Pseudo-base pairing

Palindromic base pairs that are most frequent at the two ends are green, and the pseudo-twofold symmetry axis is Indicated by a red dot. 

The protein-DNA interactions have been analyzed in detail at high resolution in the complex between the 434 repressor fragment and the ORl containing 20mer DNA. A pseudo-twofold symmetry axis relates the halves of this complex. The symmetry is not exact since the nucleotide sequence of the DNA is slightly different in each half (see Table 8.2). However, the interactions between one protein subunit and one half of the DNA are very similar to those between the second subunit and the other half of the DNA since most of the bases that interact with the protein are identical in both halves. Details of the interaction are very similar to those in the complex with the palindromic synthetic 14mer of DNA shown in Figures 8.14 and 8.15. The base pairs at one end of the DNA, 1-14, 2-13, etc. are called base pairs 1, 2, etc. 

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...

Fig. 5. Three views of the NCP from Harp et al. [31]. (a) Ventral surface view, (b) Side view, (c) View down the molecular pseudo-dyad axis. The histones are represented by Ca ribbon models of the secondary structure elements, and the DNA model indicates the base pairing between complementary strands. The DNA is positioned asymmetrically by one-half base pair on the NCP. This results in a two sides arbitrarily referred to a dorsal and ventral (the surface shown here). The ventral surface of the NCP is best recognized by the extended N-terminal H3 tail protruding to the right. In these images, the pseudo-dyad axis is represented by vertical bars for both the ventral and side view. The pseudo-dyad axis passes through the center of the dyad view orthogonal to the plane of the page, (d) Color code for histone chains in the figures in this chapter. Note the change in hue denoting the two sides of the histone octamer.

Recall that the secondary-structure model for RNA is a model - and a crude one at that. It neglects pseudo knots and other tertiary interactions, does not take deviations from the additive nearest neighbor energy model into account, and is based on thermodynamic parameters extracted from melting experiments by means of multidimensional fitting procedures. Thus, you cannot expect perfect predictions for each individual sequence. Rather, the accuracy is on the order of 50% of the base pairs for the minimum free energy structure. 

Unlike DNA and RNA, which have backbones of repeating sugar-phosphate units, the PNA molecule is built upon a pseudo-peptide backbone of N-(2-aminoethyglycine) units linked by peptide bonds, to which purine and pyrimidine bases (the specific base-pairing units of nucleic acids) are linked via methylene carbonyl bonds. 

The sugar-phosphate chains attached to atoms C(l ) are in opposite directions because of the pseudo-twofold axis of the base pairs. The two strands in DNA or RNA double helices with Watson-Crick-type base pairing are therefore always antiparallel. 

The orientation of the amino proton attached to the N2 donor on G differentiates the G C and C G base pairs from each other as well as from the A-T and T-A pairs. The latter base pairs can be discriminated by small synthetic molecules that take advantage of both the asymmetric steric structure of the adenine C2-H and the capability of the thymine 02 (with two sets of lone pair electrons) to form an additional hydrogen bond not possible with the pseudo-symmetrically related adenine N3 (37, 38). It is not yet clear whether naturally occurring, DNA-binding proteins use similar principles to distinguish between A T and T A base pairs in the minor groove. 

Figure 4.16 Xftitson-Crick pairing between thymine (T) and adenine (A) (above) and the supposed, much weaker pairing of a 2,4-difluorotoluene pseudo-base (F) with adenine (A) (below).

Figure 2-2. The pseudo base (1,2,4-triazole 3-carboxamide) of ribavirin pairs equivalently with cytosine and uracil. R denotes the polyribonucleotide strand.

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