Synthesis and nucleic-acid-binding properties of sulfamide- and 3′-N-sulfamate-modified DNAElectronic supplementary information (ESI) available: typical melting curves obtained from thermal denaturation of modified oligonucleotides with complementary DNA and RNA. See http://www.rsc.org/suppdata/p1/b1/b110603c/

2002 ◽  
pp. 485-495 ◽  
Author(s):  
Kevin J. Fettes ◽  
Nigel Howard ◽  
David T. Hickman ◽  
Steven Adah ◽  
Mark R. Player ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Thermal Denaturation ◽  
Supplementary Information ◽  
Modified Oligonucleotides ◽  
Nucleic Acid Binding ◽  
Binding Properties ◽  
Complementary Dna ◽  
Dna And Rna ◽  
Melting Curves

Stopped-flow kinetics of locked nucleic acid (LNA)–oligonucleotide duplex formation: studies of LNA–DNA and DNA–DNA interactions

2001 ◽  
Vol 354 (3) ◽  
pp. 481-484 ◽  
Author(s):  
Ulla CHRISTENSEN ◽  
Nana JACOBSEN ◽  
Vivek K. RAJWANSHI ◽  
Jesper WENGEL ◽  
Troels KOCH
Keyword(s):  
Nucleic Acid ◽  
Dissociation Constants ◽  
Locked Nucleic Acid ◽  
Stopped Flow ◽  
Complementary Dna ◽  
Conformationally Restricted ◽  
Dna And Rna ◽  
Melting Curves ◽  
Oligonucleotide Duplex ◽  
Duplex Formation

The locked nucleic acid (LNA) monomer is a conformationally restricted nucleotide analogue with an extra 2′-O,4′-C-methylene bridge added to the ribose ring. Oligonucleotides that contain LNA monomers have shown greatly enhanced thermal stability when hybridized to complementary DNA and RNA and are considered most promising candidates for efficient recognition of a given mixed sequence in a nucleic acid duplex and as an antisense molecule. Here the kinetics and thermodynamics of a series of oligonucleotide duplex formations of DNA–DNA and DNA–LNA octamers were studied using stopped-flow absorption measurements at 25°C and melting curves. The reactions of the DNA octamer 5′-CAGGAGCA-3′ with its complementary DNA octamer 5′-TGCTCCTG-3′, and with the LNA octamers 5′-TLGCTCCTG-3′ (LNA-1), 5′-TLGCTLCCTG-3′ (LNA-2) and 5′-TLGCTLCCTLG-3′(LNA-3), containing respectively one, two or three thymidine 2′-O,4′-C-methylene-(D-ribofuranosyl) nucleotide monomers, designated TL, were studied. In all cases were seen fast second-order association reactions with kobs = 2×107M-1˙s-1. At 25°C the dissociation constants of the duplexes obtained from melting curves were: DNA–DNA, 10nM; DNA–LNA-1, 20nM; DNA–LNA-2, 2nM; and DNA–LNA-3, 0.3nM; thus the greatly enhanced duplex stability induced by LNA is confirmed. Since the association rates were all equal this increase in stability is due to slower rates of dissociation of the complexes.

scholarly journals A non-cleavable hexahistidine affinity tag at the carboxyl-terminus of the HIV-1 Pr55Gag polyprotein alters nucleic acid binding properties

2017 ◽  
Vol 130 ◽  
pp. 137-145 ◽  
Author(s):  
Maria C. Bewley ◽  
Lisa Reinhart ◽  
Matthew S. Stake ◽  
Shorena Nadaraia-Hoke ◽  
Leslie J. Parent ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Carboxyl Terminus ◽  
Nucleic Acid Binding ◽  
Affinity Tag ◽  
Binding Properties ◽  
Hiv 1

scholarly journals In Silico Analysis: Annotations about Structural and Functional Features of DUF 2726 Family Member Proteins

2016 ◽  
pp. 53-58
Author(s):  
SM Sabbir Alam ◽  
M Ruhul Amin ◽  
M Anwar Hossain
Keyword(s):  
Nucleic Acid ◽  
Nuclear Localization ◽  
Nuclear Localization Signal ◽  
Bacterial Species ◽  
Nucleic Acid Binding ◽  
Protein Families ◽  
Binding Properties ◽  
Pfam Database ◽  
Localization Signal ◽  
Functional Features

Domains of unknown functions (DUFs) are a big set of protein families within the Pfam database that includes proteins of unknown function. In the absence of functional information, proteins are classified into different families based on conserved amino acid sequences and are potentially functionally important. In Pfam database, the numbers of families of DUFs are rapidly increasing and in current the fraction of DUF families had increased to about twenty two percent of all protein families. In this study we targeted DUF2726 member proteins which are mainly present in different bacterial species of Gamma-proteobacteria and have a particular domain organization. We analyzed the protein sequences of domain DUF2726 using different computational tools and databases. We found that this domain contains a nuclear localization signal peptide, which is conserved in Escherichia spp. and Shigella spp. It were also predicted that it has nucleic acid binding properties. Analyzing protein-protein interactions functional partners associated with DUF 2726 were revealed. Protein secondary structure, transmembrane helices structure were predicted. We have found that it has gene neighbourhood and co-occurrences with protein RepA and RepB. RepA and RepB are functionally associated with replication. RepA is a replication protein and RepB is a replication regulatory protein. Presence of a nucleic acid binding properties, a nuclear localization signal (NLS) signalling peptide, and possible interaction pattern with replication proteins, conjectures its possible role as a NLS like signalling peptide.Bangladesh J Microbiol, Volume 31, Number 1-2,June-Dec 2014, pp 53-58

RPA nucleic acid-binding properties of IFI16-HIN200

2008 ◽  
Vol 1784 (7-8) ◽  
pp. 1087-1097 ◽  
Author(s):  
Hongyue Yan ◽  
Kush Dalal ◽  
Benjamin K. Hon ◽  
Philippe Youkharibache ◽  
Desmond Lau ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acid Binding ◽  
Binding Properties

Polyplexes based on cationic polymers with strong nucleic acid binding properties

2012 ◽  
Vol 45 (4) ◽  
pp. 459-466 ◽  
Author(s):  
Amir K. Varkouhi ◽  
Grigoris Mountrichas ◽  
Raymond M. Schiffelers ◽  
Twan Lammers ◽  
Gert Storm ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acid Binding ◽  
Cationic Polymers ◽  
Binding Properties
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