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.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM011518-29
Application #
2168544
Study Section
Bio-Organic and Natural Products Chemistry Study Section (BNP)
Project Start
1974-05-01
Project End
1996-03-31
Budget Start
1994-04-01
Budget End
1996-03-31
Support Year
29
Fiscal Year
1994
Total Cost
Indirect Cost
Name
Purdue University
Department
Biology
Type
Schools of Arts and Sciences
DUNS #
072051394
City
West Lafayette
State
IN
Country
United States
Zip Code
47907