Base pairing in RNA

Adenine (A) A nitrogenous purine base, which bonds with thymine (T) to form the A-T base pair in DNA and the A-U base pair in RNA. 

M. Brandi, M. Meyer, and J. Siihnel, Water-mediated base-pairs in RNA a quantum-chemical Study, J. Phys. Chem. A 104, 11177-11187 (2000). 

Beside Hg, other late transition metal ions (e.g., Ag and Au ) can coordinate to DNA nucleobases to form interstrand cross-links. Several DNA coordination modes have been suggested for Ag ions, including coordination to the purine N1 and the pyrimidine N3 (86). At Ag /base pair ratios <0.5, the metal ion coordinates to the N7 position of purines, in particular to guanine, while at a Ag /bp ratio of 0.5, Ag forms cross-links between the two strands of the duplex by binding to two nucleobases (89). The Au " " ion was also shown to coordinate to solvent-exposed GC base pairs in RNA duplexes to form a G-Au-C bridge that resembles T-Hg-T (88). 

In DNA, essentially every base is part of a base pair in RNA only a portion of the bases are paired. Most of the DNA in cells is in the structure known as B-form DNA (Fig. 2.4). B-form DNA is actually a family of similar structures that vary in their detailed conformation depending on the precise sequence of individual bases along the chain. B-form DNA comprises two sugar-phosphate chains with complementary sequences such that when the two chains are wound round one another, in opposite (antiparallel) directions, to form a right-handed double helix,... 

Water-mediated base pairs in RNA A quantum-chemical study ... 

It is demonstrated that the spatial proximity of H nuclei in hydrogen bonded base-pairs in RNAs can be conveniently mapped via solid-state MAS NMR experiments involving proton spin diffusion driven chemical shift correlation of low-frequency nuclei such as the imino and amino nitrogens of nucleic acid bases.As different canonical and non-canonical base-pairing schemes encountered in nucleic acids are characterised by topologically different networks of proton dipolar couplings, different base-pairing schemes lead to characteristic cross-peak intensity patterns in such correlation spectra. The method was employed in a study of a 100 kDa RNA composed of 97 CUG repeats that has been implicated in the neuromuscular disease myotonic dystrophy. N- N chemical shift correlation studies confirmed the presence of Watson-Crick GC base pairs in (CUG)g7. 

Sponer, 1. E., Leszczynski, J., Sychrovsky, V., Sponer, 1. (2005a). The sugar edge/sugar edge base pairs in RNA. Stabilities and structures from quantum chemical calculations. Journal of Physical Chemistry B, 109,18680. 

Most of the DNA of animal cells is found in the nucleus, where DNA is the major constituent of the chromosomes. On the other hand, most of the RNA is located in the cytoplasm. Nuclear DNA exists as a thin, double helix only 2 nm wide. The double helix is folded and complexed with protein to form chromosomal strands approxim-ately 100 to 200 nm in diameter. Each chromosome contains a single DNA duplex. The human chromosomes vary in size the smallest contains approximately 4.6 X 10 base pairs of DNA, and the largest 2.4 X 10 base pairs. In contrast, the Escherichia coli chromosome has 4.5 x 106 base pairs. The DNA of die chromosomes is tightly packed and associated with both histone and nonhistone proteins. 

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). 

Figure 20.4 The bases present in RNA and DNA and the Watson-Crick base pairing relationships. Uracil is present in RNA but is replaced by thymine in DNA that is, the pairs C-G and T-A are found in DNA the pairs C-G but U-A are found in RNA. The pairing is brought about by hydrogen bonding, indicated by a broken line.

As with proteins, the nucleic acid polymers can denature, and they have secondary structure. In DNA, two nucleic acid polymer chains are twisted together with their bases facing inward to form a double helix. In doing so, the bases shield their hydrophobic components from the solvent, and they form hydrogen bonds in one of only two specific patterns, called base pairs. Adenine hydrogen bonds only with thymine (or uracil in RNA), and guanine pairs only with cytosine. Essentially every base is part of a base pair in DNA, but only some of the bases in RNA are paired. The double-helix structure... 

Most p-independent terminators have two distinguishing features. The first is a region that produces an RNA transcript with self-complementary sequences, permitting the formation of a hairpin structure (see Fig. 8-2la) centered 15 to 20 nucleotides before the projected end of the RNA strand. The second feature is a highly conserved string of three A residues in the template strand that are transcribed into U residues near the 3 end of the hairpin. When a polymerase arrives at a termination site with this structure, it pauses (Fig. 26-7). Formation of the hairpin structure in the RNA disrupts several A=U base pairs in the RNA-DNA hybrid segment and may disrupt important interactions... 

UG pairs provide a very small amount of stabilization to an RNA double helix, while the presence of unpaired bases has a destabilizing effect. The most stable hairpin loops contain four or five bases. Depending upon whether the loop is "closed" by CG or AU, the helix is destabilized by 20-30 kj/mol. "Bulge loops," which protrude from one side of a helix, have a smaller destabilizing effect. An example of the way in which Table 5-2 can be used to estimate the energies of formation of a loop in a straight-chain RNA is illustrated in Fig. 5-9. Similar analysis of base pairing in DNA can also be done.53 55... 

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