Base pair isolated

The DNA isolated from different cells and viruses characteristically consists of two polynucleotide strands wound together to form a long, slender, helical molecule, the DNA double helix. The strands run in opposite directions that is, they are antiparallel and are held together in the double helical structure through interchain hydrogen bonds (Eigure 11.19). These H bonds pair the bases of nucleotides in one chain to complementary bases in the other, a phenomenon called base pairing. 

Because of the double helical nature of DNA molecules, their size can be represented in terms of the numbers of nucleotide base pairs they contain. For example, the E. coli chromosome consists of 4.64 X 10 base pairs (abbreviated bp) or 4.64 X 10 kilobase pairs (kbp). DNA is a threadlike molecule. The diameter of the DNA double helix is only 2 nm, but the length of the DNA molecule forming the E. coli chromosome is over 1.6 X 10 nm (1.6 mm). Because the long dimension of an E. coli cell is only 2000 nm (0.002 mm), its chromosome must be highly folded. Because of their long, threadlike nature, DNA molecules are easily sheared into shorter fragments during isolation procedures, and it is difficult to obtain intact chromosomes even from the simple cells of prokaryotes. 

In contrast to the overwhelming affect of conversion of an A/T base pair in AQ-DNA(4) to a T/A base pair in AQ-DNA(5) on radical cation transport, the identical change in AQ-DNA(6) and AQ-DNA(7) has no measurable effect on the amount of strand cleavage observed at GG7 or GG2i [27]. It is apparent from consideration of these results that the effect of a change in base sequence must be considered in the context of the surrounding base pairs and not in isolation. 

The primary conclusion that follows from the effect of base sequence on the efficiency of radical cation migration through duplex DNA is that base pairs cannot be considered in isolation. For example, the effect of placing a T in a sequence of purines depends critically on the nature and number of purines. In this regard, the effect of base sequence on radical cation transport emerges from examination of collective properties of the DNA. This is a clear indication that the charge is delocalized over several base pairs, a conclusion that is supported by extensive quantum calculations. 

Figure 12. Methyladenine - Methylthymine (AT) and Methylcytosine - Methyl-guanine (CG) base pairs. The dipole moments of the isolated bases and of the base pairs are also shown.

Since one major component of the base pair interactions is of electrostatic nature, dipole moments were calculated at the HF and DFT levels for the isolated fragments and the complexes (Table VII). By proceeding from the isolated bases to the base pairs there is a change in the magnitude and direction of the resultant dipole moment. The HF results point out that for the CG pair, there is an increment of 1.42 D (27.6 %) and arotation of 11.1°,... 

The vibrational spectrum of methylguanine-methylcytosine (GC) complex consists of 99 normal modes frequencies. Differently from the AT base pair, in the GC complex the normal modes of the two bases are coupled together, thus an analysis of the shift relatively to the isolated bases is extremely complicated. This stronger coupling can possibly he ascribed to the presence of three h-bonds, rather than two as in AT. However, we tentatively discuss some significant shifts. 

The pKa is 7.0 corresponding to the H2S/SH acid base pair [76]. For this reason salts of the anion can be readily generated by strong acids, and salts M[B6H7] with large cations M can be isolated. 

Ion-exchange HPLC can also be useful in the separation of larger nucleic acid molecules. One such application is as an alternative to CsCl density gradient centrifugation in the preparation of plasmids. Plasmid molecules typically consist of between 1000 and 10 000 base pairs. The plasmid is first isolated from the bacterial cell by alkaline lysis and pure plasmid obtained from this crude extract by a one-step chromatographic separation. 

One problem with the REDOR method and other similar solid state NMR techniques is that unambiguous results only can be obtained when the spin system is based on isolated spin pairs, as shown in a recent publication . This means that the prevalent aggregates found in organolithium complexes cannot be studied by these methods. However, a recent 3D TEDOR study of uniformly labelled peptides gives some hope, provided that... 

To isolate a gene, scientists use surgical DNA scissors called restriction endonucleases (RE), proteins made by bacteria that cut DNA, based on specific rules. Each kind of RE—there are hundreds— recognizes specific sequences of 4-8 base pairs and cuts the DNA molecule at a specific spot (Figure 1.2). The biotechnologist selects... 

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