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RNA base pairing

The predictable nature of DNA and RNA base pairing make their interactions the most defined of any biological system. The specific affinity of one strand for its complementary... [Pg.64]

Transfer RNAs base-pair with mRNA codons at a three-base sequence on the tRNA called the anticodon. The first base of the codon in mRNA (read in the 5 —>3 direction) pairs with the third base of the anticodon (Fig. 27-8a). If the anticodon triplet of a tRNA recognized only one codon triplet through Watson-Criclc base pairing at all three positions, cells would have a different tRNA for each amino acid codon. This is not the case, however, because the anticodons in some tRNAs include the nucleotide inosinate (designated I), which contains the uncommon base hypoxanthine (see Fig. 8-5b). Inosinate can form hydrogen bonds with three different nucleotides (U, C, and A Fig. 27-8b), although... [Pg.1039]

DNA polymerases cannot initiate synthesis of a complementary strand of DNA on a totally single-stranded template. Rather, they require an RNA primer—that is, a short, double-stranded region consisting of RNA base-paired to the DNA template, with a free hydroxyl group on the 3 -end of the RNA strand (Figure 29.15). This hydroxyl group serves as the first acceptor of a nucleotide by action of DNA polymerase. In de novo DNA synthesis, that free 3-hydnoxyl is provided by the short stretch of RNA, rather than DNA. [Pg.400]

Telomerase consists of a protein and short RNA molecule that is complementary to the TTGGGG repeat in the telomere. This complementary RNA sequence base pairs with the telomere allowing Telomerase to add additional complementary bases to the 3 terminus of the telomere. The enzyme then translocates 6 bases towards tire 3 end so that the RNA base pairs with the last two or three nucleotides that were just synthesized.. Telomerase then adds the next set of complementary nucleotides and repeats the cycle. Human Telomerase is not yet well characterized but is believed to follow a similar mechanism. [Pg.407]

Brandi, M., Meyer, M., and Suhnel, J. (2001) Quantum-chemical analysis of C-H- - -O and C H- - -N interaidions in RNA base pairs—H-bond versus anti-H-bond pattern, J. Biomol Struct. Dyn. 18, 545-555. [Pg.291]

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. [Pg.108]

The 3 terminus of the viral RNA base pairs with the overhanging DNA strand, forming a circle-like structure. [Pg.1116]

In the following an overview on experimentally determined base polyad containing nucleic add structures deposited at the PDB is given, see Appendix (Table 2). In many cases the triplex or tetraplex fold formed jBrom on two, three or foiu strands is the major determinant of a structure. The compilation in Table 2 is int ded to be comprehensive for this structure type. On the other hand, especially in RNA structures only a few or even only one pol (s) may occur. Comprehensiveness for these structures would require a systematic anal is of dl currently known RNA structures. Recently, a database of non-canonical RNA base pairs has been set up. In addition to base pairs it also lists 331 base triads and 2S base tetrads (Mdch 7,2002). We have done a few random checks of the database and noticed that it represents a rather good starting point for further analysis but is not comprehensive. Table 2 includes only a few representative cases of polyads in RNA structures. [Pg.169]

By performing molecular dynamics simulation studies, Sykes and Levitt observed that the stability of RNA base pairs largely depends on the degree of solvation of RNA (see Figure 7.8) [11]. If the number of water molecules is inadequate for solvation then, due to insufficient inter-water HBs, water starts to form H bonds with Watson-Crick bases of the DNA, decreasing the stabUity of the base pairs by disrupting inter-base HBs. However, in the presence of a sufficient amount of water, the number of HBs found to disrupt these base pairs becomes less (see Figure 7.9). As a consequence, the base pairs exist in a stability niinimum of 20-100 water molecules, the upper limit of which corresponds to the approximate number of water molecules contained in the first hydration shell. [Pg.105]

M.T. Sykes and M. Levitt, Simulations of RNA base pairs in a nanodroplet reveal solvation-dependent stability. Proc. Natl. Acad. Sci. USA, 104 (2007), 12336-12340. [Pg.114]

RNA base pairs, are also encapsulated by using host-guest n-stacking interactions. The number of stacking planer molecules can be finely controlled by the length of aromatic pillars. ... [Pg.1452]

Sponer, ]. E., Spackova, N., Leszczynski, ]., Sponer, 1. (2005b). Principles of RNA base pairing Structures and energies of the trans Watson-Crick/sugar edge base pairs. Journal of Physical Chemistry B, 109,11399. [Pg.1274]

Sponer, J., Zgarbova, M., Jurecka, P., Riley, K. E., Sponer, J. E., Hobza, P. (2009). Reference quantum chemical calculations on RNA base pairs directly involving the 2 -OH group of ribose. Journal of Chemical Theory and Computation, 5, 1166. [Pg.1275]

Stombaugh, J., Zirbel, C. L., Westhof, E., Leontis, N. B. (2009). Frequency and isostericity of RNA base pairs. Nucleic Acid Research, 37, 2294. [Pg.1275]


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