Symmetrical nucleotide sequences

The endonucleases are a class of restriction enzymes which cleave doubly stranded DNA by recognition of specific (symmetric) nucleotide sequences [38, 39]. The enzymes are of considerable utility in studying sequence-specific interactions of proteins and small molecules with DNA. 

Fig. 4. A model of the nucleotide sequence arrangement contained within AAV DNA, Two nucleotide sequence permutations are illustrated. Plus and minus strands may anneal to form duplex linear monomers with (3 and 4) or without cohesive 3 or 5 termini (1 and 2). Duplex linear monomers with cohesive termini can then form duplex circular monomers or duplex linear oligomers. In the figure the terminal repetitions are depicted as symmetrical nucleotide sequences. In the inset two alternative types of terminal repetitions are illustrated the first has the inverted repetition subterminal to the natural repetition, the second illustrates the possibility that a strand may have either an inverted or a natural terminal repetition...

The consensus nucleotide sequence (see Figure 10.20b) used in the crystals is a symmetrized version of naturally occuring API recognition sites, but GCN4 binds to this sequence with a high affinity. Each half-site in this DNA is bound to one monomer of the GCN4 dimer by both sequence-specific and... 

The genes that respond to a specific hormone contain identical HRE (Fig. 1.6). Normally, it is a matter of short nucleotide sequences pentamers or hexamers. In the case of the ER, the sequences are found repeated in inverse order in the same strand of DNA (palindromic, or symmetrically legible sequences 5 GGACA-nnn-ACAGG 3 n is any nucleotide). In the case of the thyroid hormones and retinoic acid, the HRE at times are presented like two repeated sequences in the same order (direct repetition GGACA-GGACA). 

Nucleotide sequences recognized by restriction enzymes are usually symmetrical such that the two strands of the double helix have the same base sequences but in opposite directions. The base sequences shown here in blue, for example, are symmetrical ... 

Listed on the left are the 16 self-complementary tetranudeotides while flanking nucleotides which expand these to the 64 self-complementary hexanucleotides head the next four columns. This arrangement is useful in looking for restriction enzymes which increase the specificity of cutting at a particular tetranucleotide. Enzymes that do not have symmetrical recognition sequences are not included. 

The double helix is not symmetrical it has a broad and a narrow groove between the chains. These provide steric orientation for the processes of replication and transcription (Fig. 1). This right-handed double helix with 10 base pairs per helical turn is called B-DNA. It probably approximates closely the structure of relaxed (unstrained) DNA. It is generally accepted, however, that DNA is a dynamic molecule, with different conformations in equilibrium with one another. This equilibrium is affected by nucleotide sequence, ionic strength of the environment, presence of proteins [e. g. Histones (see) and other DNA binding proteins (see)] and the extent to which the molecule is under topological strain. 

There are three possible models to account for the data which indicate the existence of both inverted and natural terminal nucleotide sequence repetition in the population of purified AAV DNA molecules (Fig. 4). One possible structure would be that the terminal nucleotide sequence repetition is symmetrical. This possibility would be in accord with the fact that the lengths determined for both types of terminal repetition are similar. Two other alternatives are possible. The first is that the inverted and natural terminal repetitions occupy different positions along the genome. In that case the data of Berns and Kelly would probably tend to overestimate the length of the inverted nucleotide sequence repetition if it were subterminal. Likewise the estimate of the length of the natural terminal repetition (1%) by Gerry et al. would be too great if the natural terminal repetition were subterminal. An unlikely third alter-... 

The application of LSR to amino-acids has received some attention. (451-456, 498) Such studies are an essential preliminary to the use of LSR for amino-acid sequence determination in simple peptides and proteins. The latter are discussed more comprehensively in Section G. A detailed study has been made (453) of the interaction of Eu(iii), Pr(iii), Gd(iii), and La(iii) with iV-acetyl-L-3-nitrotyrosine in order to characterize the nitrotyrosine residue as a potential specific lanthanide binding site in proteins. The parameters of the dipolar interaction indicate a significant contribution from non axially symmetric terms. The conformations of the nucleotides cyclic j8-adenosine 3, 5 -phosphate (3, 5 -AMP) (457, 458) and adenosine triphosphate (ATP) (459) have been deduced using LSR. In the former case the conformation of the ribose and phosphate groups is consistent with the solid state structure. A combination of lanthanide shift and relaxation reagents was used to deduce the most favoured family of conformations for ATP in aqueous solution. One of these conformations corresponds closely to one of the crystal structure forms. 

RNA double helices are frequently interrupted by short sequences of nucleotides on both strands which cannot form standard Watson-Crick base pairs. These regions which connect two Watson-Crick helices are historically referred to as internal loops in analogy to hairpin loops which coimect the ends of helices. A symmetric internal loop has an equal number of nucleotides on opposing strands, while an asymmetric internal loop has a different number of nucleotides on the two strands. Figure 1 schematically defines internal loops. 

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