Systematic study of constraints imposed by modified nucleoside triphosphates with protein-like side chains for use in in vitro selection

2017 ◽  
Vol 15 (3) ◽  
pp. 610-618 ◽  
Author(s):  
Yajun Wang ◽  
Nicole Ng ◽  
Erkai Liu ◽  
Curtis H. Lam ◽  
David M. Perrin
Keyword(s):  
Systematic Study ◽  
In Vitro Selection ◽  
Primer Extension ◽  
Side Chains ◽  
Nucleoside Triphosphates ◽  
Modified Nucleoside

To select modified DNAzymes and aptamers, modified nucleoside triphosphates (dNTPs) must replace their unmodified counterparts in enzyme-catalyzed primer extension reactions and, once incorporated, serve as template bases in enzyme-catalyzed recopying.

scholarly journals Modified Nucleoside Triphosphates for In-vitro Selection Techniques

2016 ◽  
Vol 4 ◽  
Author(s):  
María A. Dellafiore ◽  
Javier M. Montserrat ◽  
Adolfo M. Iribarren
Keyword(s):  
In Vitro Selection ◽  
Nucleoside Triphosphates ◽  
Modified Nucleoside

Modified Nucleoside Triphosphates: Synthesis and Applications for RNA In Vitro Selection

2003 ◽  
Vol 22 (5-8) ◽  
pp. 1293-1296 ◽  
Author(s):  
Th. Schoetzau ◽  
J. Langner ◽  
E. Moyroud ◽  
I. Röhl ◽  
S. Klussmann ◽  
...  
Keyword(s):  
In Vitro Selection ◽  
Nucleoside Triphosphates ◽  
Modified Nucleoside

Modified Nucleoside Triphosphates: Synthesis and Applications for RNA in vitro Selection

ChemInform ◽  
2004 ◽  
Vol 35 (7) ◽  
Author(s):  
Th. Schoetzau ◽  
J. Langner ◽  
E. Moyroud ◽  
I. Roehl ◽  
S. Klussmann ◽  
...  
Keyword(s):  
In Vitro Selection ◽  
Nucleoside Triphosphates ◽  
Modified Nucleoside

In Vitro Selection of RNA Aptamers Carrying Multiple Biotin Groups in the Side Chains

2001 ◽  
Vol 12 (6) ◽  
pp. 850-854 ◽  
Author(s):  
Yoshihiro Ito ◽  
Akinori Suzuki ◽  
Naoki Kawazoe ◽  
Yukio Imanishi
Keyword(s):  
In Vitro Selection ◽  
Rna Aptamers ◽  
Side Chains ◽  
Selection Of

ChemInform Abstract: Synthesis of Modified Nucleoside 5′-Triphosphates for in vitro Selection of Catalytic Nucleic Acids

ChemInform ◽  
2010 ◽  
Vol 32 (49) ◽  
pp. no-no
Author(s):  
Jasenka Matulic-Adamic ◽  
Andrew T. Daniher ◽  
Alexander Karpeisky ◽  
Peter Haeberli ◽  
David Sweedler ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
In Vitro Selection ◽  
Modified Nucleoside ◽  
Catalytic Nucleic Acids ◽  
Selection Of

scholarly journals Modified nucleoside triphosphates in bacterial research for in vitro and live-cell applications

2020 ◽  
Vol 1 (5) ◽  
pp. 333-351
Author(s):  
Adeline Espinasse ◽  
Hannah K. Lembke ◽  
Angela A. Cao ◽  
Erin E. Carlson
Keyword(s):  
Genetic Material ◽  
Live Cell ◽  
Nucleoside Triphosphates ◽  
Modified Nucleoside ◽  
Enzymatic Mechanisms

Modified nucleoside triphosphates (NTPs) are invaluable tools to probe bacterial enzymatic mechanisms, develop novel genetic material, and engineer drugs and proteins with new functionalities.

Probing DNA polymerase activity with stereoisomeric 2′-fluoro-β-D-arabinose (2′F-araNTPs) and 2′-fluoro-β-D-ribose (2′F-rNTPs) nucleoside 5′-triphosphates

2008 ◽  
Vol 86 (9) ◽  
pp. 881-891 ◽  
Author(s):  
Chang G Peng ◽  
Masad J Damha
Keyword(s):  
In Vitro Selection ◽  
Dna Polymerases ◽  
Polymerase Activity ◽  
Dna Oligomers ◽  
Heterocyclic Base ◽  
Sugar Ring ◽  
Modified Nucleoside ◽  
Diagnostic Research ◽  
Enzyme Substrate Recognition

2′-Deoxy-2′-fluoro-β-D-ribonucleosides (2′F-rN) and 2′-deoxy-2′-fluoro-β-D-arabinonucleosides (2′F-araN) differ solely in the stereochemistry at the 2′-carbon of the furanose sugar ring. 2′F-rN 5′-triphosphates (2′F-rNTPs) are among the most commonly used sugar-modified nucleoside 5′-triphosphates (NTPs) for in vitro selection; however, the epimeric 2′F-araN 5′-triphosphates (2′F-araNTPs) have only recently been applied to polymerase-directed biosynthesis [C.G. Peng and M.J. Damha. J. Am. Chem. Soc. 129, 5310 (2007)]. The present study describes primer extension assays that compare, for the first time, the incorporation efficiency of the two isomeric NTPs, namely, 2′F-araNTPs or 2′F-rNTPs, by four DNA polymerases [Deep Vent (exo-), 9°Nm, HIV-1 RT, and MMLV-RT]. Under the conditions used, incorporation of 2′F-araTTP proceeded more efficiently relative to 2′F-rUTP, while the incorporation of 2′F-araCTP is comparable or slightly less efficient than that observed with 2′F-rCTP. Interestingly, these preferences were observed for all four of the DNA polymerases tested. Unexpected differences in NTP incorporation were observed for 2′F-rCTP vs. rCTP. Despite their seemingly similar conformation, they behaved striking differently in the in vitro polymerization assays. 2′F-rCTP is a much better substrate than the native counterpart (rCTP), an observation first made with human DNA polymerases [F.C. Richardson, R.D. Kuchta, A. Mazurkiewicz, K.A. Richardson. Biochem. Pharmacol. 59, 1045 (2000)]. In contrast, 2′F-rUTP behaved like rUTP, providing poor yield of full-length products. Taken together, this indicates that 2′F-rCTP is very unusual with regard to enzyme/substrate recognition; an observation that can be exploited for the production of DNA oligomers enriched with both ribose and arabinose modifications. These findings are timely given the significant interest and growing need to develop chemically modified oligonucleotides for therapeutic and diagnostic research. By examining the structure-activity relationship (SAR) of the ribose and arabinose sugar, this study furthers our understanding of how the nature of the 2′ substituent (e.g., α vs. β; F vs. OH) and the heterocyclic base affect NTP selection (specificity) by DNA polymerases.Key words: 2′F-rNTPs, 2′F-araNTPs, DNA polymerases, biosynthesis, modified nucleoside triphosphates.

scholarly journals DNAzymes for Amine and Peptide Lysine Acylation

2020 ◽  
Author(s):  
Tianjiong Yao ◽  
Jack Przybyla ◽  
Peter Yeh ◽  
Austin Woodard ◽  
Hannah Nilsson ◽  
...  
Keyword(s):  
Chemical Reactions ◽  
In Vitro Selection ◽  
Side Chains ◽  
Amino Group ◽  
Biologically Relevant ◽  
Protein Substrates ◽  
Peptide Modifications ◽  
Selection For ◽  
Acyl Donors

DNAzymes were previously identified by in vitro selection for a variety of chemical reactions, including several biologically relevant peptide modifications. However, finding DNAzymes for peptide lysine acylation is a substantial challenge. By using suitably reactive aryl ester acyl donors as the electrophiles, here we used in vitro selection to identify DNAzymes that acylate amines, including lysine side chains of DNA-anchored peptides. Some of the DNAzymes can transfer a small glutaryl group to an amino group. These results expand the scope of DNAzyme catalysis and suggest the future broader applicability of DNAzymes for sequence-selective lysine acylation of peptide and protein substrates.

In Vitro Selection of a Ligase Ribozyme Carrying Alkylamino Groups in the Side Chains

2000 ◽  
Vol 11 (6) ◽  
pp. 744-748 ◽  
Author(s):  
Naozumi Teramoto ◽  
Yukio Imanishi ◽  
Yoshihiro Ito
Keyword(s):  
In Vitro Selection ◽  
Side Chains ◽  
Selection Of

scholarly journals DNAzymes for Amine and Peptide Lysine Acylation

2020 ◽  
Author(s):  
Tianjiong Yao ◽  
Jack Przybyla ◽  
Peter Yeh ◽  
Austin Woodard ◽  
Hannah Nilsson ◽  
...  
Keyword(s):  
Chemical Reactions ◽  
In Vitro Selection ◽  
Side Chains ◽  
Amino Group ◽  
Biologically Relevant ◽  
Protein Substrates ◽  
Peptide Modifications ◽  
Selection For ◽  
Acyl Donors

DNAzymes were previously identified by in vitro selection for a variety of chemical reactions, including several biologically relevant peptide modifications. However, finding DNAzymes for peptide lysine acylation is a substantial challenge. By using suitably reactive aryl ester acyl donors as the electrophiles, here we used in vitro selection to identify DNAzymes that acylate amines, including lysine side chains of DNA-anchored peptides. Some of the DNAzymes can transfer a small glutaryl group to an amino group. These results expand the scope of DNAzyme catalysis and suggest the future broader applicability of DNAzymes for sequence-selective lysine acylation of peptide and protein substrates.

Sign in / Sign up

Export Citation Format

Share Document