Stability of the pH-Dependent Parallel-Stranded d(CGA) Motif

Abstract

Non-canonical DNA structures that retain programmability and structural predictability are increasingly being used in DNA nanotechnology applications, where they offer versatility beyond traditional Watson-Crick interactions. The d(CGA) triplet repeat motif is structurally dynamic and can transition between parallel-stranded homo-base paired duplex and anti-parallel unimolecular hairpin in a pH-dependent manner. Here, we evaluate the thermodynamic stability and nuclease sensitivity of oligonucleotides composed of the d(CGA) motif and several structurally related sequence variants. These results show that the structural transition resulting from decreasing the pH is accompanied by both a significant energetic stabilization and decreased nuclease sensitivity as unimolecular hairpin structures are converted to parallel-stranded homo-base paired duplexes. Furthermore, the stability of the parallel-stranded duplex form can be altered by changing the 5′nucleobase of the d(CGA) triplet and the frequency and position of the altered triplets within long stretches of d(CGA) triplets. This work offers insight into the stability and versatility of the d(CGA) triplet repeat motif and provides constraints for using this pH-adaptive structural motif for creating DNA-based nanomaterials. STATEMENT OF SIGNIFICANCE This article addresses the stability of the d(CGA) triplet motif and variants in solution. Our study reveals changes in thermodynamic stability and nuclease resistance in response to pH. The identity of the 5′-nucleobase within each triplet and the position and frequency of different triplets within stretches of d(CGA) triplets can tune parallel-stranded duplex stability. This tunability can be used for nanotechnological applications where the specificity of the 5′-nucleobase pairing interaction is .

Characterization of Parallel-Stranded DNA Duplexes by Surface-Enhanced Raman Spectroscopy and Bromide-Modified Gold Nanoparticles

“…Besides, PS A and H produce a positive band at ∼280 nm. In contrast, the antiparallel W showed a negative band at ∼245 nm and a positive band at ∼280 nm. − These structures also exhibit a hyperchromic shift at 260 nm along with an increase in temperature and melting temperatures ( T m ), as shown in Figure S2. All the results above have confirmed the formation of parallel/antiparallel dsDNA.…”

“…Thus, optimal and tailor-made Au BMNPs are discovered to be suitable for label-free SERS detection of parallel dsDNA. PS CGA (formed through ssDNA SS CGA ), 25,26 and H (formed through ssDNA Pu and RPy), as well as antiparallel dsDNA W (formed through ssDNA Pu and Py) 27 (Figure 1). As a result, the featured bands from parallel dsDNA can unambiguously distinguish parallel dsDNA from antiparallel dsDNA when the base composition of DNA strands is the same.…”

“…Scheme shows the detection procedure. By utilizing this SERS substrate, we obtained high-quality signals corresponding to parallel dsDNAs, including PS A [formed through single-stranded DNA (ssDNA) SS A ], PS CGA (formed through ssDNA SS CGA ), , and H (formed through ssDNA Pu and RPy), as well as antiparallel dsDNA W (formed through ssDNA Pu and Py) (Figure ). As a result, the featured bands from parallel dsDNA can unambiguously distinguish parallel dsDNA from antiparallel dsDNA when the base composition of DNA strands is the same.…”

Conditionally designed luminescent DNA crystals doped by Ln3+(Eu3+/Tb3+) complexes or fluorescent proteins with smart drug sensing property

“…Self-assembled DNA nanostructures have the advantages of modularity, structural programmability, and the resulting extraordinary devices and materials can be used in various research fields. 2–13 The ability to accurately program the secondary structure of oligonucleotide assemblies via base pairing has resulted in the creation of extraordinary devices and materials. Seeman proposed that DNA lattices could host proteins of unknown structure and thereby facilitate structure determination.…”

All-or-None Selectivity in Probing Polarity-Determined Trinucleotide Repeat Foldings with a Parity Resolution by a Beyond-Size-Matching Ligand

“…Nucleotide conformations in a folded duplex play an important role in ligand binding, enzyme recognition, and DNA transcription/translation. − Trinucleotide repeats (TNRs) of CNG and GNC (5′-to-3′, N = T, A, G, C) with abnormal amplification have been identified as the main cause of neurodegenerative diseases. ,− These TNRs can form hairpin structures looping out of the main duplex during replication, in which context, CG/GC base pairs subsequently accommodate N–N mismatches. ,− It has been found that the hairpin foldings of TNRs are dependent on the repeat parity. ,− Namely, the detailed hairpin structures of TNRs are determined by the even/odd repeat number, and slippage complicates further the hairpin structures . Furthermore, the strand polarity of TNRs also defines the detailed structures.…”