Polynucleotide Minor Bases

Various minor or unusual bases occur in DNA and (to a greater extent) in RNA samples from natural sources. These additional nucleotide components are mostly simple derivatives of the main bases and occur only to the extent of 1 or 2%, for example. Table 10.17. Their significance is not yet fully understood but they do contribute to irregularities of structure and behaviour (Chapter 11.5). 

In a polynucleotide of natural origin (nucleic add), the proportion and sequence of bases along the chains is highly important and is characteristic of the source. It does not change with age, nutritional state or external environment. 

The DNA contains about equal quantities of purine and pyrimidine bases, that is. 

Some Unusual (Foreign) Bases Eound in Natural Nucleic Acids 

Note Small proportions of minor bases ignored.  

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For polynucleotides, an hypochromic effect of the order of 10-50% is frequently observed. The intact double helix DNA absorbs roughly 30% less than a mixture of the component monomers. A few of minor bases found in tRNA show > 300mn, such as the Y base (Xnrnx = 325 nm) and 4-thiouridine (Vax = 340 nm), which can be exploited to investigate these molecules. 

A hypothetical DNA chain containing equal numbers of the four different bases (as in the tetra-nucleotide fragment (10.72)), and no minor bases, could be assigned the empirical formula C35H4g024NigP4. This approximation can be used for some purposes to represent a polynucleotide chain. 

Several unusual "minor" bases occur in tRNA. Most of these are synthesized by secondary modification of bases previously Incorporated into a polynucleotide strand, since the minor bases are critical for the function of certain tRNAs, it is possible that a new type of drug might be developed which interferes selectively with the synthesis of one or more of the minor bases, thus modifying the function of specific tRNAs. 

Identification of the component pentose sugar confirms whether the polynucleotide chain is RNA or DNA. Both RNA and DNA contain the same two purine bases, adenine (A) and guanine (G) whereas they differ in their content of the pyrimidine bases. RNA contains cytosine (C) and uracil (U) but DNA contains cytosine and the 5-methyl derivative of uracil called thymine (T). In addition to these bases, called major bases, DNA and RNA also contain altered or less common bases called minor bases. In DNA, the minor bases are usually methylated derivatives of the major bases which play a special role in the functioning of the polynucleotide. RNAs, especially transfer RNAs, also contain minor bases, e.g. inosine, pseudouridine (in which uracil is linked through C-5, not N-1, to ribose), dihydrouridine, ribosylthymine and methylated derivatives of nucleosides (Figure 7.2). Minor bases are mainly modified versions of major bases. 

Only two kinds of modification of the classical Crick-Watson polynucleotide structure (Figures 10.38 and 10.39) have to this point been considered. These are (1) the occurrence of minor or unusual bases in natural samples of DNA and RNA, and (2) the oecurrence of alternative inter-base H bonding schemes in synthetic oligonucleotides. The latter can be associated with mismatched and no-matched base pairs, or the formation of triple, quadruple or other helical arrangements. 

FIGURE 5 This figure illustrates that the entire analysis of mixture of polynucleotide fragments of from 67 to 622 base pairs can be accomplished in 160 sec. Also, the reproducibility from channel to channel allows the easy discrimination of minor changes In composition between samples. [From Woolley etal. (1997). Anal. Chem. 69,2183-2184. Reprinted with permission of the American Chemical Society, Washington, DC.]... 

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