Base-pairing rules

In principle, the Maxam-Gilbert method can provide the total sequence of a dsDNA molecule just by determining the purine positions on one strand and then the purines on the complementary strand. Complementary base-pairing rules then reveal the pyrimidines along each strand, T complementary to where A is, C complementary to where G occurs. (The analogous approach of locating the pyrimidines on each strand would also provide sufficient information to write the total sequence.)... 

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 genetic information within the nucleotide sequence of DNA is transcribed in the nucleus into the specific nucleotide sequence of an RNA molecule. The sequence of nucleotides in the RNA transcript is complementary to the nucleotide sequence of the template strand of its gene in accordance with the base-pairing rules. Several different classes of RNA combine to direct the synthesis of proteins. 

Mismatch Repair. Mispairs that break the normal base-pairing rules can arise spontaneously due to DNA biosynthetic errors, events associated with genetic recombination and the deamination of methylated cytosine (Modrich, 1987). With the latter, when cytosine deaminates to uracil, an endonuclease enzyme, /V-uracil-DNA glycosylase (Lindahl, 1979), excises the uracil residue before it can pair with adenine at the next replication. However, 5-methyl cytosine deaminates to form thymine and will not be excised by a glycosylase. As a result, thymine exits on one strand paired with guanine on the sister strand, that is, a mismatch. This will result in a spontaneous point mutation if left unrepaired. For this reason, methylated cytosines form spontaneous mutation hot-spots (Miller, 1985). The cell is able to repair mismatches by being able to distinguish between the DNA strand that exists before replication and a newly synthesized strand. 

Wobble Base pairing rules used for position... 

Figure 12-1. Codon-anticodon base pairing. Special wobble base-pairing rules apply to the third (3 ) position of the codon. The first (S ) position of the tRNA anticodon is frequently inosine (I) to provide this flexibility in hydrogen bonding.

Early work on DNA polymerase I led to the definition of two central requirements for DNA polymerization. First, all DNA polymerases require a template. The polymerization reaction is guided by a template DNA strand according to the base-pairing rules predicted by Watson and Crick where a guanine is present in the template, a cytosine deoxynucleotide is added to the new strand, and so on. This was a particularly important discovery, not only because it provided a chemical basis for accurate semiconservative DNA replication but also because it represented the first example of the use of a template to guide a biosynthetic reaction. 

Here kf and kb do not have solely their usual meanings as forward and backward chemical rate constants, because the free monomer concentration has been included as a factor in kf and the concentrations of the byproducts of the forward reaction (inorganic pyrophosphate and water) have been absorbed into kb. Since there are actually four different types of monomer, each template site specifying, according to the Watson-Crick base-pairing rules, which type is to be incorporated at that site, this use of the same kf for each step is strictly valid only if all four monomer concentrations are equal, as well as essentially invariant during the duration of the process, and if the true rate constant for the incorporation of each type of monomer is independent not only of the nature of the monomer to be added but also of the nature of the sequence already incorporated. 

According to base-pairing rules, adenine pairs with ... 

The structure of the IRE that occurs in the sequence of ferritin mRNA appears in Figure 10.34. The iron response element is a small region of RNA, and it is distinguished in that it spontaneously folds upon itself to form a hairpin shape. The ribonucleotides of RNA follow similar base-pairing rules as in DNA. In RNA, guanine binds to cytosine, and adenine binds to uracil. It is accurate to state that within the hairpin the RNA occurs as double-stranded RNA. To repeal, one might note that DNA contains a sequence of DNA bases that is used to code for the iron response clement, but these DNA bases do not bind the IRF... 

The molar content of the four bases in DNA (called the base composition) always satisfies the equalities [A] = [T] and [G] = [C] where [ ] denotes molar concentration. These equalities arise because of the base pairing rules in... 

DNA which require that A pair with T and G pair with C in the double-stranded DNA molecule (Figure 23-3). Because of the base pairing rules it follows that [purines] = [pyrimidines] in all DNA molecules. 

The two strands in the double helix are complementary because of the base pairing rules that dictate A = T and G = C. Because of the base... 

The nitrogenous bases of the codons are complementary to those of the anticodons. As a result they are able to hydrogen bond to one another according to the base pairing rules. 

The bases in RNA are adenine (A), guanine (G), cytosine (C), and uracil (U). These are the same bases as DNA except that the base uracil is used in place of thymine (T). Unlike DNA, RNA is rarely composed of two strands base paired with each other. Instead, RNA exists as a single-stranded entity, though extensive regions of many RNAs may form double helices within themselves by the base pairing rules. 

The base pairing rules for making RNA from DNA are the following ... 

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