Do Nucleic Acids Have Sulfur? Surprising Roles in Gene Expression

Nucleic acids, such as DNA and RNA, are primarily composed of carbon, hydrogen, oxygen, nitrogen, and phosphorus. Unlike proteins, which contain sulfur in amino acids like cysteine and methionine, nucleic acids generally lack this element. However, exceptions exist where sulfur plays a role in their structure and function.

Understanding sulfur’s role in nucleic acids provides insights into gene regulation and molecular biology. Researchers have identified both natural and synthetic sulfur modifications that influence genetic processes.

Naturally Occurring Sulfur Substitutions

While sulfur is not a standard component of nucleic acids, certain biological systems incorporate it into DNA and RNA through specialized modifications. One well-documented example is phosphorothioate (PS) substitution, where a non-bridging oxygen in the phosphate backbone is replaced by sulfur. This modification occurs naturally in some bacterial and archaeal genomes, enhancing DNA stability and resistance to enzymatic degradation.

Bacteria such as Escherichia coli and Streptomyces species enzymatically introduce phosphorothioate modifications into their DNA through the dnd (DNA degradation) gene cluster. First identified in Streptomyces lividans, this system acts as a form of epigenetic regulation, marking specific DNA sequences with sulfur-containing groups. These modifications influence gene expression by altering DNA-protein interactions, affecting transcription and chromosomal architecture. Studies show that phosphorothioate modifications occur at specific sequence motifs, suggesting a targeted regulatory role.

Sulfur modifications also appear in RNA, particularly in transfer RNA (tRNA) and ribosomal RNA (rRNA). In RNA, sulfur substitution often occurs at nucleosides, forming thiolated nucleotides such as 4-thiouridine (s4U) and 2-thiocytidine (s2C). These modifications are critical for tRNA stability and function, particularly in codon-anticodon interactions during translation. In Escherichia coli, 4-thiouridine in tRNA acts as a photoreceptor, sensing ultraviolet (UV) light and triggering stress responses. This suggests that sulfur incorporation in RNA extends beyond structural stability, playing a role in environmental adaptation and cellular signaling.

Synthetic Sulfur Modified Nucleic Acids

The incorporation of sulfur into nucleic acids has gained traction in synthetic biology and therapeutic research, improving stability, binding affinity, and enzymatic resistance. One extensively studied modification involves phosphorothioate (PS) linkages, where sulfur replaces a non-bridging oxygen in the phosphate backbone. This alteration disrupts nuclease recognition sites, increasing resistance to enzymatic degradation. As a result, phosphorothioate-modified oligonucleotides have become integral to antisense therapies, RNA interference (RNAi), and splice-switching interventions.

Phosphorothioate-modified antisense oligonucleotides (ASOs) are widely used in clinical settings to modulate gene expression. These molecules bind to target mRNA sequences, promoting degradation via RNase H-mediated cleavage or blocking translation. Drugs such as nusinersen, an FDA-approved ASO for spinal muscular atrophy, employ phosphorothioate modifications to enhance bioavailability and prolong systemic circulation. PS linkages are also incorporated into small interfering RNAs (siRNAs) and aptamers to improve pharmacokinetics and reduce degradation, underscoring their therapeutic potential.

Beyond phosphorothioates, other synthetic sulfur modifications fine-tune nucleic acid properties. Thionucleosides, where sulfur replaces oxygen in nucleobases or ribose sugars, improve hybridization efficiency and resistance to hydrolytic cleavage. Thiolated uridines and cytidines have been incorporated into mRNA therapeutics to increase stability and translation efficiency, a strategy used in some next-generation vaccines. Additionally, sulfur-functionalized nucleotides facilitate chemical crosslinking studies, enabling precise structural mapping of transcriptional and translational machinery.

Techniques To Locate Sulfur In DNA And RNA

Detecting sulfur within nucleic acids requires specialized analytical techniques due to its low natural abundance and the subtle structural changes it introduces. Traditional methods like UV-Vis spectroscopy and standard gel electrophoresis lack the sensitivity and specificity needed to distinguish sulfur modifications. Researchers have developed refined approaches that leverage sulfur’s unique chemical properties for precise identification and quantification in DNA and RNA.

Mass spectrometry (MS), particularly liquid chromatography-tandem mass spectrometry (LC-MS/MS), is one of the most effective strategies. This technique exploits the distinct mass shift introduced by sulfur substitution, allowing high-resolution detection of phosphorothioate linkages and thiolated nucleosides. By fragmenting nucleic acid samples into smaller ionized components, MS differentiates between sulfur-containing and unmodified bases, providing structural insights at the molecular level. High-performance liquid chromatography (HPLC) is often coupled with MS to enhance separation efficiency.

X-ray absorption spectroscopy (XAS) is valuable for elucidating the oxidation states and bonding environments of sulfur atoms within nucleic acids. This method exploits sulfur’s ability to absorb X-rays at specific energy levels, generating spectral fingerprints that distinguish different sulfur-containing species. Synchrotron radiation sources enhance XAS sensitivity, enabling analysis of sulfur modifications in complex biological samples. Similarly, Raman spectroscopy detects sulfur substitutions by measuring vibrational shifts in molecular bonds, providing a non-destructive means of probing nucleic acid modifications in real time.

Functional Roles In Gene Expression

Sulfur modifications in nucleic acids influence gene expression by altering molecular interactions, structural dynamics, and enzymatic processes. These modifications fine-tune transcription, translation, and RNA stability, making them important regulatory elements. When sulfur replaces oxygen in nucleotides, it modifies the electrostatic properties of DNA and RNA, impacting interactions with proteins such as transcription factors, polymerases, and ribosomes. This shift can enhance or inhibit binding affinity, directly affecting gene transcription and translation.

In bacterial systems, sulfur-containing nucleotides influence transcriptional efficiency. Phosphorothioate-modified DNA exhibits altered interactions with RNA polymerase, leading to changes in promoter recognition and transcription initiation rates. This suggests that sulfur modifications serve as epigenetic-like markers, dictating gene accessibility for transcription. In RNA, thiolated nucleotides such as 4-thiouridine contribute to translation fidelity by stabilizing codon-anticodon pairing, reducing errors during protein synthesis. This is particularly relevant under stress conditions, where precise gene expression is crucial for cellular adaptation.