Structure of RNA aptamer complexed with an RNA-binding peptide of Tat with aid of residue-specific 13C, 15N labeling

Matsugami, Akimasa; Tochio, Hidehito; Niyada, Emi; Tamura, Yasumasa; Kudo, Michiko; Misono, Tomoko; Kumar, Penmetcha K. R.; Katahira, Masato

doi:10.1093/nass/49.1.69

Cited by 2 publications

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“…[5][6][7] The in vitro selection procedure is called "systemic evolution of ligands by exponential enrichment" (SELEX), and the products were named "aptamers". ssDNA and RNA aptamers selectively bind to their target amino acids, [8][9][10] peptides, 11 proteins, 12 nucleotides, 7 carbohydrates, 13 and other molecules. 14,15 The binding of aptamers and their ligand often rely on the secondary and tertiary structural elements of the nucleic acid.…”

Section: Introductionmentioning

confidence: 99%

Microcalorimetrics Studies of the Thermodynamics and Binding Mechanism between l-Tyrosinamide and Aptamer

et al. 2008

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In recent years, several high-resolution structures of aptamer complexes have shed light on the binding mode and recognition principles of aptamer complex interactions. In some cases, however, the aptamer complex binding behavior and mechanism are not clearly understood, especially with the absence of structural information. In this study, it was demonstrated that isothermal titration calorimetry (ITC) and circular dichroism (CD) were useful tools for studying the fundamental binding mechanism between a DNA aptamer and L-tyrosinamide (L-TyrNH2). To gain further insight into this behavior, thermodynamic and conformational measurements under different parameters such as salt concentration, temperature, pH value, analogue of L-TyrNH2, and metal ion were carried out. The thermodynamic signature along with the coupled CD spectral change suggest that this binding behavior is an enthalpy-driven process, and the aptamer has a conformational change from B-form to A-form. The results showed that the interaction is an induced fit binding, and the driving forces in this binding behavior may include electrostatic interactions, hydrophobic effects, hydrogen bonding, and the binding-linked protonation process. The amide group and phenolic hydroxyl group of the L-TyrNH2 play a vital role in this binding mechanism. In addition, it should be noted that Mg(2+) not only improves binding affinity but also helps change the structure of the DNA aptamer.

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Section: Introductionmentioning

confidence: 99%

Microcalorimetrics Studies of the Thermodynamics and Binding Mechanism between l-Tyrosinamide and Aptamer

et al. 2008

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“…For most aptamers, tight binding to RT appears to be governed by the folded structure rather than the sequence of the nucleic acids. This method has since been used to isolate aptamers that can bind several different proteins, including viral therapeutic targets and a few HIV proteins (Gold, 1995;Brody and Gold, 2000;Matsugami et al, 2005;Metifiot et al, 2005;Held et al, 2006a;Kolb et al, 2006). Many of these aptamers…”

Section: Introductionmentioning

confidence: 99%

Novel Aptamer Inhibitors of Human Immunodeficiency Virus Reverse Transcriptase

DeStefano

Nair

2008

Oligonucleotides

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Primer-template-based double-stranded nucleic acids capable of binding human immunodeficiency virus reverse transcriptase (HIV-RT) with high affinity were used as starting material to develop small singlestranded loop-back DNA aptamers. The original primer-templates were selected using a SELEX (Systematic Evolution of Ligands by EXponential enrichment) approach and consisted of 46-and 50-nt primer and template strands, respectively. The major determinant of the ~10-fold tighter binding in selected sequences relative to control primer-templates was a run of 6-8 G residues at the 3′ primer end. Sixty, thirty-seven, twenty-seven, and twenty-two nucleotide loop-back single-stranded versions that retained the base pairs near the 3′ primer terminus were constructed. Both the 60-and 37-nt versions retained high affinity for RT with K d values of ~0.44 nM and 0.66 nM, respectively. Random sequence primer-templates of the same length had K d s of ~20 nM and ~161 nM. The shorter 27-and 22-nt aptamers bound with reduced affinity. Several modifications of the 37-nt aptamer were also tested including changes to the terminal 3′ G nucleotide and internal bases in the G run, replacement of specific nucleotides with phosphothioates, and alterations to the 5′ overhang. Optimal binding required a 4-to 5-nt overhang, and internal changes within the G run had a pronounced negative effect on binding. Phosphothioate nucleotides or the presence of a 3′ dideoxy G residue did not alter affinity. The 37-nt aptamer was a potent inhibitor of HIV-RT in vitro and functioned by blocking binding of other primertemplates.

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Structure of RNA aptamer complexed with an RNA-binding peptide of Tat with aid of residue-specific 13C, 15N labeling

Cited by 2 publications

References 0 publications

Microcalorimetrics Studies of the Thermodynamics and Binding Mechanism between l-Tyrosinamide and Aptamer

Microcalorimetrics Studies of the Thermodynamics and Binding Mechanism between l-Tyrosinamide and Aptamer

Novel Aptamer Inhibitors of Human Immunodeficiency Virus Reverse Transcriptase

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