Kinetic and thermodynamic analysis of triplex formation between peptide nucleic acid and double-stranded RNA

2018 ◽  
Vol 16 (7) ◽  
pp. 1178-1187 ◽  
Author(s):  
Takaya Sato ◽  
Naonari Sakamoto ◽  
Seiichi Nishizawa
Keyword(s):  
Nucleic Acid ◽  
Thermodynamic Analysis ◽  
Thermodynamic Data ◽  
Peptide Nucleic Acid ◽  
Double Stranded Rna ◽  
Triplex Formation ◽  
Kinetic And Thermodynamic Analysis

We revealed an association mechanism for PNA–dsRNA triplex formation based on a set of kinetic and thermodynamic data.

The detrimental effect of orotic acid substitution in the peptide nucleic acid strand on the stability of PNA2:NA triple helices

2005 ◽  
Vol 83 (10) ◽  
pp. 1731-1740 ◽  
Author(s):  
Robert HE Hudson ◽  
Filip Wojciechowski
Keyword(s):  
Nucleic Acid ◽  
Carboxylic Acid ◽  
Peptide Nucleic Acid ◽  
Triple Helix ◽  
Orotic Acid ◽  
Uv Spectroscopy ◽  
Triplex Formation ◽  
Helix Formation ◽  
Triple Helix Formation ◽  
The Stability

We have investigated the incorporation of C6 derivatives of uracil into polypyrimidine peptide nucleic acid oligomers. Starting with uracil-6-carboxylic acid (orotic acid), a peptide nucleic acid monomer compatible with Fmoc-based synthesis was prepared. This monomer then served as a convertible nucleobase whereupon treatment of the resin-bound methyl orotate containing hexamers with hydroxide or amines cleanly converted the ester to an orotic acid or orotamide-containing peptide nucleic acid. Peptide nucleic acid hexamers containing the C6-modified nucleobase hybridized to both poly(riboadenylic acid) and poly(deoxyriboadenylic acid) via triplex formation. Complexes formed with poly(riboadenylic acid) were more stable than those formed with poly(dexoyriboadenylic acid), as measured by temperature-dependent UV spectroscopy. However, both of these complexes were destabilized relative to the complexes formed by an unmodified peptide nucleic acid oligomers. Internal or doubly substituted hexamers are destabilized more strongly than a terminally substituted one, and the type of substitution (carboxamide, ester, carboxylic acid) affects the overall triplex stability. These results clearly show that incorporation of a C6-substituted uracil into polypyrimidine PNA is detrimental to triplex formation. We have also extended this chemistry to incorporate uracil-5-methylcarboxylate into a peptide nucleic acid hexamer. After on-resin conversion of the C5 ester to the 3-(N,N-dimethylamino)propylamide, significant stabilization of the triplex formed with poly(riboadenylic acid) was observed, which illustrates the compatibility of C5 substitution with peptide nucleic acid directed triple helix formation. Key words: peptide nucleic acid, triple helix, orotic acid, orotamide, PNA.

Metallo-regulation of the bimolecular triplex formation of a peptide nucleic acid

2013 ◽  
Vol 42 (45) ◽  
pp. 16006 ◽  
Author(s):  
Hiroshi Shimada ◽  
Toshihiko Sakurai ◽  
Yusuke Kitamura ◽  
Hirotaka Matsuura ◽  
Toshihiro Ihara
Keyword(s):  
Nucleic Acid ◽  
Peptide Nucleic Acid ◽  
Triplex Formation

scholarly journals Extended Peptide Nucleic Acid Nucleobases Based on Isoorotic Acid for the Recognition of A–U Base Pairs in Double‐Stranded RNA

2021 ◽  
Author(s):  
Nikita Brodyagin ◽  
Aubrey L. Maryniak ◽  
Ilze Kumpina ◽  
John M. Talbott ◽  
Martins Katkevics ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Peptide Nucleic Acid ◽  
Base Pairs ◽  
Double Stranded Rna

Molecular insights on the dynamic stability of peptide nucleic acid functionalized carbon and boron nitride nanotubes

2021 ◽  
Vol 23 (1) ◽  
pp. 219-228
Author(s):  
Nabanita Saikia ◽  
Mohamed Taha ◽  
Ravindra Pandey
Keyword(s):  
Nucleic Acid ◽  
Boron Nitride ◽  
Nucleic Acids ◽  
Dynamic Stability ◽  
Peptide Nucleic Acid ◽  
Rational Design ◽  
Peptide Nucleic Acids ◽  
Boron Nitride Nanotubes ◽  
Molecular Hybrids ◽  
Single Wall Nanotubes

The rational design of self-assembled nanobio-molecular hybrids of peptide nucleic acids with single-wall nanotubes rely on understanding how biomolecules recognize and mediate intermolecular interactions with the nanomaterial's surface.

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