Expanded-size bases in naturally sized DNA: evaluation of steric effects in Watson-Crick pairing

Journal of the American Chemical Society
Jianmin GaoEric T Kool

Abstract

We describe physicochemical properties in DNA of altered-size nucleobases that retain Watson-Crick analogous hydrogen-bonding ability. Size-expanded analogues of adenine and thymine (xA and xT, respectively, which are expanded by benzo-fusion) were incorporated into natural DNA oligonucleotides, and their effects on helix stability were measured. Base stacking studies revealed that the two stretched analogues stack much more strongly than do their naturally sized counterparts. In contrast to this, pairing studies showed that single substitutions of the new bases are destabilizing to the natural helix as compared to A or T in standard A-T pairs in the same context, unless multiple adjacent substitutions are used. Interestingly, the size-expanded bases displayed selective recognition of the hydrogen-bonding complementary partners, suggesting that Watson-Crick analogous pairs were still formed despite local backbone strain. In an attempt to compensate for the added size of the expanded adenine, we tested a formamide deoxynucleoside, which Leonard proposed as a shortened thymine analogue (F(o)). Data showed, however, that this compound adopts a conformation unfavorable for pairing. On the basis of the combined thermodynamic data, w...Continue Reading

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Citations

Feb 21, 2007·Accounts of Chemical Research·Andrew T KruegerEric T Kool
Jun 1, 2012·ACS Chemical Biology·Armando R HernándezEric T Kool
Mar 9, 2010·Chemical Reviews·Renatus W SinkeldamYitzhak Tor
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Jul 13, 2006·Journal of the American Chemical Society·Alex H F Lee, Eric T Kool
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