Design and synthesis of capped DNA duplexes

Maneesh R Pingle, Purdue University

Abstract

The work describes the design and synthesis of aromatic linker molecules to cap short DNA duplexes in order to improve their thermal stability. The core aromatic moieties were based on naphthalene diimide and terthiophene. The cap molecules were incorporated into short four base pair oligonucleotide duplexes using modified automated oligonucleotide synthesis procedures. Control sequences, containing either four-nucleotide loops (either A or T) or a pentaethylene glycol linker replacing the caps, were also synthesized. Sequences were designed such that the cap molecules were adjacent to either a 5′-CG-3 ′ or a 5′-AT-3′ base pair. Thermal melting experiments were performed on the oligonucleotide samples at multiple concentrations. Oligonucleotide duplexes with naphthalene diimide based caps showed substantially higher Tm values when the cap was adjacent to a CG base pair. The terthiophene containing oligonucleotides showed higher Tm values when the cap was adjacent to an AT base pair. Naphthalene diimide caps were, in general, more effective in increasing the stability of the oligonucleotide duplexes as compared to the terthiophene caps. The length of the aliphatic chains emanating from the naphthalene diimide core showed a preference for an odd number of carbon atoms in the chain. Circular dichroism spectra of the oligonucleotides indicate that the capped oligonucleotides adopt a B-DNA like conformation.

Degree

Ph.D.

Advisors

Bergstrom, Purdue University.

Subject Area

Molecular biology|Organic chemistry

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