Geometry Watson-Crick pairing

The 3 terminal redundancy of the genetic code and its mechanistic basis were first appreciated by Francis Crick in 1966. He proposed that codons and anticodons interact in an antiparallel manner on the ribosome in such a way as to require strict Watson-Crick pairing (that is, A-U and G-C) in the first two positions of the codon but to allow other pairings in its 3 terminal position. Nonstandard base pairing between the 3 terminal position of the codon and the 5 terminal position of the anticodon alters the geometry between the paired bases Crick s proposal, labeled the wobble hypothesis, is now viewed as correctly describing the codon-anticodon interactions that underlie the translation of the genetic code. 

It has been found that 6-aminopyrazinone (Scheme 2), when incorporated as a pyrimidine base analog into an ohgonucleotide, might participate in a nonstandard base pair that retains Watson-Crick geometry [14],... 

Fig. 8 Ab initio ground and excited state potential curves for a dAdT Watson/Crick nucleoside pair along the N6(A)-H stretching coordinate. At each point along the curve, the ground-state geometry was optimized constraining the sugars to their positions in a B-DNA chain.

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... 

Overlap Geometry at the Intercalation Site We shall attempt to utilize the nucleic acid base and anthracycline ring proton com-plexation shifts to deduce which anthracycline aromatic ring(s) overlap with nearest neighbor base pairs in the daunomycin poly-(dA-dT) intercalation complex. It should be noted that the nonplanarity of ring A in the antibiotic requires that the aromatic portion of the anthracycline chromophore cannot intercalate with its long axis colinear to the direction of the Watson-Crick hydrogen bonds at the intercalation site as was demonstrated for proflavine-nucleic acid complexes. 

At the HF and DFT level, the ground state geometries of the Watson-Crick (WC) base pairs are generally planar including the amino group [38, 39, 97-100], However, at the MP2 level the amino groups of the WC GC and AT base pairs are revealed pyramidal with smaller basis set, but with larger basis sets the... 

The anionic Watson-Crick guanine-cytosine base pair behaves in a different manner [75], Namely, out of several possible configurations, differing with the position of proton(s), the geometry with proton transferred from the N1 atom of guanine to the N3 atom of cytosine turned out to be the global minimum. This structure is more stable than the Watson-Crick anion by 2.9 (B3LYP) and... 

The Structure of DNA and RNA Double Helices is Determined by Watson-Crick Base-Pair Geometry... 

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