Results 11 to 20 of about 34,496 (157)

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 ...
Dirks, Robert M., Bois, Justin S., Schaeffer, Joseph M., Winfree, Erik, Pierce, Niles A.   +4 more
openaire   +6 more sources

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.
P, Prabakaran, J, An, M M, Gromiha, S, Selvaraj, H, Uedaira, H, Kono, A, Sarai   +6 more
openaire   +2 more sources

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, An Jacobs, Wahyu Wijaya Hadiwikarta, Tom Venken, Dirk Valkenborg, Nadine Van Roy, Jo Vandesompele, Jef Hooyberghs   +7 more
doaj   +1 more source

Novel isoguanine derivative of unlocked nucleic acid-Investigations of thermodynamics and biological potential of modified thrombin binding aptamer. [PDF]

PLoS ONE, 2018
Thrombin binding aptamer (TBA), is a short DNA 15-mer that forms G-quadruplex structure and possesses anticoagulant properties. Some chemical modifications, including unlocked nucleic acids (UNA), 2'-deoxy-isoguanosine and 2'-deoxy-4-thiouridine were ...
Weronika Kotkowiak, Tomasz Czapik, Anna Pasternak   +2 more
doaj   +1 more source

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
openaire   +3 more sources

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, Jhimli Bhattacharyya   +1 more
doaj   +1 more source

Design principles for ligand-sensing, conformation-switching ribozymes. [PDF]

PLoS Computational Biology, 2009
Nucleic acid sensor elements are proving increasingly useful in biotechnology and biomedical applications. A number of ligand-sensing, conformational-switching ribozymes (also known as allosteric ribozymes or aptazymes) have been generated by some ...
Xi Chen, Andrew D Ellington
doaj   +1 more source

Hachimoji DNA and RNA: A genetic system with eight building blocks [PDF]

, 2019
Reported here are DNA and RNA-like systems built from eight (hachi-) nucleotide letters (-moji) that form four orthogonal pairs. This synthetic genetic biopolymer meets the structural requirements needed to support Darwinism, including a polyelectrolyte ...
Bates, Alison M., Benner, Steven A., DasGupta, Saurja, Ellington, Andrew D., Georgiadis, Millie M., Hoshika, Shuichi, Karalkar, Nilesh B., Kim, Hyo-Joong, Kim, Myong-Jung, Kim, Myong-Sang, Leal, Nicole A., Meyer, Adam J., Piccirilli, Joseph A., SantaLucia, Holly A., SantaLucia, John, Jr., Watkins, Norman E., Jr.   +15 more
core   +1 more source

Physico-chemical foundations underpinning microarray and next-generation sequencing experiments [PDF]

, 2013
Hybridization of nucleic acids on solid surfaces is a key process involved in high-throughput technologies such as microarrays and, in some cases, next-generation sequencing (NGS).
A. Buhot, A. E. Pozhitkov, A. Halperin, A. Harrison, A. Ott, Amend, B. M. Pettitt, Berger, Binder, Binder, Binder, Binder, Bolstad, Bullard, Burden, Burden, C. Gibas, C. J. Burden, Chou, Chou, Czypionka, D. P. Kreil, D. Tautz, E. Carlon, Fasold, Fasold, Fiche, Fuchs, H. Binder, Halperin, Harr, Harrison, He, Heim, Held, Hooyberghs, Huettel, Iltumur, Irizarry, Irizarry, Irizarry, Irving, J. Hooyberghs, Kane, L. J. Gamble, Lee, Lee, Letowski, Li, Liebich, Lockhart, Luebke, Marshall, Matveeva, Mueckstein, Mulders, Naiser, Naiser, P. A. Noble, Pingel, Pozhitkov, R. Levicky, Relogio, Rouillard, Tanaka, Trapp, Upton, Vainrub, Wodicka, Yu, Zhang   +70 more
core   +3 more sources

HiTRACE: High-throughput robust analysis for capillary electrophoresis [PDF]

, 2011
Motivation: Capillary electrophoresis (CE) of nucleic acids is a workhorse technology underlying high-throughput genome analysis and large-scale chemical mapping for nucleic acid structural inference. Despite the wide availability of CE-based instruments,
Bylund, Cormen, Cover, Das, Das, Deigan, Ewing, Ewing, Hanjoo Kim, Jinkyu Kim, Justine Hum, Kay, Kazmi, Kladwang, Kladwang, Laederach, Levenberg, Marquardt, Merino, Mitra, Nielsen, Oppenheim, Peattie, Pravdova, Rhiju Das, Robinson, Ruiz-Martinez, Seunghyun Park, Sungroh Yoon, Tijerina, Tomasi, Vasa, Walczak, Watts, Weeks, Wilkinson, Wipapat Kladwang, Wong, Woolley, Xi   +39 more
core   +1 more source