Results 11 to 20 of about 10,354 (218)

A Mathematical Model of Nucleic Acid Thermodynamics

, 2018
The DNA denaturation, the double-stranded DNA unwinding process, is a vital process for cells. The percentage of the denaturation is used as an index of organism complexity and it is the base of the DNA hybridisation technique, which provides a great deal of information.
Franco Pastrone, Sonia Guarguagli
core   +2 more sources

Thermodynamic analysis of Zα domain-nucleic acid interactions [PDF]

Biochemical Journal, 2022
Abstract DNA/RNA molecules adopting the left-handed conformation (Z-form) have been attributed with immunogenic properties. However, their biological role and importance has been a topic of debate for many years. The discovery of Z-DNA/RNA binding domains (Zα domains) in varied proteins that are involved in the innate
Bharath Srinivasan, Krzysztof Kuś, Alekos Athanasiadis   +2 more
openaire   +2 more sources

Thermodynamic Analysis of Nylon Nucleic Acids [PDF]

ChemBioChem, 2008
AbstractThe stability and structure of nylon nucleic acid duplexes with complementary DNA and RNA strands was examined. Thermal denaturing studies of a series of oligonucleotides that contained nylon nucleic acids (1–5 amide linkages) revealed that the amide linkage significantly enhanced the binding affinity of nylon nucleic acids towards both ...
Yu, Liu, Risheng, Wang, Liang, Ding, Ruojie, Sha, Philip S, Lukeman, James W, Canary, Nadrian C, Seeman   +6 more
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NTDB: Thermodynamic Database for Nucleic Acids [PDF]

Nucleic Acids Research, 2001
A new thermodynamic database for normal and modified nucleic acids has been developed. This Thermodynamic Database for Nucleic Acids (NTDB) includes sequence, structure and thermodynamic information as well as experimental methods and conditions. In this release, there are 1851 sequences containing both normal and modified nucleic acids.
Wing Lok Abe Kurtz Chiu, Chun Ngai Sze, Lai Nang Ip, Sze Ki Chan, Steve Chik Fun Au-Yeung   +4 more
openaire   +2 more sources

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, Justin S. Bois, Joseph M. Schaeffer, Erik Winfree, Niles A. Pierce   +4 more
openaire   +2 more sources

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, Matthew R, Jones, Kevin L, Kohlstedt, Resham J, Banga, Monica, Olvera de la Cruz, George C, Schatz, Chad A, Mirkin   +6 more
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Thermodynamic database for protein–nucleic acid interactions (ProNIT) [PDF]

Bioinformatics, 2001
Abstract Motivation: Protein–nucleic acid interactions are fundamental to the regulation of gene expression. In order to elucidate the molecular mechanism of protein–nucleic acid recognition and analyze the gene regulation network, not only structural data but also quantitative binding data are necessary.
Ponraj Prabakaran, Jianghong An, M. Michael Gromiha, Samuel Selvaraj, Hatsuho Uedaira, Hidetoshi Kono, Akinori Sarai   +6 more
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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, Chun Ngai Sze, Nap Tak Ma, Lai Fan Chiu, Chung Wai Leung, Steve Chik Fun Au-Yeung   +5 more
openaire   +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, Shinobu, Sato, Ken-ichi, Yamashita, Satoshi, Obika, Takeshi, Imanishi, Shigeori, Takenaka   +5 more
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Nucleic acid-lipid membrane interactions studied by DSC

Journal of Pharmacy and Bioallied Sciences, 2011
The interactions of nucleic acids with lipid membranes are of great importance for biological mechanisms as well as for biotechnological applications in gene delivery and drug carriers. The optimization of liposomal vectors for clinical use is absolutely
Sarantis Giatrellis, George Nounesis
doaj   +1 more source