Base-pairing schemes

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]. 

Fig. 37. Possible base-pairing scheme for 34 and four cytosine-containing derivatives. Reproduced with permission from Ref. (58). Copyright 2000, Wiley-VCH.

Fig. 52. Suggested base-pairing scheme for metal derivatized M-DNA where the imino protons of N3-T and Nl-G are replaced by a divalent metal ion. Adapted from Ref. (177).

Cytosine is generally represented in the lactam-amine form 2 both as a free molecule and in its nucleoside or nucleotide. This is also the form considered to be involved in the base-pairing scheme in DNA. 

Tn orcTer to extend these conformational energy studies to the analysis of multi-stranded nucleic acid systems, it is necessary to devise a procedure to identify the arrangements of the polynucleotide backbone that can acconmodate double, triple, and higher order helix formation. As a first step to this end, a computational scheme is offered here to identify the double helical structures compatible with given base pairing schemes. 

Figure 4. Proposed base-pairing schemes that accommodate the A-DNA-like...

Since the IR spectrum of an RNA molecule has numerous features, IR spectroscopy is not limited to the determination of the fraction folded only. Depending upon the wavenumber of the transition, IR spectroscopy can distinguish A-U base pairs from G-C base pairs as well as the more complex base pairing schemes found in triple helices (Banyay et al., 2003 Brauns and Dyer, 2005). Similarly, base stacking interactions can be distinguished from base pairing interactions. It has even been shown that transfer RNAs of different species can be distinguished from their IR spectra (Thomas, 1969). 

The above-mentioned purine-pyrimidine base-pairing scheme consists, as it is well known, of hydrogen bonding between specific, complementary base pairs, namely, adenine-thymine [or uracil in ribonucleic acid (RNA)] and guanine-cytosine (Fig. 1) (shorthand notations A-T or A-U and G-C). The specificity of the bonding concerns both this exclusiveness and the steric arrangement which is... 

Fig. 3. The effect of rare tautomeric forms on the change in the base-pairing scheme and its perpetuation through DNA replication.

Complexes formed between different homo-polynucleotides usually adopt the Watson-Crick base-pairing scheme as, for instance, poly(C) poly(G), poly(C) poly(I), poly(A) poly(U), poly(dA) poly(dT), etc. They are consequently right-handed double helices with antiparallel polynucleotide strands. 

Tautomerism in the bases commands interesting prominence in the history of the elaboration of the structure of DNA by James Watson and Francis Crick. When in the early 1950s Watson was attempting to identify structurally compatible base pairing schemes using simple two-dimensional cardboard models of the bases, he inadvertently deployed the rare tautomeric states until the chemist Jerry Donahue pointed out this error to him. 

An alternative to these two tautomer models for point mutations assumes non-Watson-Crick base pairing schemes between normal tautomer forms in which the glycosidic bonds are displaced relative to their normal position in DNA. In other words, incorporation of these wobble mispairs requires appropriate adjustment of the DNA backbone resulting in glycosidic distances different from the usual 10.7 A. 

Figure 4 (sl, b) Hoogsteen and (c-e) wobble base-pairing schemes. I =inosine... 

Figure 9 Base-pairing schemes in Y RY motif (a) T AT and (b) C -GC triads. The arrows indicate the relative 5 - 3 directionalities of the three strands...

Figure 10 Base-pairing schemes in R RY motif (a) A AT, (b) G GC and (c) T AT triads. Note the reverse HG mode for the third-strand T in (c) as compared to T AT in Figure 9...

P2, Z = 2 Dx = 1.413 R = 0.07 for 2,874 reflections. The adenine and uracil bases participate in the Hoogsteen base-pairing scheme, with the uracil and adenine bases of two, different, ApU molecules. The N-6-H of adenine is hydrogen-bonded to 0-4 of uracil, and the... 

A-, B-, and Z-DNA DNA is found as a base-paired duplex. A-, B-, and Z-DNA are different duplex structures with the same base-pairing scheme, but different three-dimensional structures. A- and B-DNA are right-handed helices Z-DNA is lefthanded. B-DNA is the predominant structure of DNA in cells A-DNA is found in duplex structures containing RNA. 

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