Enhanced Diagnostic Tools
PNA is a synthetic analogue of DNA and RNA, developed more than a decade ago, in which the naturally occurring sugar phosphate backbone has been replaced by the N-(2-aminoethyl) glycine units, Scheme 1.10 PNA can hybridize to complementary DNA or RNA strand through Watson-Crick base-pairing; because of the unnatural backbone, PNA can neither be recognized nor easily degraded by proteases or nucleasessall of which make PNA an attractive reagent for biotechnology applications.11 However, unlike DNA or RNA in the unhybridized state (single strand) whose structure, to a large degree, is extended in solution due to the negatively charged phosphate backbone, PNA tends to fold into complex globular structures, 12,13 presumably due to the collapse of the hydrophobic nucleobases. In fact, this conformational collapse has been exploited in the development of stemless PNA molecular beacons, taking advantage of the proximity between the two termini in the unhybridized state.12,14-16 Several modifications have been made to the PNA N-(2-aminoethyl) glycine backbone in attempts to increase its rigidity;17,18 however, only a few such modifications showed improvements in the hybridization properties19-24 many of which require either elaborate
synthesis19-22 or the use of relatively expensive D-amino acids as starting materials.23,24 Of the various backbone modifications that have been made, only a few were made at the γ-position.25-27 A systematic study correlating structure with function at this position has not yet been established. To fill this void, we have developed a research program to explore the structural effects of γ-backbone modifications on the conformation and hybridization properties of PNA.
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