Guanine-cytosine Watson-Crick base pair

O.V. Shishkin et al., Intramolecular flexibility of DNA bases in adenine-thymine and guanine-cytosine Watson-Crick base pairs. J. Mol. Struct. 477, 15-21 (1999)... 

GC, guanine—cytosine Watson—Crick base pair. 

Figure 11 Substituent effects on H-bond energy in methylated GC pair. GC, guanine-cytosine Watson—Crick base pair. Reproduced with permission from (2002JPCA(106) 3207). Copyright 2002 American Chemical Society.

It has been shown that photoexcitation of the guanine-cytosine (G-C) base pair leads to proton transfer [231], Watson-Crick (WC) base pairs have excited state lifetimes much shorter than other non-WC base pairs indicating once again that the natural occurring WC base pairs are more photostable than other alternative configurations [115, 118, 232-235], Much work has been done in the gas phase where many different base pair isomers exist. The ultrafast relaxation of the WC base pair has also been confirmed in solution using fluorescence up-conversion measurements [117]. 

In molecular biology, a set of two hydrogen-bonded nucleotides on opposite complementary nucleic acid strands is called a base pair. In the classical Watson-Crick base pairing in DNA, adenine (A) always forms a base pair with thymine (T) and guanine (G) always forms a base pair with cytosine (C). In RNA, thymine is replaced by uracil (U). 

FIG U RE 3.4 Watson-Crick base pairing in DNA. Adenine is complementary to thymine, and guanine is complementary to cytosine. 

Draw the structures of the Watson-Crick base pairs guanine-cytosine (GC) and adenine-thymine (AT). Also draw the GU pair, which is not a Watson-Crick pair. 

Keywords Cytosine, Guanine, Watson-Crick Base-Pair, DNA Oligomers, Conical Intersection,... 

In this chapter we have reviewed computations that help to explain the photostability and lifetimes of the DNA nucleobases, using cytosine and the cytosine-guanine Watson-Crick base-pair as examples. 

In the cytosine-guanine Watson-Crick base-pair, radiationless decay occurs instead via an intermolecular charge transfer state, and is triggered by proton transfer. The locally excited states that were studied in the isolated cytosine are rapidly displaced to higher energy along the proton transfer coordinate. Here the protein environment causes a part of the conical intersection seam to become accessible which cannot be reached in the gas phase. 

Guanine-cytosine. Guanine has an acceptor-donor-donor sequence which is complementary to the donor-acceptor-acceptor sequence of cytosine, so that the three-bond Watson-Crick base pair GC23 can form (Fig. 16.11). In addition, there are seven more two-bond configurations (see scheme 1, page 262). 

In the nucleic acids, only XC22 is possible due to substitution. This base pair corresponds to the guanine-cytosine Watson-Crick combination GC23 (Fig. 16.11). 

In this section, we present the results of computational studies of the five nucleic acid bases cytosine 13, guanine 14, adenine 15, thymine 16, and uracil 17. The canonical structures, those that are involved in the Watson-Crick base pairing within DNA, are drawn below. Other tautomers for each base can be energetically competitive with the canonical structure, and these other tautomers are invoked in some models of DNA mutations and anomalous DNA structures. The ensuing discussion focuses on the relative energies of the tautomers, in both the gas and solution phases. Structural changes that accompany this phase change are also noted. 

Classic Watson-Crick base pairs are formed by unique hydrogen-bonding interactions between the nitrogenous bases of DNA and RNA. The purine adenine associates specifically with the pyrimidine thymine in DNA (or the related unmethylated analog, macil, in RNA), and the pmine guanine interacts with the pyrimidine cytosine. These complementarity rules. 

Figure 1.3. Watson-Crick Base Pairs. Adenine pairs with thymine (A-T), and guanine with cytosine (G-C). The dashed lines represent hydrogen bonds.

Type B PCET systems of Fig. 17.3 may also be assembled using the three-point hydrogen bond of Watson-Crick base pairs such as guanine (G) and cytosine (C). Sessler and coworkers provided the first example of this assembly with 5, for which only energy transfer is observed [101,102]. A Type B PCET is realized when the cytosine of the GC base pair is appended with an Ae functional group. In 6, a Zn porphyrin serves as De and p-benzoquinone as Ae [103]. Time resolved fluorescence quenching experiments reveal that the rate of ET across the GC interface... 

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