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Protocols

RNAJunction specifications

Information


Unique identifier OMICS_03254
Name RNAJunction
Restrictions to use None
Maintained Yes

Publication for RNAJunction

RNAJunction citations

 (6)
library_books

Advancement of the Emerging Field of RNA Nanotechnology

2017
ACS Nano
PMCID: 5333189
PMID: 28045501
DOI: 10.1021/acsnano.6b05737

[…] ch vertex of the 3WJ (A-i:11–14). (5) Construction of RNA Nanoparticle via Tectonics. Increasing knowledge of RNA folding and availability of databases such as the nucleic acid database (NAD) and the RNAjunction database have increased the power of tectonics, as the number of motifs that can be used as potential tectoRNAs is quite large. Examples include the tectoRNA squares and cubes designed fro […]

call_split

RNA as a stable polymer to build controllable and defined nanostructures for material and biomedical applications

2015
PMCID: 4707685
PMID: 26770259
DOI: 10.1016/j.nantod.2015.09.003
call_split See protocol

[…] hree-dimensional cubic RNA-based scaffolds can be successfully designed and engineered with precise control over their shape, size and composition []. Moreover, online RNA structure databases such as RNAJunction database also provides useful RNA structures for designing RNA nanostructures []. […]

library_books

In Silico Design and Enzymatic Synthesis of Functional RNA Nanoparticles

2014
Acc Chem Res
PMCID: 4066900
PMID: 24758371
DOI: 10.1021/ar400329z

[…] is driven by an input set of junctions, that is, RNA structure fragments, including internal, multibranch, and kissing loops, with short helical stubs emanating from them, such as those stored in our RNAJunction database (Figure ). First, junctions are placed in a 3D workspace, followed by creation of linker helices. The third strategy (Figure c) combinatorially produces a set of closed-shape stru […]

library_books

A Boost for the Emerging Field of RNA Nanotechnology

2011
ACS Nano
PMCID: 3102291
PMID: 21604810
DOI: 10.1021/nn200989r

[…] uences that can self-assemble into 3D RNA nanocomplexes (also see http://www-ccrnp.ncifcrf.gov/∼bshapiro/)., Dr. Shapiro presented elements of a computational RNA nanodesign pipeline,, discussing the RNAJunction Database,() NanoTiler,() RNA2D3D algorithms,() and RNA Dynamics,, which are used to build RNA nanoconstructs that incorporate individual RNA motifs adhering to defined user specifications […]

library_books

ModeRNA: a tool for comparative modeling of RNA 3D structure

2011
Nucleic Acids Res
PMCID: 3105415
PMID: 21300639
DOI: 10.1093/nar/gkq1320

[…] supports the explicit combination of fragments taken from different templates. Several databases with specialized RNA structural motifs facilitate the search for an appropriate fragment. For example RNAJunction provides over 12 000 3D fragments of junction and kissing-loop structures (), and the structural classification of RNA (SCOR) () supports queries for RNA motifs like kink turns and GNRA lo […]

library_books

Sequence–structure relationships in RNA loops: establishing the basis for loop homology modeling

2009
Nucleic Acids Res
PMCID: 2817452
PMID: 19923230
DOI: 10.1093/nar/gkp1010

[…] needs to be established. Examples of current RNA 3D structural motif databases that can form a possible foundation for such a knowledge base are the Structural Classification of RNA database (), the RNAjunction database (), the RNA FRABASE () and the DARTS database (). Second, the sequence–structure relationships have to be explored. Up to what degree of sequence divergence can RNA loops be expec […]

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RNAJunction institution(s)
Basic Research Program, SAIC-Frederick and Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD, USA

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