Unusual DNA Structure and DNA Damage Recognition: Structure and Dynamic Markers

Abstract

Nucleic acids play a central role in many biological processes, including information storage, gene expression, serving as messengers or structural components and even catalysis. Their diverse roles have made them targets of interest to diagnose and treat an array of human disorders such as infections, degenerative diseases and cancer. Nature has evolved proteins and ligands that recognize specific nucleic acid sequences or structures and control their function, demonstrating that this can be efficiently accomplished. This has led to the development of wide variety of synthetic molecules that selectively bind to nucleic acids. In turn, this has precipitated numerous studies which showed that nucleic acid structures and their dynamic properties must be understood in order to efficiently target specific sequences or structures.

Recognition of Damaged DNA: Structure and Dynamic Markers

“…Moreover, the repair efficiency is only in part determined by the identity of the mismatch and is also affected by the flanking sequence. 122,123 This suggests that recognition is not solely relying on specific base contacts.…”

LNA units present in [RP-PS]-(DNA#LNA) chimeras enhance the thermal stability of parallel duplexes and triplexes formed with (2′-OMe)-RNA strands

“…20 Hp-DNA duplexes seem to be involved in regulation of cell processes and evolution of neurodegenerative diseases. [21][22][23] Since natural DNA molecules are easily degraded by phosphodiesterases, several modications of the sugar-phosphate backbone have been proposed. Among them, phosphorothioate analogs of DNA (PS-DNA) were found to be very useful because their electronic and steric properties are remarkably close to those of DNA.…”

Adaptively Recognizing Parallel-Stranded Duplex Structure for Fluorescent DNA Polarity Analysis

“…Although being less stable than the antiparallel-stranded DNA duplex (aps-DNA), parallel-stranded DNA duplex (ps-DNA) is believed to still exist in loops and regions of trinucleotide repeats for regulation of cell process and evolution of neurodegenerative diseases. ,, Various covalent modifications, including base surrogate/isomer, − base cross-linkage, intramolecular 3′-3′ or 5′-5′ phosphodiester linkage, and spin label, have been used to investigate the structure and property of ps-DNA. Furthermore, many efforts have also been made to stabilize ps-DNA using exogenous ligands including actinamycin, actinomin, netropsin, distamycin, DAPI, ethidium bromide, benzimidazole, and benzopyridoindole derivatives. ,− Unfortunately, these ligands also serve as the universal groove and intercalation binders of aps-DNA.…”