Book of Abstracts: Albany 2009

category image Albany 2009
Conversation 16
June 16-20 2009
© Adenine Press (2008)

Exploration of Structural Building Block Properties for RNA Nanostructures

Our group is pursuing computer-aided strategies for designing RNA-based nanostructures. As part of this effort we have developed an RNAJunction database, which provides a large set of RNA junctions (internal loops and loop-loop interactions). These can be used as building blocks for larger, biologically functionalized nanostructures. Our programs, NanoTiler and RNA2D3D, can utilize them, together with idealized fragments of A-form helices, to produce the desired 3D shapes. Up to this stage the building blocks are treated as rigid or near-rigid objects. However, experimental data shows that RNA structures are flexible and capable of accommodating their shape to the constraints of larger structural contexts. Here we present examples of the RNA-based nanostructure designs, stressing the characterization of the structural flexibility of the building blocks and potential strategies for controlling these characteristics. We present examples of the characterization of various reprogrammed (edited) kissing loops (KL) based on the HIV-1 KL complex, as well as the use of modified nucleotides to change its characteristics. We contrast them with the dynamic behavior of other kissing loops. Larger characterized structures include tectosquare building blocks, in which the flexible KLs appear to be necessary for the assembly, and a triangle and its individual large building block monomers.

Funded in part by NCI contract N01-CO-12400. This research was supported by the Intramural Research Program of the NIH, National Cancer Institute, Center for Cancer Research.

Wojciech Kasprzak1
Eckart Bindewald1
Tae-Jin Kim2
Bruce A. Shapiro2

1Basic Science Program
SAIC-Frederick, Inc.
NCI at Frederick
Frederick, MD, 21702
2Center for Cancer Research Nanobiology Program
National Cancer Institute at Frederick
Frederick, MD, 21702

Tel: 301 846 5536
Fax: 301 846 5598
Email: bshapiro@ncifcrf.gov