Thermal Stability of Modified i‐Motif Oligonucleotides with Naphthalimide Intercalating Nucleic Acids

Abstract

In continuation of our investigation of characteristics and thermodynamic properties of the i‐motif 5′‐d[(CCCTAA)3CCCT)] upon insertion of intercalating nucleotides into the cytosine‐rich oligonucleotide, this article evaluates the stabilities of i‐motif oligonucleotides upon insertion of naphthalimide (1H‐benzo[de]isoquinoline‐1,3(2H)‐dione) as the intercalating nucleic acid. The stabilities of i‐motif structures with inserted naphthalimide intercalating nucleotides were studied using UV melting temperatures (Tm) and circular dichroism spectra at different pH values and conditions (crowding and non‐crowding). This study indicated a positive effect of the naphthalimide intercalating nucleotides on the stabilities of the i‐motif structures compared to the wild‐type structure which is in contrast to a previous observation for a pyrene‐intercalating nucleotide showing a decrease in Tm values.

i-Clamp phenoxazine for the fine tuning of DNA i-motif stability

“…In turn, different porphyrin-containing nucleotide and non-nucleotide derivatives were placed into the fragment of the sequence that did not participate in iM core formation, and they provoked strong stabilization (average T m was 53°C, whereas T m of the unmodified sequence was <25°C) at pH 5.0 owing to porphyrin–porphyrin interactions ( 41 ). Naphthalimide derivatives were introduced into the TAA loop of iM-forming sequence and one of them showed nearly equal stabilizing effects of 6°C at different pH (5.2 and 6.2) under crowding and noncrowding conditions ( 42 ). In addition, a shift of pH transition values up to 0.5 was observed.…”

Synthesis, Characterization and Docking Study of Novel Pyrimidine Derivatives as Anticancer Agents

“…From the modern therapeutic organic synthesis point of view and our previous work to modify DNA, [4][5][6] synthesis of modified DNA bases guanosine 1 and adenosine 6 derivatives was carried out. The Sonogashira reaction was carried out on the 2-pent-4-ynyl-isoindole-1,3-dione 2 with bromoguanosine 1 and bromoadenosine 6 using copper iodide and tetrakis(triphenylphosphine) palladium(0) Pd(PPh3)4 in the presence of triethyl amine to synthesize compound 3 and 7 (Scheme 1).…”

“…Modification of DNA and RNA oligonucleotides with new synthesized heterocyclic compounds have drawn significant interest owing to their ability to imitate new gene chemical probes that play an important role in the drug discovery process [1][2][3][4][5][6][7]. Gene-therapy in recent research was based on DNA and its modification [8][9][10].…”

“…Gene-therapy in recent research was based on DNA and its modification [8][9][10]. The thymidine ring is a DNA building block that interests many researchers to focused their research on the synthesis of new pyrimidine rings as anti-cancer agents such as 5-fluorouracil [1][2][3][4][5][6][7][8][9][10][11][12][13][14], and anti-HIV like AZT, D4T, Nikavir [15][16][17][18][19][20][21], Lamivudina [22] and Emtricitabina [16,[23][24]. The Nitrogen containing heterocycles like pyrimidines and their derivatives have received great attention for their considerable exciting biological activities [25][26][27][28].…”

High definition polyphosphoesters: between nucleic acids and plastics

“…86 Naphthalimide systems can also stabilise i-motifs. 87 Häner also performed important foundational work in this area by substituting a single base in a duplex with an aromatic unit (phenanthrene) building block -this was destabilising when placed opposite a canonical base in a duplex, but stabilising when opposite itself. 88 Structure-based photophysical effects became clear when moving to a pyrene system; with careful choice of linker length, a pyrene dimer across the duplex forms, giving excimer emission and no reduction in Tm (Fig.…”