Uracil single base pair

One of the most prominent hydrogen-bonded systems is DNA. Despite numerous experimental and theoretical investigations on vibrational spectra of nucleic acid bases [7-13], information on inter- and intramolecular interactions in base pairs and DNA oligomers is still limited [14-25]. A recent example is the work on single adenine-uracil (AU) base pairs in the Watson-Crick geometry in solution, which showed an enhancement of vibrational energy... 

Many spontaneous mutations are point mutations, which involve a change in a single base pair in the DNA sequence. One of the most frequent point mutations comes from deamination of a cytosine (C) base, which converts it into a uracil (U) base. In addition, the common modified base 5-methyl cytosine forms thymine when it is deaminated. If these alterations are not corrected before the DNA is replicated, the cell will use the strand containing U or T as template to form a U-A or T-A base pair, thus creating a permanent change to the DNA sequence (Figure 23-25). 

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. 

The structures of RNA molecules consist of a single polymer chain of nucleotides with the same bases as DNA, with the exception of thymine, which is replaced by uracil, which forms a complementary base pair with adenine (Figure 1.33(a)). These chains often form single stranded hairpin loops separated by short sections of a distorted double helix formed by hydrogen bonded complementary base pairs (Figure 1.33(b)). 

Solvation of DNA bases/base pairs is of fundamental importance to biological processes as they take place in aqueous media. The effect of hydration on neutral bases or base pairs has been addressed using quantum chemical methods [106-112] as well as molecular dynamics (MD) simulations [113, 114], It is known that unlike the gas phase, dipole bound anions do not exist in condensed environments because such diffuse states are destabilized in the aqueous phase [115]. The drastic change in the nature of excess electron binding in the presence of water molecules with uracil has been observed experimentally by Bowen and co-workers [95b] using negative electron photoelectron spectroscopy (PES). They observed that even with a single water molecule the dipole bound state of uracil anion in gas phase... 

RNA is single-stranded, but the strands loop back on themselves and the bases pair guanine with cytosine and adenine with uracil. 

When not replicating, DNA serves as the code for synthesis of proteins. During protein synthesis, a small portion of DNA is copied by complementary base pairing of RNA nucleotides (adenine, guanine, cytosine and uracil instead of thymine) to form single stranded messenger ribonucleic acid (mRNA) in the nucleus of the cell. This process is known as transcription and is catalysed by an enzyme called RNA polymerase. 

Although RNA molecules are single-stranded, base pairing between uracil and adenine and between guanine and cytosine can still occur. We will show the importance of this property as we examine the way in which RNA molecules are involved in the expression of the genetic information in DNA. 

The bases in RNA are adenine (A), guanine (G), cytosine (C), and uracil (U). These are the same bases as DNA except that the base uracil is used in place of thymine (T). Unlike DNA, RNA is rarely composed of two strands base paired with each other. Instead, RNA exists as a single-stranded entity, though extensive regions of many RNAs may form double helices within themselves by the base pairing rules. 

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