Bases, DNA and RNA

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. 

Introduction Advances in Plasmid DNA Purification Advances in Electrophoretic DNA Separations Advances in Affinity-Based DNA and RNA Recovery Conclusions References... 

Firefly lucifenn is an example of an azole that contains a benzene ring fused to the five membered ring Such structures are fairly common Another example is benzimidazole present as a structural unit m vitamin B12 Some compounds related to benzimidazole include purine and its ammo substituted derivative adenine one of the so called het erocychc bases found m DNA and RNA (Chapter 28)... 

These relationships are general Hydroxyl substituted purines and pyrimidines exist in their keto forms ammo substituted ones retain structures with an ammo group on the ring The pyrimidine and punne bases m DNA and RNA listed m Table 28 1 follow this general rule Beginning m Section 28 7 we 11 see how critical it is that we know the cor rect tautomeric forms of the nucleic acid bases... 

Although experimental studies of DNA and RNA structure have revealed the significant structural diversity of oligonucleotides, there are limitations to these approaches. X-ray crystallographic structures are limited to relatively small DNA duplexes, and the crystal lattice can impact the three-dimensional conformation [4]. NMR-based structural studies allow for the determination of structures in solution however, the limited amount of nuclear overhauser effect (NOE) data between nonadjacent stacked basepairs makes the determination of the overall structure of DNA difficult [5]. In addition, nanotechnology-based experiments, such as the use of optical tweezers and atomic force microscopy [6], have revealed that the forces required to distort DNA are relatively small, consistent with the structural heterogeneity observed in both DNA and RNA. 

Viral vectors are usually classified by the characteristics of the parental viius. Based on the viral genome, one can distinguish between DNA and RNA viruses (for details see [1, 2]). 

Molecules of DNA and RNA are polynucleotides, polymeric species built from nucleotide units. Polymerization takes place when the phosphate group of one nucleotide (which is the conjugate base of an organic phosphoric acid) condenses... 

The processes of DNA and RNA synthesis are similar in that they involve (1) the general steps of initiation, elongation, and termination with y to 3 polarity (2) large, multicomponent initiation complexes and (3) adherence to Watson-Crick base-pairing rules. These processes differ in several important ways, including the... 

The structures of DNA and RNA are similar in that each has a sugar-phosphate backbone with one organic base bound to each sugar. However, there are four distinct differences between RNA and DNA ... 

Fig. 3 Schematic representation of triplex form with chemical structures of base triplets of DNA and RNA triplexes. Reprinted from [80] with permission from Wiley InterScience...

DNA and RNA are formed of nucleotides. Each nucleotide or nucleoside is composed of a purine or pyrimidine base linked to the 1-position of a ribose sugar in the case of RNA and a 2 -deoxyribose sugar in the case of DNA.155 The 5 position is phosphorylated in the case of a nucleotide, while the nucleoside is not phosphorylated therefore, nucleotides are nucleoside phosphates. Phosphorylation can include one, two, or three phosphate groups. The most familiar example of a phosphorylated nucleotide is phosphorylated adenosine, which occurs as the mono-, di-, and triphosphate (AMP, ADP, and ATP, respectively) and is a principal means of energy storage in biological systems. 

Ozonolysis of organic compounds in water also has biological and environmental93 interest. Ozone preferentially attacks the base moiety of pyrimidine nucleotides in water.94 For example, the reaction of ozone with uracil in water, having no substitutent at 1-position, gave the ozonolysis products in Scheme 3.6.95 The reactions of DNA and RNA with O3 in an aqueous environment are linked to the damage of... 

Piccirilli, J. A., et al. (1990). Enzymatic incorporation of a new base pair into DNA and RNA extends the genetic alphabet. Nature 343,33-37. 

Ullrich S, Schultz T, Zgierski MZ, Stolow A (2004) Electronic relaxation dynamics in DNA and RNA bases studied by time-resolved photoelectron spectroscopy. Phys Chem Chem Phys 6 2796... 

Canuel C, Mons M, Piuzzi F, Tardinel B, Dimicoli I, Elhanine M (2005) Excited states dynamics of DNA and RNA bases characterization of a stepwise deactivation pathway in the gas phase. J Chem Phys 122 074316... 

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