Thermodynamic Analysis of Interacting Nucleic Acid Strands

NUPACK: Analysis and design of nucleic acid systems

UNLABELLED The Nucleic Acid Package (NUPACK) is a growing software suite for the analysis and design of nucleic acid systems. The NUPACK web server (http://www.nupack.org) currently enables: ANALYSIS thermodynamic analysis of dilute solutions of interacting nucleic acid strands. DESIGN sequence design for complexes of nucleic acid strands intended to adopt a target secondary structure at eq...

A partition function algorithm for interacting nucleic acid strands

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...

Electronic, optical, thermodynamic parameter, NMR analysis on fullerene interacting with glycine by DFT methods

A thermodynamic approach to designing structure-free combinatorial DNA word sets

An algorithm is presented for the generation of sets of non-interacting DNA sequences, employing existing thermodynamic models for the prediction of duplex stabilities and secondary structures. A DNA 'word' structure is employed in which individual DNA 'words' of a given length (e.g. 12mer and 16mer) may be concatenated into longer sequences (e.g. four tandem words and six tandem words). This a...

Synthesis, Characterization and interaction Studies of 1-(3-bromophenyl azo) 2,7-dihydroxy naphthalene, (BPADHN) with calf thymus deoxy ribo nucleic acid (ct-DNA)

In this study at first , an azo dye, 2,7- naphthalenediol, 2-[(4-Bromophenyl)azo (BPAND) as a ligand has been synthesized by addition of p-Bromoaniline to the modified montomorillonite K10 clay. This ligand was characterized using 1H-NMR, UV-Vis and IR spectroscopies. Subsequently, its interaction with calf thymus deoxyribonucleicacid ,ct-DNA was investigated in 5 mM phosphate buffer solution, ...