Sequence dependency

The key question we want to answer is what are the intrinsic sequence dependent factors tliat not only detennine tire folding rates but also tire stability of tire native state It turns out tliat many of tire global aspects of tire folding kinetics of proteins can be understood in tenns of tire equilibrium transition temperatures. In particular, we will show tliat tire key factor tliat governs tire foldability of sequences is tire single parameter... 

Packer M J, M P Dauncey and C A Hunter 2000. Sequence-dependent DNA Structure Dinucleotide Conformational Maps. Journal of Molecular Biology 295 71-83. 

I Wojcik, I-P Mornon, I Chomilier. New efficient statistical sequence-dependent structure prediction of short to medium-sized protein loops based on an exhaustive loop classification. I Mol Biol 289 1469-1490, 1999. 

While each mode is a separate function, the order of mode sequence depends on specific conditions. 

Equation (4-210) is known as the sampling theorem. It states that any time function limited to a frequency W can be uniquely determined by its values at sample points spaced 1/2W apart. Thus if both the input and output from a channel are limited to a frequency W, then we can represent the input and output as sequences of real numbers spaced at intervals of 1/2 W. If each output in this sequence depends on only one input, then the results for continuous input, continuous output channels can be applied. One particularly important case in which ... 

Yoon, S. C., Choi, M. H., 1999. Local sequence dependence of polyhydroxyalkanoic acid... 

Certain heteroatom-substituted aliphatic phosphites have also been employed in these sequences, depending on their stability. Generally, phosphites bearing a-substituents led to higher yields than were obtained with phosphites having p-subsdtuents (27). For example, bis-p-cyanoethyl phosphite gave a relatively modest yield (-25%) of coupled triester product (34,35), whereas a very good yield (83%) of desired product was isolated ftom reactions with bis-a-cyanopropyl phosphite (36). 

Let us also notice that i) the changes in the activity sequences with the temperature show the necessity to compare the activities at various temperatures, not only near the light-off temperature ii) since the activity sequences depend also on the mixture, for example on the presence or on the absence of H2O, it is necessary to study complex realistic mixtures. 

The analogy drawn between -stacked solids and duplex DNA has provided a useful starting point for experiments to probe and understand DNA-medi-ated CT. As with the -stacked solids, the DNA base pair array can provide an effective medium for long range CT. Mechanistically, however, the differences between DNA and these solid state materials may be even more important to consider. Duplex DNA, as a molecular -stacked structure, undergoes dynamical motion in solution. The time-dependent and sequence-dependent structures that arise serve to modulate and gate CT. Indeed in probing DNA CT as a function of sequence and sequence-dependent structure, we may better understand mechanistically how CT proceeds and how DNA CT may be utilized. 

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]. 

Fig. 7. (A) Secondary chemical shifts, corrected for sequence-dependent contribu-...

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