Base pair opening

In double-stranded DNA, electron abstraction from the guanine radical cation can be associated with an extremely fast shift of the N1 proton to its Watson-Crick partner cytosine (Scheme 2a) [9]. The equilibrium constant for the protonation of C (pfCa=4.3) with the concomitant deprotonation of G estimated from the pK values of the free nucleosides, is about 2.5 [49]. Within these constraints, the guanine radical should retain some radical cation character [82] and the complete deprotonation of G would require a base pair opening event occurring on a millisecond timescale [74]. An alternative mechanism of G deprotonation is the release of the N2 proton (Scheme 2b). This mechanism was experimentally established for 1-methyl-guanosine conductometric results showed that in neutral solutions, the radical cation of this nucleoside rapidly deprotonates with the formation of the neutral radical [48]. Although the exact mechanism of the G deprotonation in double-stranded DNA requires further clarification, electron abstraction... 

As the polymerase traverses the DNA, it must continually cause a melting or strand separation of the DNA so that a single DNA template strand is available at the active site of the enzyme. During elongation, one base pair re-forms behind the active site for every base pair opened in front of it. The short transient RNA-DNA hybrid duplex that forms between the newly synthesized RNA and the unpaired region of the DNA helps to hold the RNA to the elongating complex. 

Gueron, M., Kochoyan, M., and Leroy, J. L. (1987). A single mode of DNA base pair opening drives imino proton exchange. Nature 328(6125), 89—92. 

Full circles are H-bonded bases in base pairs. Open circles are bases not in clover-leaf base pairs. H-bonds in base pairs are represented by big dots. R = purine base. Y = pyrimidine base. indicates that the nucleotide may be modified. Base-paired regions (stems) are numbered a to e and non base-paired bases are in loops I to IV. The dotted part of loops 1 and III indicate variation on number of nucleotides. 

A subtle (24°) base-pair opening of Ai3-Ti9 is induced by contacts of Hin recombinase (50) with the minor-groove edge of T19 (NDB entry pde009 Fig. 4c). By contrast, the major-groove capture of cytosine by Hhal DNA cytosine-5-methyltransferase... 

Chen, C., Jiang, L., Michalczyk, R. and Russu, LM. (2006) Structural energetics and base-pair opening dynamics in sarcin-ricin domain RNA. Biochemistry, 45, 13606-13613. 

The occurrence of structural/dynamic deviations from the ideal base pair in real base pairs of DNA is not random. Certain sequences of the DNA bases and base pairs are more predisposed than others to adopt certain propeller twist angles, are more fluctional in base-pair opening, and so forth. This is the fundamental basis for the sequence-directed structure and dynamics that are the subject of this chapter. 

Base local motion Rotation/twisting Sugar ring motion Global tumbling Base-pair opening... 

Ramstein, J., Lavery, R. Energetic coupling between DNA bending and base pair opening. Proc. Natl. Acad. Sci. USA 1988,85(19), 7231-5, October. 

Giudice, E., Vamai, P., 8c Lavery, R. (2003). Base pair opening within B-DNA Free energy pathways for GC and AT pairs from umbrella sampling simulations. Nucleic Acids Research, 31,1434. 

The ENCAD force field has been mainly used for protein simulations but some limited applications to nucleic acids have also been reported DNA dodecamer. Tip rep-DNA, and Homeo rep-DNA complexes. The quality of this force field and its performance in the nucleic acid simulations are yet to be confirmed. One of the problems with this force field, which could be noticed here, is for example the irreversible base pair opening in DNA observed during molecular dynamics simulations. ... 

Bryant and DeLuca (5) purified and characterized a Type I nitroreductase from Enterobacter cloacae. The protein is a monomer of approximately 27 kDa, it has a loosely bound FMN cofactor and uses NAD(P)H as an electron donor. The substrate range of the enzyme includes nitrofurans, nitrobenzenes, nitrotoluenes and quinones. The enzyme appears to produce the hydroxylamino derivative of nitroflirazone under aerobic conditions, but the product was not thoroughly characterized. Under anaerobic conditions the product is the amine. The authors did not test the effect of metals on enzyme activity, and no inhibition studies were reported. Therefore, it is not known if this enzyme is a metalloprotein. The gene encoding the Enterobacter reductase was cloned and sequenced (7). The authors found a 651 base pair open reading frame corresponding to a protein of 23.9 kDa. Comparison of the Enterobacter and Salmonella amino acid sequences revealed 88% sequence identity between the two proteins (7). 

Other RNA structures include the RNA claw from the DNA packaging motor from bacteriophage (p29/ the conformation of an RNA structural switch/ structures of miRNA/ the structure of the A730 loop from the Neurospora VS ribozyme/ structures or rRNA, the structure of RNA containing an internal UU loop from myotonic dystrophy type base pair opening found in the adenine tract of an RNA... 

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