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...

In its standard implementation, the suppression of the undesired one-bond correlations is far from complete using a one-step low-pass J filter HMBC pulse sequence. Effective modifications are needed to achieve this goal when there is a wide range of Vch values. There are several kinds of pulse... 

A comprehensive list of behavioral phenomena and physical attributes affecting the strength and stability of steel frames is compiled in White 1991. Some of the items listed include initial imperfections, residual stresses, initial strains, construction sequence, effects of simultaneous axial force, shear and moment on section capacities, P-dclta effect, local buckling and spread of inelastic zones in members. A similar list of items could be compiled for reinforced concrete and other structural materials. It is clear that a comprehensive advanced analysts can become quite... 

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. 

At higher temperatures retro-Diels-Alder reaction may also occur in the opposite sense to addition, as in the reaction of methyl pyrrole-1-carhoxylate with dimethyl acetylenedicarboxylate at 200°, which affords acetylene and the pyrrole triester (56). The decomposition of the suspected intermediate Diels-Alder adduct (11) at 170° has been separately established. Compounds 19 and 20 are intermediates in similar addition-elimination reactions leading to pyrrole-l,3,4-triesters, in which removal of acetylene from the system makes the reaction sequence effectively irreversible. 

This sequence effectively breaks off at atomic mass 7 because the heirs of helium are so incurably unstable. In particular. 

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... 

For the Tar—Tar kissing loops, the P—B calculations are unable to discern their propensity to accumulate counterions accumulation at the loop—loop interface (data not shown). This is because the fully hydrated ions as defined by the Stem layer cannot penetrate into the central cation binding pocket (data not shown). Similarly, the axial spine of counterion density observed in the A-RNA helix (Fig. 20.5) is not captured by the P—B calculation (Fig. 20.7). No noticeable sequence specificity is observed in the counterion accumulation patterns in the P—B calculations, even though the sequence effects are explicitly represented in the P—B calculation through the appropriate geometry and assignment of point-charges. This is because the sequence specificity observed in the molecular dynamics simulations usually involves first shell interactions of base moieties with partially dehydrated ions, which cannot be accurately represented in the P—B framework. 

The relationship between age and pharmacokinetics were assessed by an analysis of variance (ANOVA) on AUCs, MRT and Cmax with adjustments for treatment, period, sequence and subject within sequence effects by age class using the natural log transformed values to compare treatments within age class. Point estimates and 95 % confidence intervals were calculated for me treatment ratios per age class. 

The primary parameter AUCo-oo was subjected to an analysis of variance (ANOVA) including sequence, subject nested within sequence (subject (sequence)), period and treatment (non-fasting/fasting) effects. The sequence effect was tested using the subject (sequence) mean square from the ANOVA as an error term. All other main effects were tested against the residual error (error mean square) from the ANOVA. The ANOVA was performed on ln-transformed data. Lor ratios 90 % confidence intervals were constructed. The point estimates and confidence limits were calculated as antilogs and were expressed as percentages. The... 

The DANTE-Z sequence effectively suppresses the sine oscillations that occur using the simple DANTE sequence or Gaussian pulses. 

Every M sequence is joined to two M2 sequences in the interior of the copolymer. The number of sequences of each type cannot differ by more than one, therefore. For long polymer molecules, which will contain a large number of sequences of each type, this difference is negligible and the number of Mi sequences effectively equals the number of M2 sequences. Then the ratio of Mi units to M2... 

On adding water to the acetonium ion (26), however, the bridge is attacked rapidly to give the two monoacetates of the 2/9,3j -diol [ioy,xo8]. This reaction sequence effects m-hy-droxylation from the more hindered side of the olefinic bond, and so gives the as-glycol of configuration opposite to that obtained with osmium tetroxide. Unfortunately, the process does not seem to be applicable to more highly substituted olefins. 

In the CABBY-2 sequence the numbers in parentheses indicate the amplitude of the individual rf pulses in units of kilohertz, scaled for applications at 600 MHz. With an rf amplitude of 1.6 kHz, the CABBY-4 sequence effects selective transfer between the 3, 4, 5, and 5" protons in the deoxyribose moiety of DNA at 600 MHz. Additional highly selective and band-selective sequences based on doubly selective irradiation schemes are discussed in Section X.C. 

Where Kunf and Kfiuct are the equilibrium constants for the unfolding transitions and fluctuations respectively. For simplicity, both the unfolded and the fluctuated conformations are assumed to exchange with the rate determined from unstructured dipeptides (Bai et al., 1993 Connelly et al., 1993). This may be a poor assumption, especially for the fluctuated form, but it allows the rates to be normalized for temperature, pH and amino acid sequence effects. Kpp, the equilibrium constant determined from kobs / is then given by... 

---