Uracil base pairing

Shukla MK, Leszczynski J (2002) A theoretical investigation of excited-state properties of die adenine-uracil base pair. J Phys Chem A 106 1011—1018... 

The uracil-uracil base-pair configuration UUS2 (Fig. 16.2) is not observed with the monomer bases, but in the modified nucleoside 5-dimethylaminouridine [DMURID], and it has been proposed to occur in the double helix formed by the... 

Similarly, we can write the interaction matrix for the possible hypoxanthine-uracil base pairs ... 

Figure 3 Supramolecular dimers, trimers, and oligomers generated by H-bonding self-assembly of (a) adenine, (b) uracil, and (c) adenine-uracil base-pair. (R = sugar, alkyl, etc.)...

D. RNA contains uracil instead of thymine. Uracil base-pairs with adenine. 

How many hydrogen bonds link a guanine-c)ftosine base pair an adenine-uracil base pair Would you expect any difference in strength between guanine-cytosine bonding and adenine-uracil bonding Explain. 

Fig 5. Ceo-uracil base paired complexes used in the preparation of Langmuir and... 

The DNA base pairs guanine (G), cytosine (C), adenine (A) and thymine (T). The uracil-2,6-diaminopyridine pair can also form three hydrogen bonds but has a much lower association constant than G-C. 

The mode of action has been a subject for research for a number of years. While it was originally thought that maleic hydrazide replaced uracil in the RNA sequence, it has been deterrnined that the molecule may be a pyrimidine or purine analogue and therefore base-pair formation is possible with uracil and thymine and there exists the probabiHty of base-pair formation with adenine however, if maleic hydrazide occurs in an in vivo system as the diketo species, then there remains the possibiHty of base-pairing with guanine (50). Whatever the mechanism, it is apparent that the inhibitory effects are the result of a shutdown of the de novo synthesis of protein. 

Fig. 6. Elements of RNA stmcture (a) uracil (b) a Watson-Crick A—U base pair and (c) a polynucleotide chain which reads from 5 — 3 ACUG, and...

The substituent effects on the H-bonding in an adenine-uracil (A-U) base pair were studied for a series of common functional groups [99JPC(A)8516]. Substitutions in the 5 position of uracil are of particular importance because they are located toward the major groove and can easily be introduced by several chemical methods. Based on DFT calculation with a basis set including diffuse functions, variations of about 1 kcal/mol were found for the two H-bonds. The solvent effects on three different Watson-Crick A-U base pairs (Scheme 100) have been modeled by seven water molecules creating the first solvation shell [98JPC(A)6167]. 

Although most of an RNA molecule is single-stranded, there often are some double-stranded regions. Intramolecular base pairing between guanine and cytosine and between adenine and uracil creates loops and kinks in the RNA molecule. The structure of one kind of RNA molecule is shown in Figure 13-30. 

Sarai, A., and M. Saito. 1984. Theoretical Studies on the Interaction of Proteins with Base Pairs. I. Ab Initio Calculation for the Effect of H-Bonding Interaction of Proteins on the Stability of Adenine-Uracil Pair, Int. J. Quantum Chem. 25, 527-533. 

A sequence, in general, is the relative order of base pairs, whether in a fragment of a protein, DNA, a gene, a chromosome, or an entire genome. DNA is composed of two antiparallel strands of deoxynucleotides held together by hydrogen bonds between purine (adenine, A and guanine, G) and pyrimidine (thymidine, T uracil, U and cytosine, C) bases. 

Uracil A nitrogenous base normally found in RNA but not in DNA it bonds with adenine to form the A-U base pair. 

A = Adenine = purine T = Thymine = pyrimidine G = Guanine = purine C = Cytosine = pyrimidine U = Uracil = pyrimidine AT/GC base pairs Antiparallel strands Major groove-minor groove A-, B-, and Z-DNA... 

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. 

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). 

Cytosine can become deaminated spontaneously or by reaction with nitrous acid to form uracil. This leaves an improper base pair (G-U), which is eliminated by a base excision repair mechanism (Figure 1-2-5). Failure to repair the improper base pair can convert a normal G-C pair to an A-T pair. 

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.

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