Hostname: page-component-848d4c4894-hfldf Total loading time: 0 Render date: 2024-06-01T01:28:11.499Z Has data issue: false hasContentIssue false
  • English
  • Français

Optimization of nucleic acid scaffold design using fluorescence measurements

Published online by Cambridge University Press:  28 January 2019

Jessica Anderson ,
McKenze Moss ,
Nancy Nguyen ,
Natalie Hughes ,
Amira Gee  and
Mehnaaz F. Ali
Jessica Anderson
Affiliation:
Department of Chemistry, Xavier University of Louisiana, 1, Drexel Drive, New Orleans LA70125
McKenze Moss
Affiliation:
Department of Chemistry, Xavier University of Louisiana, 1, Drexel Drive, New Orleans LA70125
Nancy Nguyen
Affiliation:
Department of Chemistry, Xavier University of Louisiana, 1, Drexel Drive, New Orleans LA70125
Natalie Hughes
Affiliation:
Department of Chemistry, Xavier University of Louisiana, 1, Drexel Drive, New Orleans LA70125
Amira Gee
Affiliation:
Department of Chemistry, Xavier University of Louisiana, 1, Drexel Drive, New Orleans LA70125
Mehnaaz F. Ali*
Affiliation:
Department of Chemistry, Xavier University of Louisiana, 1, Drexel Drive, New Orleans LA70125
*
*(Email: mali2@xula.edu)
Get access

Abstract

The current work focuses on optimizing aptamer scaffolds that are tailored to allow for the formation of binding pockets for both a redox active signaling molecule and the target miR-92a. These newly designed allosteric nucleic acid systems are studied for efficacy to undergo a target based conformational switch. Two hairpin scaffolds were designed with differing stem stabilities and were explored using fluorescence quenching measurements. The dose dependent data for the detection of miR-92a shows the importance of scaffold design where the stability of the intra-molecular hairpin structure has to be optimized for target binding. Additional experiments explored the selectivity of the aptamer scaffolds in the presence of competing miR’s and mismatched sequences. These results provide an important precursor to constructing nucleic acid scaffolds for the detection of miR’s using label-free redox signaling.

Keywords

luminescencenanoscaleresponsivesensor
Type
Articles
Information
MRS Advances , Volume 4 , Issue 23: Biomaterials and Soft Materials , 2019 , pp. 1349 - 1354
Copyright
Copyright © Materials Research Society 2019 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

REFERENCES

Soukup, G. A. and Breaker, R. R., TIBTech 17, 469 (1999).CrossRefGoogle Scholar
Lodmell, J. S. and Dahlberg, A. E., Science 277, 1262 (1997).CrossRefGoogle Scholar
Gowda, K. and Zwieb, C., Nucleic Acids Res 25, 2835 (1997).CrossRefGoogle Scholar
Sanghavi, S. S. B., Griep, M., Karna, S., Ali, M. F., Swami, N. S., Anal. Chem. 85, 8158 (2013).CrossRefGoogle Scholar
Sitaula, S., Branch, S. D., and Ali, M. F., Chem. Commun. 48, 9284 (2012).CrossRefGoogle Scholar
Johnson, J. J., Loeffert, A. C., Stokes, J., Olympia, R. P., Bramley, H., and Hicks, S. D., JAMA Pediatr. 172 , 65 (2018).CrossRefGoogle Scholar
Mitchell, P. S., Parkin, R. K., Kroh, E. M., Fritz, B. R., Wyman, S. K., Pogosova-Agadjanyan, E. L., et al. , PNAS 105, 10513 (2008).CrossRefGoogle Scholar
Skinner, J. P., Keown, A. A., and Chong, M. M., PLoS One 9, p. e88997 (2014).CrossRefGoogle Scholar
Marzi, M. J., Ghini, F., Cerruti, B., de Pretis, S., Bonetti, P., Giacomelli, C., et al. , Genome Res, 26, 554, (2016).CrossRefGoogle Scholar
Burgstaller, P. and Famulok, M., Bioorg. Med. Chem. Lett. 6, 1157, (1996).CrossRefGoogle Scholar