Book of Abstracts: Albany 2007

category image Albany 2007
Conversation 15
June 19-23 2007

Non-Self-Complementary Four and Five Unit-Tangle DNA and DNA-RNA Hybrid Switchback Motifs

Non-self-complementary four unit-tangle and five unit-tangle switchback (SB) DNA and DNA-RNA hybrid motifs have been constructed. They have been characterized using non-denaturing polyacrylamide gel electrophoresis (PAGE), atomic force microscopy (AFM), and Circular Dichroism (CD) spectroscopy. PAGE analyses confirm that non-self-complementary SB 5-tangle DNA and DNA-RNA hybrid motifs have been prepared successfully. By contrast, non-self-complementary SB 4-tangle DNA and DNA-RNA hybrid motifs form large aggregates of paranemic crossover (PX) DNA and PX-like motifs, respectively. AFM imaging reveals that the PX aggregates from non-self-complementary 4-tangle SB DNA motif have roughly 40% linear and 60% cyclic 1D structures, with an average circumference of 600 nm. The aggregates formed with the non-self-complementary SB 4-tangle DNA-RNA hybrid motif are approximately 90% linear and 10% cyclic 1D structures, with an average length of 450 nm. The CD spectra suggest that both 4- and 5-tangle non-self-complementary SB DNA motifs have CD profiles similar to control B-form Watson-Crick double-stranded DNA duplexes. The CD spectra of non-self-complementary SB DNA-RNA hybrid motifs resemble those of A-form Watson-Crick double-stranded RNA duplexes and DNA-RNA hybrid duplexes.

This research supported by NIGMS, NSF, ARO and the W.M. Keck Foundation.

Tanashaya Ciengshin
Roberto Rossetti
Pamela E. Constantinou
Hao Yan
Zhiyong Shen
Nadrian C. Seeman*

Department of Chemistry
New York University
New York NY 10003

*Phone: 212-998-8395
Fax: 212-260-7905
Email: ned.seeman@nyu.edu