Pairing rule

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.)... 

Fig. 3.2 Pairing rules for polyamide recognition of all four Watson—Crick base pairs of DNA. Putative hydrogen bonds are shown as dashed lines. Circles with dots represent lone pairs of N(3) of purines and 0(2) of pyrimi-...

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. 

The following pairing rules apply to triple strands ... 

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. 

Figure 3. Spectrum of Lyapunov exponents of a dynamical system of 33 hard spheres of unit diameter and mass at unit temperature and density 0.001. The positive Lyapunov exponents are superposed to minus the negative ones showing that the Lyapunov exponents come in pairs L, —L, as expected in Hamiltonian systems. Eight Lyapunov exponents vanish because the system has four conserved quantities, namely, energy and the three components of momentum and because of the pairing rule. The total number of Lyapunov exponents is equal to 6 x 33 = 198.

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.

The complementary antiparallel strands of DNA follow the pairing rules proposed by Watson and Crick. The base-paired antiparallel strands differ in base composition the left strand has the composition A3 T2 G, the right, A2 T3 G3 C,. They also differ in sequence when each chain is read in the 5 — 3 direction. Note the base equivalences A = T and G = C in the duplex. 

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. 

The replication is directed by the template according to the Watson-Crick pairing rules. 

DNA polymerases have just one binding site for all four combinations of base pairing—AT, TA, GC, and CG. The specificity of these sites is dictated by the Watson-Crick pairing rules, in that the sites themselves appear to recognize just the overall shape of a correct purine-pyrimidine pair, with the precise specificity resulting from the complementary nature of the base pairing. The polymerase catalyzes the transfer of a complementary deoxynucleoside monophosphate from its triphosphate to the 3 -hydroxyl of the primer terminus (equation 14.1). 

Pair-rule genes—define seven bands runt (runt) hairy (h) fushi tarazu (ftz) even skipped (eve ) paired (prd) odd paired (opa)... 

The gap gene products regulate the position-specific expression of other genes, those belonging to the pair-rule class of segmentation genes. 

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