Hydrogen-bonded base pairing, alternative

The implication is that under the conditions of deep UV irradiation, which likely existed on the early earth, selective chemistry may have taken place in favor of species with the shortest excited state lifetimes. Benner and coworkers, for example, have proposed a molecular lexicon of 12 alternate bases that can produce 6 base pairs with virtually identical geometries as the guanine-cytosine (GC) triply hydrogen bonded base pair [1], Several of these alternate bases have been observed as products in simulation experiments that test the feasibility of synthesis of such compounds under primitive conditions [77, 78], This raises the... 

Circular DNA is a type of double-stranded DNA in which the two ends of each strand are joined by phosphodiester bonds [Figure 20.11 (a)]. This type of DNA, the most prominent form in bacteria and viruses, is also referred to as circular duplex (because it is double-stranded) DNA. One strand of circular DNA may be opened, partially unwound, and then rejoined. The unwound section introduces a strain into the molecule because the nonhelical gap is less stable than hydrogen-bonded, base-paired helical sections. The strain can be localized in the nonhelical gap. Alternatively, it may be spread uniformly over the entire circular DNA by the introduction of superhelical twists, one twist for each turn of a helix unwound. The circular DNA shown in Figure 20.11 (b) has been unwound by four complete turns of the helix. The strain introduced by this unwinding is spread uniformly over the entire molecule by the introduction of four superhelical twists [Figure 20.11 (c)]. Interconversion of relaxed and supercoiled DNA is catalyzed by groups of enzymes called topoisomerases and gyrases. 

Where nucleic acids are concerned, the enhanced hydrophobicity of abiotic polyfluorinated aromatic bases (e.g., tetrafluorobenzene or tetrafluoroindole deoxyribose derivatives) was exploited as an alternative to natural hydrogen bonding to achieve selective and stable nucleic acid base pairing in duplex DNA [85], The DNA replication was examined using polyfluorinated-nucleotide analogs as substrates. A DNA polymerase active site was able to process the polyfluorinated base pairs more effectively than the analogous hydrocarbon pairs, demonstrating hydrophobic selectivity of polyfluorinated bases for other polyfluorinated bases [86]. 

An alternative form of hydrogen bonding between base pairs is designated Hoogsteen. This type of bonding cannot readily occur in nature because the purine and pyrimidine bases are constrained to long chains that must interact at numerous points. 

Figure 6.2. Molecular architecture of DNA. Each strand of DNA is composed of alternating pentose sugar (deoxyribose) and phosphate moieties linked to each other via phosphodiester linkage. The first carbon position of the sugar is attached to one of the four nitrogenous bases (A, T, G, or C). The two strands are in opposite orientation to each other with respect to a 5 or 3 phosphate group attached to the sugar moiety. Cytosine (C) pairs with guanine (G) via three hydrogen bonds, and adenine (A) pairs with thymine (T). (Reproduced from Textbook of Biochemistry with Clinical Correlations, T. M. Devlin, ed., Wiley, New York, 1982.)...

Complementary base pairs are joined by hydrogen bonds and are best represented by a centered dot dA-dT and dG-dC are the canonical pairings in double-stranded DNA, although alternate pairings, DNA-RNA hybrids, triplexes, and other variations may occur. 

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