Nucleotides and Nucleic Acids

Chapter 10 . Nucleotides and Nucleic Acidscoefficient. Stacked bases have a lower extinction coefficient than unstacked bases. Thus,denaturation is accompanied by an increase in ultraviolet light absorption, a phenomenonknown as the hyperchromic effect. The ultraviolet absorbance of denatured DNA isapproximately 40% higher than that of native DNA.7. BamHI produces 5'-overhangs as shown below:5' 3' 5' 5' 3'GGATCC G GATCC+CCTAGG CCTAG G3' 5' 3' 5' 3'Bgl II also produces 5'-overhangs as shown below:5' 3' 5' 5' 3'AGATCT A GTACT+TCTAGA TCTAG C3' 5' 3' 5' 3'The overhangs are compatible but the hybrid site formed by joining a BamHI half site with aBglII half site is not recognized by either. The junction is no longer a 6-base palindrome.5' 5' 3' 5' 3'G GATCT GGATCT+CCTAG A CCTAGA3' 5' 5' 5' 3'BamHI BglII hybridhalf-site half-site siteSummaryThe nucleic acids, ribonucleic acid (RNA) and deoxyribonucleic acid (DNA), are importantbiopolymers of nucleotides, compounds containing nitrogenous bases, a five-carbon sugar(ribose or deoxyribose) and phosphate. This chapter describes the basic biochemistry of nucleicacids and nucleotides. The nitrogenous bases come in two types, pyrimidines and purines.Pyrimidines are 6-membered, heterocyclic, aromatic ring structures containing two nitrogens.There are three principal pyrimidines: cytosine, uracil and 5-methyluracil or thymine. Cytosineis found in both DNA and RNA whereas uracil is in RNA and thymine in DNA. The generalstructure of a purine is a 5-membered imidazole ring fused to a pyrimidine ring. In DNA andRNA, there are two common purines, namely adenine and guanine. Both purines andpyrimidines contain numerous groups that can participate in hydrogen bonds as donors oracceptors or both. In fact, complementary groups exist on adenine and uracil (or thymine) andon guanine and cytosine such that they can form hydrogen-bonded pairs. This base-pairing isthe foundation for the structure of double-stranded DNA.Because the bases have extensive, conjugated double bonds, they absorb light strongly in theUV range. The conjugated bond system allows delocalization of π-electrons, forming electronclouds above and below the base plane. Delocalized π-electrons can interact by base stacking,another force stabilizing double-stranded DNA. Base stacking also affects the efficiency ofelectronic transitions of π-electrons, such that stacked bases absorb less UV light thanunstacked bases. The transition from an ordered nucleic acid structure stabilized by hydrogenbonds and base stacking to an unordered structure is accompanied by an increase in UVabsorbance. This transition is known as denaturation and it results in a hyperchromic shift inUV absorption.Purines and pyrimidines have low water solubility which improves when they are attached toeither ribose or deoxyribose sugars through N-glycosidic bonds. The resulting compounds are157