Base quadruplets

Fig. 16.17. The base quadruplets formed by two Watson-Crick base pairs have not yet been directly observed experimentally...

Although the base triplets are of only minor importance in double-stranded nucleic acids, they have a structural role in determining and stabilizing the tertiary structure of transfer RNA, as discussed in Chapter 20. Base quadruplets where two Watson-Crick base pairs are associated as shown in Fig. 16.17 have been invoked to play a role in DNA-DNA aggregation and DNA recombination, but there is no direct evidence for their occurrence. 

The most commonly adopted approach, the nearest neighbor (NN) model, is based on a very simple idea since pairing and stacking always act together, the minimum entity which contains both effects is a quadruplet formed by two consecutive nucleotides on one strand and the corresponding nucleotides on the other strand. An example is given in Fig. 2, where the rectangles outline three such quadruplets. Note that the quadruplets overlap. The rationale of this approach is that... 

Base Pairs Can Combine to Form Triplets and Quadruplets... 

Secondary-ion mass spectrometry (SIMS) of a thin layer of nucleic acid bases deposited on a silver foil under bombardment with Ar ions at 3 kV gives intense pseudomolecular ions [M H] but practically no simple bond cleavage fragments. Another new technique is that of (pulsed) laser induced desorption (LD). When applied to nucleotide bases such as cytosine or adenine (266 nm, quadruplet neodymium laser or 347 nm, ruby laser) the technique has good detection limits, particularly for ions with a short lifetime (up to 100 nsec). The technique makes use of a time-of-flight instrument and is utilized in both modes, positive (PI) and negative ions (NI). Both bases exhibit an intense [BH]" ion. These results are similar to those obtained by Cf plasma desorption (PD). 

If the genetic code were based on quadruplet codons rather than triplet codons, and the first two 50 nucleotides in the tRNA anticodon were wobble positions, would there need to be more or less different tRNAs for protein... 

B. Moore, C.C. Nelson, B.C. Persson, R.F. Gesteland, J.F. Atkins, Decoding of tandem quadruplets by adjacent tRNAs with eight-base anticodon loops, Nucleic Acids Res. 2000, 28, 3615-3624. 

Nilakantan et described a similarity measure based also on the interatomic distances between all sets of three nonhydrogen atoms, using a bit-string representation of molecular shape. It is also possible to consider doublets or quadruplets of nonhydrogen atoms (the doublets give rise to similarity measures which are related to the distance-distribution measure described by Pepperrell and Willett see also Ref. 86). 

The single criterion shown in Table 10.2 is based on the formulation of stereoisograms, which respectively contain enantiomeric, / ,S-diastereomeric, and holantimeric relationships. Each of these relationships is capable of producing a definite assembly. Moreover, these relationships are integrated into an RS-stereoisomeric relationship, which is also capable of producing a definite assembly (a quadruplet of l 5-stereoisomers in a stereoisogram). Thereby, the dichotomy between l 5-stereoisomers and others to cover stereoisomerism has been developed as shown in the solid-lined boxes in Fig. 10.11. 

The efiectiveness of the BNB and NBN measures was assessed by simulated property-prediction experiments. These experiments involved the QSAR data sets studied previously by Pepperrell and Willetti" for the evaluation of distance-based similarity measures and a large set of 6-deoxyhexopyranose carbohydrates, which had previously been classified into 14 shape classes using numerical clustering methods based on torsional dissimilarity coefficients. The comparison encompassed the Bemis-Kuntz and Lederle measures, including not just the atom-triplet but also the atom-pair and atom-quadruplet versions of the former measure. The results were equivocal, in that it was impossible to... 

This is a familiar form of the binding isotherm derived for hemoglobin, based on the assumption of total pairwise additivity of both the triplet and the quadruplet potential of average force, as presented in (3.6.48)-(3.6.50). 

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