Nucleic acids base pairs

J.M. Wong and E. Bateman. TBP-DNA interactions in the minor groove discriminate between A T and T A base pairs. Nucleic Acids Res 22 (1994) 189C)-6. 

Ikuta, S., Takagi, Wallace, R. B., and Itakura, K. (1987) Dissociation kinetics of 19 base paired oligonucleotide -DNA duplexes containing different single mismatched base pairs. Nucleic Acid Res. 15,797-811. 

Kimoto M, Kawai R, Mitsui T, Harada Y, Sato A, Yokoyama S, Hirao 1 (2005) Site-specific incorporation of fluorescent probes into RNA by specific transcription using uimatural base pairs. Nucleic Acids Symp Ser 49 287-288. doi 10.1093/nass/49.1.287... 

Moriyama K, Kimoto M, Mitsui T, Yokoyama S, Hirao I (2005) Site-specific biotinylation of RNA molecules by transcription using unnatural base pairs. Nucleic Acids Res 33(15) el29. doi 10.1093/ nar/gnrl28... 

Chuprina, V. R, Poltev, V. I. (1983). Possible conformations of double-helical polynucleotides containing incorrect base pairs. Nucleic Acids Research, 11, 5205. 

Stombaugh, J., Zirbel, C. L., Westhof, E., Leontis, N. B. (2009). Frequency and isostericity of RNA base pairs. Nucleic Acid Research, 37, 2294. 

Figure 5-6 Outlines of the purine and pyrimidine bases of nucleic acids showing van der Waals contact surfaces and some of the possible directions in which hydrogen bonds may be formed. Large arrows indicate the hydrogen bonds present in the Watson-Crick base pairs. Smaller arrows indicate other hydrogen bonding possibilities. The directions of the green arrows are from a suitable hydrogen atom in the base toward an electron pair that serves as a hydrogen acceptor. This direction is opposite to that in the first edition of this book to reflect current usage.

The bases in nucleic acids can interact via hydrogen bonds. The standard Watson-Crick base pairs are G-C, A T (in DNA), and A U (in RNA). Base pairing stabilizes the native three-dimensional structures of DNA and RNA. 

Nucleic acid bases constituent bases of nucleic acids. N.a.b. are fundamental to the storage and transfer of genetic information by nucleic acids They are Adenine (see). Guanine (see), Cytosine (see). Thymidine (see). Uracil (see) and others that occur less frequently (see Rare nucleic acid components). See also Nucleic acids. Genetic code. Base pairing. 

Ab initio evaluations of the structures and energetics of H-bonded and stacked nucleic acids base pairs carried out since 1994 have provided for the first time a reliable picture of these interactions. This could not be achieved by any other experimental or theoretical technique. These calculations are important in understanding the role of molecular interactions of DNA bases in nucleic acids and allow for a parameterization and verification of the empirical force fields. Intense research of the various aspects of interactions between metal cations and bases and base pairs is under way. 

A FIGURE 21.15 Base Pairing in DNA The bases in nucleic acids are complementary. Each pyrimidine base pairs with only one purine base (G with C, A with T) via specific hydrogen bonds that occur between the two bases. 

The probability of finding a nucleic acid unit in the certain conformation according to our results is never equal to the unit. It agrees with the idea that NAs are not static but fluctuating, breathing , objects [23]. For example, in RNA molecule with 10 base pairs at the room temperature about 510 base pairs do not take part in the stacking and are not connected with H -bonds [2]. 

Transfer RNA (tRNA) Transfer RNAs are relatively small nucleic acids containing only about 70 nucleotides They get their name because they transfer ammo acids to the ribosome for incorporation into a polypeptide Although 20 ammo acids need to be transferred there are 50-60 tRNAs some of which transfer the same ammo acids Figure 28 11 shows the structure of phenylalanine tRNA (tRNA ) Like all tRNAs it IS composed of a single strand with a characteristic shape that results from the presence of paired bases m some regions and their absence m others... 

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