A recent study examined how surface-enhanced Raman spectroscopy (SERS) can characterize parallel double-stranded DNA (dsDNA).
Characterizing parallel double-stranded DNA (dsDNA) is possible by using surface-enhanced Raman spectroscopy (SERS), according to a recent study published in Analytical Chemistry (1).
Parallel double-strand DNA refers to a structural arrangement of the DNA molecule where both strands run in the same direction, unlike the antiparallel arrangement found in the classic Watson-Crick model (2). In this configuration, both strands of the double helix have their 5' to 3' directionality oriented in the same direction (2). This conformation has been proposed in some non-canonical DNA structures and synthetic DNA molecules, although it contrasts with the predominant antiparallel orientation found in natural DNA. The implications of parallel double-strand DNA extend to its potential use in nanotechnology, particularly in DNA-based computing, molecular machines, and materials science (2). Researchers seek to understand the unique properties and behaviors of parallel double-strand DNA because the consensus is that it could unlock novel applications in biotechnology and nanoscience, driving innovation in various fields.
Read More: Studying Epigenetic Modifications of DNA Using UV Resonance Raman Spectroscopy
However, the lack of robust characterization techniques has hindered its exploration. The research team, led by lead authors Xiaoxuan Xiang, Yang Tian, and Xinhua Guo, attempted to present a solution to this ongoing issue. Comprised of researchers from Jilin University and East China Normal University, the research team demonstrated a novel method that could characterize parallel dsDNA using SERS with gold nanoparticles modified by bromine and magnesium ions (Au BMNPs) as substrates (1).
Blue and red particles DNA helix glowing over dark blue background. | Image Credit: © vladimircaribb - stock.adobe.com
In their study, the research team showed the success of their new method could help improve molecular biology, diagnosis, therapy, and molecular assembly. The researchers showed that there was a series of intensive characteristic Raman bands specific to three types of parallel dsDNA (1). These structures were stabilized by various molecular interactions, including reverse Hoogsteen A+·A+ base pairs, hemiprotonated C+·C and G·G minor groove edge interactions, Hoogsteen A·A base pairs, and Hoogsteen T·A and C+·G base pairs (1).
The technique demonstrated in this study distinguished itself from traditional ones in two important ways. For one, the method used in the study was able to distinguish parallel dsDNA from antiparallel structures (1). The second key advantage is that it was able to identify the orientation of strands within the dsDNA (1). This level of precision in DNA analysis is significant because it had never been achieved before, according to the authors that led the study (1). As a result, their method could be valuable in fields that require precise DNA characterization.
Read More: Optimizing SERS DNA Sensors: Impact of Sandwich-Type Construction and Plasmonic Metal Revealed
The implications of this research are broad. In molecular biology, it could lead to a deeper understanding of DNA-based processes, such as replication and transcription (1). In diagnostics, the ability to accurately differentiate between various DNA conformations could enhance the detection of genetic mutations and diseases. Moreover, in therapy, it could facilitate the design of more targeted and effective treatments (1).
As this technique gains traction, it is expected to catalyze further advancements in DNA analysis, which is critical for our understanding of biological functions.
(1) Zhang, Y.; Xiang, X.; Bao, Y.; et al. Characterization of Parallel-Stranded DNA Duplexes by Surface-Enhanced Raman Spectroscopy and Bromide-Modified Gold Nanoparticles. Anal. Chem. 2024, 96 (12), 4884–4890. DOI: 10.1021/acs.analchem.3c05356
(2) Szabat, M.; Kierzek, R. Parallel-Stranded DNA and RNA Duplexes - Structural Features and Potential Applications. FEBS J. 2017, 284 (23), 3986–3998. DOI: 10.1111/febs.14187
New Method for Rapid SERS Detection of Pesticides in Agricultural Products Unveiled
August 22nd 2024A recent study led by Xaolin Cao at Yantai University demonstrated a rapid and highly sensitive method using magnetic molecularly imprinted polymers combined with surface-enhanced Raman spectroscopy (MMIPs-SERS) for detecting neonicotinoid pesticides in agricultural products.
Best of the Week: AI in Analytical Chemistry, Strock Award
July 12th 2024Top articles this week on Spectroscopy covered topics such as Raman spectroscopy in cultural heritage applications, surface-enhanced Raman spectroscopy (SERS) in pesticide detection, and the impact of artificial intelligence on spectroscopy.
LEGO Bricks: A New Standard for Evaluating Fluorescence in Raman Spectroscopy
July 1st 2024Researchers have proposed an innovative approach to tackling fluorescence interference in Raman spectroscopy by using LEGO blocks as standard samples. This new method offers a low-cost, rugged, and reproducible alternative to the complex liquid mixtures traditionally used in such studies, marking a significant advancement in the field of spectroscopic analysis.