Structural Properties of G,T‐Parallel Duplexes

Abstract

The structure of G,T-parallel-stranded duplexes of DNA carrying similar amounts of adenine and guanine residues is studied by means of molecular dynamics (MD) simulations and UV- and CD spectroscopies. In addition the impact of the substitution of adenine by 8-aminoadenine and guanine by 8-aminoguanine is analyzed. The presence of 8-aminoadenine and 8-aminoguanine stabilizes the parallel duplex structure. Binding of these oligonucleotides to their target polypyrimidine sequences to form the corresponding G,T-parallel triplex was not observed. Instead, when unmodified parallel-stranded duplexes were mixed with their polypyrimidine target, an interstrand Watson-Crick duplex was formed. As predicted by theoretical calculations parallel-stranded duplexes carrying 8-aminopurines did not bind to their target. The preference for the parallel-duplex over the Watson-Crick antiparallel duplex is attributed to the strong stabilization of the parallel duplex produced by the 8-aminopurines. Theoretical studies show that the isomorphism of the triads is crucial for the stability of the parallel triplex.

Structural Aspects of the Antiparallel and Parallel Duplexes Formed by DNA, 2’-O-Methyl RNA and RNA Oligonucleotides

“…The use of CD spectroscopy to study the geometry of DNA and RNA molecules is well established [ 21 , 35 ]. CD spectra were performed at pH 5.0 and 7.0 in RB buffer containing 100 mM NaCl at 4°C ( Table 1 , Fig 2 ).…”

Integration of Demethylation-Activated DNAzyme with a Single Quantum Dot Nanosensor for Sensitive Detection of O6-Methylguanine DNA Methyltransferase in Breast Tissues

“…Methylation-specific PCR (MSP) can assess MGMT promoter methylation in glioblastoma, but it involves cumbersome operating steps and requires a long period of time. , The enzyme-linked immunosorbent assay (ELISA) uses antibodies to quantify MGMT, but it requires expensive antibodies and suffers from poor specificity . Alternatively, fluorescent biosensors based on fluorophore-labeled protein ligands have been developed to detect MGMT, , but they suffer from low sensitivity due to the incomplete fluorescence quenching-induced high background and the lack of signal amplification strategies. Recently, PvuII endonucleases have been introduced to detect MGMT activity, − which can selectively recognize and cleave the demethylated 5′-CAGCTG-3′ sequence .…”

“…14,15 The enzyme-linked immunosorbent assay (ELISA) uses antibodies to quantify MGMT, but it requires expensive antibodies and suffers from poor specificity. 16 Alternatively, fluorescent biosensors based on fluorophorelabeled protein ligands have been developed to detect MGMT, 17,18 activity, 19−21 which can selectively recognize and cleave the demethylated 5′-CAGCTG-3′ sequence. 22 However, PvuII is susceptible to the environmental conditions, resulting in low amplification efficiency and unsatisfactory sensitivity.…”