Sequence overlapping

Fig. 3.6 Polyamide-DNA binding motifs targeting longer DNA sequences. Overlapped and slipped homodimers depending on the sequence context, six-ring polyamides with central p-Ma residues can bind to DNA as fully overlapped homodimers, recognizing 11 bp, or as slipped homodimers, recognizing 13 bp. Extended hairpin extended conformation increases binding site size (to 9 bp) and enhances binding affinity. Cooperative dimer a cooperatively binding hairpin polyamide can...

The primary goal of peptide mapping is the verification of the amino acid sequence deduced from the genetic code of the recombinant protein. The protein backbone gets cleaved by typically two or three different endoproteinases like Lys-C, trypsin, and Glu-C to achieve maps with sequence-overlapping peptide fragments. These peptide mixtures can then be separated by LC or CE and analyzed on-line by MS to obtain sequence information. Often simple mass analysis matches the predicted primary sequence of the protein. However, sometimes mutations can lead to isobaric masses of peptides that can be overseen, if no further sequence analysis like N-terminal Edman sequencing and MS/MS is carried out. 

Figure 2a compares the time-resolved Stokes shift of the normal sequence and the abasic sequence. For ease of comparison, the data is shifted to overlap the sequences at early times. In the first nanosecond, the Stokes shifts from both sequences overlap almost perfectly. This results suggests that there is not a large scale collapse of the normal DNA structure at the abasic site. However after 1 ns, the abasic sequence has additional dynamics beyond those of the normal sequence. The fit of the abasic sequence has the same logarithmic component of the normal sequence fit, but with an additional exponential term for the fast rise in the Stokes shift after 1 ns S(t) = S0 + A0 logl0(t/t0) + 4,(l-exp(-f/r)), with an exponential time constant r of 25 ns. 

The complete 297 amino acid sequence of the adenine nucleotide transporter has been determined [185] and deductions have been made about the two-dimensional structure in the plane perpendicular to the membrane. Some of these deductions have been made using computer analyses of the amino acid sequence [186], Using a computer program to locate sequence homologies, three domains have been identified within the sequence with significant sequence overlap. The three repeating areas are characterized by a conserved region centered on a cysteine residue found in three... 

B) Study Designs 5 and 9 (Fixed Sequence Overlapping Panel Designs) Study Design 5 (Doubling with Two-Panel Overlap)... 

This protocol will result in a linearized, dephosphorylated vector with a sequence overlap with your insert of at least 50 bp. No ligation with the insert will be necessary, as the yeast will recombine the vector and insert through homologous recombination (see Note 1 for tips on choosing an appropriate vector). 

In practice, it is rarely possible to sequence lengths of more than 20 or so amino acids by these methods because the mixtures become too complex, and degradation patterns are uneven. However, a range of short sequences from a collection of different peptides from the one protein ( peptide mapping ) is often sufficient to identify the protein. If the different peptide sequences overlap, then the entire protein sequence can be determined. 

Lemma 0. Let 1, 1,, . .., be a sequence of intervals such that every pair of consecutive intervals are related. Then no intervals in this sequence overlap. 

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