The conformations of loop nucleotides in DNA hairpins are to be determined in relation to loop size and sequence, and the effects of these conformations on hairpin stability will be investigated. The study will involve the use of oligonucleotides whose sequences are designed to discourage hairpin-duplex transitions at the high concentrations required for NMR and X-ray diffraction analyses. A new DNA sequence analysis method to be developed will allow, in contrast to currently used methods, the visualization of each nucleotide in the chain, and thus will be useful in the study of the locations and biological roles of modified bases in DNA. Removable affinity handles for DNA will be designed and applied to a number of molecular biological problems. Each affinity handle will consist of the 2',3' cis-diol group of a ribonucleoside attached through a 5'-5' phosphodiester linkage to the synthetic DNA. Attachment will be effected in a DNA synthesizer using an appropriately derivatized ribonucleoside during the final addition cycle. For natural DNA, oligonucleotide linkers containing a terminal ribonucleoside moiety will be synthesized, and these will be joined to the DNA terminals using enzymatic ligation.
