Thermodynamic Analysis of Interacting Nucleic Acid Strands
نویسندگان
چکیده
منابع مشابه
Thermodynamic Analysis of Interacting Nucleic Acid Strands
Motivated by the analysis of natural and engineered DNA and RNA systems, we present the first algorithm for calculating the partition function of an unpseudoknotted complex of multiple interacting nucleic acid strands. This dynamic program is based on a rigorous extension of secondary structure models to the multistranded case, addressing representation and distinguishability issues that do not...
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UNLABELLED Recent interests, such as RNA interference and antisense RNA regulation, strongly motivate the problem of predicting whether two nucleic acid strands interact. MOTIVATION Regulatory non-coding RNAs (ncRNAs) such as microRNAs play an important role in gene regulation. Studies on both prokaryotic and eukaryotic cells show that such ncRNAs usually bind to their target mRNA to regulate...
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DNA nanotechnology is an emerging field which utilizes the unique structural properties of nucleic acids in order to build nanoscale devices, such as logic gates, motors, walkers, and algorithmic structures. Predicting the structure and interactions of a DNA device requires good modeling of both the thermodynamics and the kinetics of the DNA strands within the system. The kinetics of a set of D...
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We describe an algorithm for designing the equilibrium base-pairing properties of a test tube of interacting nucleic acid strands. A target test tube is specified as a set of desired "on-target" complexes, each with a target secondary structure and target concentration, and a set of undesired "off-target" complexes, each with vanishing target concentration. Sequence design is performed by optim...
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Protein-nucleic acid interaction plays an essential role in the regulation of gene expression. Structural and binding information provides insight into the mechanism of protein-nucleic acid recognition. Although there are structural databases for protein-nucleic acid complexes, there exists no database for protein-nucleic acid binding. Thus, we have decided to develop the Thermodynamic Database...
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ژورنال
عنوان ژورنال: SIAM Review
سال: 2007
ISSN: 0036-1445,1095-7200
DOI: 10.1137/060651100