the focus was to develop specific-sequence DNA to improve the diffraction quality of NCP crystals. The positioning of the DNA on the histone core has to be precise so that all the NCPs are identical. A project was undertaken to understand the DNA sequence effects on nucleosome phasing [25]. Second, a DNA palindrome was developed to extend the two-fold symmetry of the histone core to the DNA. The objective was to eliminate the two-fold disorder caused by the indeterminacy of packing of an asymmetric particle into the crystal lattice. A palindrome based on one-half of the primary candidate sequence was constructed and methods were developed to produce the palindrome fragment in large quantities for reconstitution of NCPs. 

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