Results 21 to 30 of about 2,687,425 (254)
Thermodynamic Analysis of Interacting Nucleic Acid Strands [PDF]
SIAM Review, 2007 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 ...
Robert M. Dirks +4 more
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Monovalent metal ion binding promotes the first transesterification reaction in the spliceosome
Nature Communications, 2023 Cleavage and formation of phosphodiester bonds in nucleic acids is accomplished by large cellular machineries composed of both protein and RNA. Long thought to rely on a two-metal-ion mechanism for catalysis, structure comparisons revealed many contain ...
Jana Aupič +4 more
doaj +1 more source
Thermodynamic framework to assess low abundance DNA mutation detection by hybridization. [PDF]
PLoS ONE, 2017 The knowledge of genomic DNA variations in patient samples has a high and increasing value for human diagnostics in its broadest sense. Although many methods and sensors to detect or quantify these variations are available or under development, the ...
Hanny Willems +7 more
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What Controls the Hybridization Thermodynamics of Spherical Nucleic Acids?* [PDF]
Journal of the American Chemical Society, 2015 The hybridization of free oligonucleotides to densely packed, oriented arrays of DNA modifying the surfaces of spherical nucleic acid (SNA)-gold nanoparticle conjugates occurs with negative cooperativity; i.e., each binding event destabilizes subsequent binding events. DNA hybridization is thus an ever-changing function of the number of strands already
Pratik S, Randeria +6 more
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Polymer Concepts in Cellular Function. [PDF]
Adv Sci (Weinh)Advanced Science, EarlyView.
Yu M +7 more
europepmc +2 more sources
Binding of threading intercalator to nucleic acids: Thermodynamic analyses [PDF]
Nucleic Acids Symposium Series, 2002 The constant melting temperature upon the change in the oligonucleotide concentration showed that the oligonucleotide d(CGCTTTGCG) formed a intramolecular hairpin rather than a duplex with an internal loop. We examined the thermodynamic properties of the interaction between the threading intercalator, naphthalene diimides designated as NDI, and a ...
Hidetaka, Torigoe +5 more
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Algorithms for Nucleic Acid Sequence Design [PDF]
, 2010 Motivated by a growing field of research focused on programming function into biomolecules, we seek to decrease the cost of high-quality rational nucleic acid sequence design while increasing its versatility and availability.
Zadeh, Joseph N.
core +1 more source
On binding mechanism exploration of organic amphoteric dye Rhodamine B with natural polymeric DNA
Discover Materials, 2023 Nucleic acids, like DNA and RNA, are molecules that are present in any life form. Their most notable function is to encode biological information.
Senchumbeni Yanthan +1 more
doaj +1 more source
NTDB: Thermodynamic Database for Nucleic Acids, Version 2.0 [PDF]
Nucleic Acids Research, 2003 The second release of Thermodynamic Database for Nucleic Acids, NTDB 2.0, includes more than 4600 entries (250% increase over release 1.0). It contains sequence types and details of several thermodynamic parameters (enthalpy, DeltaH; entropy, DeltaS; Gibbs free energy, DeltaG; melting temperature, T(m)), experimental models and methods for extracting ...
Wing Lok Abe Kurtz Chiu +5 more
openaire +3 more sources
Stochastic Simulation of the Kinetics of Multiple Interacting Nucleic Acid Strands [PDF]
, 2013 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
Schaeffer, Joseph Malcolm
core +1 more source