Base pairing Table

We turn now to consider recent work on PtR and discuss here only the four most representative PtR models, 1-4, along with a model, Model 4bi, derived from Model 4 with different hydrogen bonding of the base pairs (Table 4). All of the PtR models have helical kinks as determined experimentally (Fig. 15 for the representative Model 4bi). These models fall either within the LL family (1) or between the NP and LL families with mainly LL (2) or NP (3,4, and 4bi, Fig. 16) features. Since the key structural chang-... 

In this regard, significant chemical modification is required to effect either keto-enol or amino-imino tautomerism of the nitrogenous bases, with the consequent formation of A C and G T mispairs that fit into the canonical double-helical structure. Notably, the N6-methoxy A C mispairs and the 06-methylated G T mispairs, which are observed in crystalline duplex structures, are isomorphous with standard A T and G C base pairs (Tables 1 and 2) NDB entries bd0009, bdlb26, and bdlb58 (19-21). 

Some tRNAs bond to one codon exclusively, but many of them can recognize more than one codon because of variations in the allowed pattern of hydrogen bonding. This variation is called wobble (Figure 12.4), and it applies to the first base of an anticodon, the one at the 5 end, but not to the second or the third base. Recall that mRNA is read from the 5 to the 3 end. The first (wobble) base of the anticodon hydrogen-bonds to the third base of the codon, the one at the 3 end. The base in the wobble position of the anticodon can base-pair with several different bases in the codon, not just the base specified by Watson-Crick base pairing (Table 12.2). 

Most viruses are much smaller than bacteria and are therefore not seen in the light microscope. The dimensions of virus particles generally lie in the range of about 100-3000 A, and the nucleic acid chains have a molecular weight 10 containing up to 10 or more base pairs (Table 11.24). 

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... 

Approximately 10 base pairs are required to make one turn in B-DNA. The centers of the palindromic sequences in the DNA-binding regions of the operator are also separated by about 10 base pairs (see Table 8.1). Thus if one of the recognition a helices binds to one of the palindromic DNA sequences, the second recognition a helix of the protein dimer is poised to bind to the second palindromic DNA sequence. 

The protein-DNA interactions have been analyzed in detail at high resolution in the complex between the 434 repressor fragment and the ORl containing 20mer DNA. A pseudo-twofold symmetry axis relates the halves of this complex. The symmetry is not exact since the nucleotide sequence of the DNA is slightly different in each half (see Table 8.2). However, the interactions between one protein subunit and one half of the DNA are very similar to those between the second subunit and the other half of the DNA since most of the bases that interact with the protein are identical in both halves. Details of the interaction are very similar to those in the complex with the palindromic synthetic 14mer of DNA shown in Figures 8.14 and 8.15. The base pairs at one end of the DNA, 1-14, 2-13, etc. are called base pairs 1, 2, etc. 

A clue to the chemical basis of base pairing in DNA came from the analysis of the base composition of various DNAs by Erwin Chargaff in the late 1940s. His data showed that the four bases commonly found in DNA (A, C, G, and T) do not occur in equimolar amounts and that the relative amounts of each vary from species to species (Table 11.3). Nevertheless, Chargaff noted that certain pairs of bases, namely, adenine and thymine, and guanine and cytosine, are... 

An alternative form of the right-handed double helix is A-DNA. A-DNA molecules differ in a number of ways from B-DNA. The pitch, or distance required to complete one helical turn, is different. In B-DNA, it is 3.4 nm, whereas in A-DNA it is 2.46 nm. One turn in A-DNA requires 11 bp to complete. Depending on local sequence, 10 to 10.6 bp define one helical turn in B-form DNA. In A-DNA, the base pairs are no longer nearly perpendicular to the helix axis but instead are tilted 19° with respect to this axis. Successive base pairs occur every 0.23 nm along the axis, as opposed to 0.332 nm in B-DNA. The B-form of DNA is thus longer and thinner than the short, squat A-form, which has its base pairs displaced around, rather than centered on, the helix axis. Figure 12.13 shows the relevant structural characteristics of the A- and B-forms of DNA. (Z-DNA, another form of DNA to be discussed shortly, is also depicted in Figure 12.13.) A comparison of the structural properties of A-, B-, and Z-DNA is summarized in Table 12.1. 

Consider the weak acids in Table 13.2. Which acid-base pair would behest for a buffer at apH of... 

TABLE P a 10.3 Conjugate Acid-Base Pairs Arranged by Strength Acid name Acid formula Base formula Base name PKb... 

A practical problem in solution preparation usually requires a different strategy than our standard seven-step procedure. The technician must first identify a suitable conjugate acid-base pair and decide what reagents to use. Then the concentrations must be calculated, using pH and total concentration. Finally, the technician must determine the amounts of starting materials. The technician needs a buffer at pH = 9.00. Of the buffer systems listed in Table 18-1. the combination of NH3 and NH4 has the proper pH range for the required buffer solution. 

C18-0053. From Table 18-1. select the best conjugate acid-base pairs for buffer solutions at pH 3.50 and 12.60. If you were going to add HCl solution as part of the buffer preparation, what other substance should you use in each case ... 

The results of the various semi-empirical calculations on the reference structures contained within the JSCH-2005 database (134 complexes 31 hydrogen-bonded base-pairs, 32 interstrand base pairs, 54 stacked base pairs and 17 amino acid base pairs) are summarised in Table 5-10. The deviations of the various interaction energies from the reference values are displayed in Figure 5-5. As with the S22 training set, the AMI and PM3 methods generally underestimate the interactions whereas the dispersion corrected method (PM3-D) mostly over-estimates the interactions a little. Overall the PM3-D results are particularly impressive given that the method has only... 

In a another experiment, we confirmed that the hole migration from the G+ to the remote GG step through four intervening AT base pairs is extremely difficult (Table 2 and Fig. 4). These observations are consistent with... 

Receptor sites. The intercalation and kinked sites in DNA used in this study are listed in Table V. Three theoretically determined intercalation sites (I, II and III) permit the study to be conducted with the DNA unwound by 7°-12°, lU-l8° and 25°-32° with parallel base pairs separated by 6.76 A and with alternating (a) sugar puckers (67,68) Attention will be confined to site I because it was found to be the most favorable in the present studies. Several kink (K) sites have been identified (66). The constraint that proper hybridization exists about N2(g) and CIO of BPDEs stimulated an investigation in kinked DNA. In an idealized structure the pyrene moiety is approximately parallel to one of the base pairs as shown... 

The energy required to adjust the DNA to these receptor sites is given in Table VI. The DNA can kink equally well in both grooves with base pairs held at a distance sufficient for intercalation (Az = 6.76 A, ax = 0°) and for kinks (Az > 6.76 A, ax 0°). These receptor sites are constructed by operations on a pair of initially coincident base pairs. Each is rotated by +ax/2 and -ax/2 about a kink axis. This axis is perpendicular to the helix and dyad axes of the base, and parallel to the Cl (py)-Cl (pu) axis. It lies approximately along the C6(py)-C8(pu) axis. Then each base pair is rotated about the helix axis by +az/2 and -az/2 and separated by Az. The combinations of ax, az, and Az which permit the construction of a phosphate backbone defines families of receptor sites. With this approach, the base pairs adjacent to the BPDE are symmetrically... 

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