Duplex pair overlaps

Base Pair Overlaps The chemical shifts in the duplex state,... 

Figure 3). These upfield shifts reflect the base pair overlap geometries in the duplex state and result predominantly from ring current contributions due to nearest and next-nearest neighbor base pairs (33,34) These contributions can be computed for the B-DNA overlap geometry and are compared with the experimental upfield chemical shifts on duplex formation of poly(dA-dT) and the related synthetic DNA pol.y(dA-dU) in Table II.

We observe similar base pair overlaps for poly(dA-dT) in 1 M Na+ and TMA+ solution based on a comparison of the base proton chemical shifts of the synthetic DNA in the duplex state as a function of counterion. 

Overlap Geometry A schematic representation of the proposed overlap geometry for proflavine intercalated into a deoxy pyrimidine(3 -5 )purine site is presented below with the (o) symbols representing the location of the phenanthridine ring protons. The mutual overlap of the two base pairs at the intercalation site involves features observed in the crystal structures of a platinum metallointercalator miniature dC-dG duplex complex (55) and the more recent proflavine miniature dC-dG duplex complex (48), as well as features derived in a linked-atom conformational calculation of the intercalation site in the proflavine DNA complex (51). [4]... 

The relative magnitude of the large proflavine upfield complexation shifts requires that the dye intercalate into the duplex with its long axis colinear to the direction of the Watson-Crick hydrogen bonds of adjacent base pairs. This results in significant overlap of the proflavine ring system and base pairs at the intercalation site. 

The large upfield shifts of 1.6 ppm for both phenolic protons which are located between rings B and C of the anthra-cycline ring chromophore demonstrates that the anthracycline ring intercalates into the nucleic acid duplex and experiences ring current contributions from adjacent base pairs. This in turn requires that anthracycline rings B and C overlap with adjacent base pairs at the intercalation site. 

From a chemical perspective, the double-helix produced by two intertwining strands of oligomeric DNA is a fascinating and unique molecular structure. (See Fig. 1 for a structural model of a 12-base pair duplex of B-form DNA.) In it nucleic acid bases are stacked in pairs one on top of the other with a slight twist reminiscent of a spiral staircase [16]. The unique stacking and overlapping of the n- and Tr-electrons of DNA bases may provide a preferred path for electron transfer. Similarly, the exceptional closeness of the stacked bases may have important consequences for charge motion in DNA duplexes. Additionally, the... 

By overlap of the geometrically more extended purine base over the preceding pyrimidine base of the same strand (C72) with the purine base (Gl) of the opposite strand, both nucleotides of the terminal base pair of the stem are locked together more strongly than without this non-paired nucleotide. In this way the overall duplex stability is enhanced, and at the same time the opening rate of the terminal base pair and consequently the imino proton exchange rate of the Gl are considerably reduced. 

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