Base-pairs

The hydrogen-bonded base pairs, of which the Watson-Crick forms are most commonly found in native DNA and RNA, were examined by Sponer and Hobza using high-level computations. The geometries were optimized at 

TABLE 7.16 Relative Energies (in Real mol ) of Uracil Tautomers (16a-m) 

Calculated using the relative energies in (a) and thermodynamic quantities computed at MP2/6-31G. Ref. 102. 

Tautomer and one water molecule calculated at RI-MP2/TZVPP//RI-MP2/TZVPP. 

UV with an onset around 36000cm. No spectroscopic detail could be extracted from these broad spectra, and certainly tautomeric information was limited for a long time to bulk measurements. 

Microwave measurements of uracil in a heated cell had suggested the diketo form as the most abundant [70]. Brown et al. [71] had reported the first microwave measurements in a seeded molecular beam and also concluded that the diketo form was predominant. Viant et al. [72] reported the first rotationally resolved gas-phase IR spectra of uracil. This work employed a sht nozzle, an IR diode laser, and a multipass arrangement to obtain high-resolution IR absorption spectra of the out-of-phase Vg(C2=0, C4=0) stretehing vibration. The rotational analysis unambiguously assigned the species to the diketo tautomer. 

Brown et al. [73] also observed the diketo form of thymine in a seeded molecular beam, based on the hyperfine structure in the 14 jj transition. 

I 7 Tautomer-Selective Spectroscopy of Nucleobases, Isolated in the Cas Phase 

Keto-keto (0) Keto-keto (309) Keto-keto (899) Keto-enol-c/s (1343) 

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V (the potential) is identified with the enthalpy, i.e. the number n of base pairings (contacts), and T corresponds to the entropy. At each stage in the folding process, as many as possible new favourable intramolecular interactions are fonned, while minimizing the loss of confonnational freedom (the principle of sequential minimization of entropy loss, SMEL). The entropy loss associated with loop closure is (and the rate of loop closure exp... 

In addition to conventional applications in conducting polymers and electrooptical devices, a number of recent novel applications have emerged. Switching of DNA electron transfer upon single-strand/double-strand hybridization fonns the basis for a new medical biosensor teclmology. Since the number of base pairs of length 20... 

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]. 

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. 

Figure 28 4 supplements Figure 28 3 by showing portions of two DNA strands arranged side by side with the base pairs m the middle... 

FIGURE 28 5 (a) Tube and (b) space filling models of a DNA double helix The carbohydrate-phosphate backbone is on the out side and can be roughly traced in (b) by the red oxygen atoms The blue atoms belong to the purine and pyrimidine bases and he on the inside The base pairing is more clearly seen in (a)... 

FIGURE 28 10 During transcription a molecule of mRNA is assembled from a DNA template Transcription begins at a promoter sequence and proceeds in the 5 3 direction of the mRNA until a termination sequence of the DNA is reached Only a region of about 10 base pairs is unwound at any time... 

Among the 76 nucleotides of tRNA are two sets of three that are especially important The first is a group of three bases called the anticodon, which is comple mentary to the mRNA codon for the ammo acid being transferred Table 28 3 lists two mRNA codons for phenylalanine UUU and UUC (reading m the 5 3 direction) Because base pairing requires the mRNA and tRNA to be antiparallel the two anticodons are read m the 3 5 direction as AAA and AAG... 

The mam use of PCR is to amplify or make hundreds of thousands—even mil lions—of copies of a portion of the polynucleotide sequence m a sample of DNA Sup pose for example we wish to copy a 500 base pair region of a DNA that contains a total of 1 million base pairs We would begin as described m Section 28 14 by cleaving the DNA into smaller fragments using restriction enzymes then use PCR to make copies of the desired fragment... 

Base pair (Section 28 7) Term given to the punne of a nu cleotide and its complementary pyrimidine Adenine (A) is complementary to thymine (T) and guanine (G) is comple mentary to cytosine (C)... 

Dou ble hel ix (Section 28 8) The form in which DNA normally occurs in living systems Two complementary strands of DNA are associated with each other by hydrogen bonds be tween their base pairs and each DNA strand adopts a helical shape... 

Adding as little as 0.1 mb of concentrated HCl to a liter of H2O shifts the pH from 7.0 to 3.0. The same addition of HCl to a liter solution that is 0.1 M in both a weak acid and its conjugate weak base, however, results in only a negligible change in pH. Such solutions are called buffers, and their buffering action is a consequence of the relationship between pH and the relative concentrations of the conjugate weak acid/weak base pair. 

A solution containing a conjugate weak acid/weak base pair that is resistant to a change in pH when a strong acid or strong base is added. 

In the human cell there are 23 pairs of chromosomes containing approximately 3000 million base pairs of DNA. Short sequences of DNA, perhaps with as few as 20 nucleotide units and sometimes radiolabeled, can be obtained either by chemical synthesis (gene machine) or from cloning. These short sequences can be used to probe for a complementary sequence by looking for the position to which they bind to any DNA sample under investigation, from blood for example. Such probes can detect as little as 100 fg of DNA and are the basis of forensic genetic fingerprinting tests. 

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