DNA vs. RNA: Structural and Functional Differences in Molecular Diagnostics

DNA and RNA are nucleic acids that carry genetic information, but they differ in sugar composition, nitrogenous bases, strand structure, and functional roles. DNA serves as the long-term storage molecule for genetic information, while RNA acts as an intermediary that transfers genetic instructions for protein synthesis and performs regulatory functions. In molecular diagnostics, these structural differences determine which nucleic acid target is selected, how assays are designed, and what clinical questions can be answered. This article provides a side-by-side comparison of DNA and RNA for laboratory students, technicians, researchers, and diagnostic professionals, with emphasis on how these differences affect PCR, reverse transcription, and other detection platforms.

The Chemical Basis of Nucleic Acid Differences

Sugar Component: Deoxyribose versus Ribose

The backbone of both DNA and RNA consists of alternating sugar and phosphate groups. The sugar in DNA is 2-deoxyribose, which lacks a hydroxyl group at the 2-carbon position. RNA contains ribose, which has a hydroxyl group at the same position. This single chemical difference has profound consequences for molecular stability. The 2-hydroxyl group in RNA makes the molecule more susceptible to alkaline hydrolysis and enzymatic degradation, which is why RNA requires more careful handling in the laboratory than DNA.

The presence of the 2-hydroxyl group also affects the three-dimensional conformation of RNA molecules. RNA can adopt complex secondary structures through intramolecular base pairing, while DNA typically exists in a more regular double helical form. These structural properties influence how nucleic acids interact with enzymes, probes, and detection reagents in diagnostic assays.

Nitrogenous Base Composition

Both DNA and RNA contain four nitrogenous bases, but the specific bases differ. DNA contains adenine, guanine, cytosine, and thymine. RNA contains adenine, guanine, cytosine, and uracil instead of thymine. Uracil is chemically similar to thymine but lacks the methyl group found at the 5-position of thymine.

The base pairing rules remain consistent across both molecules. Adenine pairs with thymine in DNA or uracil in RNA, and guanine pairs with cytosine in both molecules. This complementary base pairing is the foundation for hybridization-based detection methods, probe design, and primer annealing in amplification assays.

The substitution of uracil for thymine has diagnostic relevance. When designing primers or probes for RNA targets, the sequence must reflect uracil instead of thymine. Conversely, when designing assays that distinguish DNA from RNA, the base composition provides one point of differentiation.

Strand Structure: Double-Stranded DNA versus Single-Stranded RNA

DNA exists primarily as a double-stranded molecule with antiparallel strands held together by hydrogen bonds between complementary bases. This double-stranded structure provides stability and protects the genetic information from damage. RNA exists primarily as a single-stranded molecule, although it can fold into complex secondary structures through intramolecular base pairing.

The single-stranded nature of RNA has important implications for diagnostic assays. Single-stranded nucleic acids can hybridize with complementary probes more readily than double-stranded DNA, which requires denaturation before hybridization. However, the secondary structures formed by RNA can sometimes interfere with primer binding or probe hybridization, requiring careful assay design.

Some viruses contain single-stranded DNA or double-stranded RNA genomes, which adds complexity to diagnostic testing. The identification of a single-stranded DNA virus associated with citrus chlorotic dwarf disease demonstrates that nucleic acid structure varies across biological systems and that diagnostic approaches must account for this diversity.

Functional Roles in the Central Dogma

DNA as the Genetic Archive

DNA functions as the stable repository of genetic information in most organisms. The double-stranded structure provides a template for replication, allowing genetic information to be passed faithfully from one cell generation to the next. The relative chemical stability of DNA, conferred by the absence of the 2-hydroxyl group, supports its role as a long-term storage molecule.

In diagnostic testing, DNA targets are often used to detect the presence of pathogens, identify genetic mutations, or determine genetic identity. DNA-based assays such as polymerase chain reaction amplify specific DNA sequences to detectable levels. The stability of DNA makes it a practical target for clinical samples that may be subjected to transport, storage, or repeated freeze-thaw cycles.

RNA as the Functional Messenger and Regulator

RNA performs multiple roles in gene expression. Messenger RNA carries genetic instructions from DNA to ribosomes for protein synthesis. Ribosomal RNA forms structural and catalytic components of ribosomes. Transfer RNA delivers amino acids during translation. Regulatory RNAs control gene expression at multiple levels.

The precise regulation of gene expression is crucial for bacteria to respond to changing environmental conditions, and RNA molecules participate in these regulatory networks. In diagnostic contexts, RNA targets provide information about gene expression levels, viral replication activity, and cellular responses that DNA targets cannot reveal.

RNA-based diagnostics require reverse transcription to convert RNA into complementary DNA before amplification. This additional step introduces complexity but enables detection of RNA viruses, measurement of gene expression, and analysis of transcriptional activity.

Transcription and Its Diagnostic Significance

Transcription is the process by which RNA is synthesized from a DNA template. This process is fundamental to gene expression and is tightly regulated in all organisms. The regulation of transcription involves complex interactions between RNA polymerase, promoter sequences, and regulatory proteins.

The structure-function comparisons of (p)ppApp vs (p)ppGpp for Escherichia coli RNA polymerase binding sites illustrate how nucleotide signaling molecules influence transcription. These regulatory mechanisms affect which genes are expressed and at what levels, information that can be captured through RNA-based diagnostic testing.

For diagnostic professionals, understanding transcription is essential for interpreting RNA measurements. RNA levels reflect also the presence of a gene but also its activity. Changes in RNA abundance can indicate disease states, treatment responses, or pathogen replication.

At a Glance: DNA versus RNA Comparison

Molecular Diagnostic Applications

DNA-Based Detection Methods

DNA-based diagnostics are widely used for pathogen identification, genetic testing, and forensic analysis. Polymerase chain reaction amplifies specific DNA sequences using thermostable DNA polymerase, primers that flank the target region, and nucleotides for chain extension. The double-stranded nature of DNA provides a template that can be denatured, annealed, and extended in repeated cycles.

DNA-based assays offer several advantages in diagnostic settings. DNA is relatively stable, allowing samples to be collected, transported, and stored with less stringent cold-chain requirements. DNA targets are often present at consistent copy numbers per cell, facilitating quantitative measurements. The DNA-based detection rate of metagenomic next-generation sequencing was slightly higher than that of bronchoalveolar lavage culture in a study of pediatric pneumonia, demonstrating the utility of DNA-based approaches for pathogen detection.

DNA-based metagenomic next-generation sequencing can identify multiple pathogens simultaneously from a single clinical sample. This approach has been applied to diagnosis and lung microbiome probing of pediatric pneumonia through bronchoalveolar lavage fluid, providing comprehensive information about infectious agents and microbial community composition.

RNA-Based Detection Methods

RNA-based diagnostics require reverse transcription to convert RNA into complementary DNA before amplification. This process uses reverse transcriptase enzymes and is the basis for reverse transcription PCR, commonly known as RT-PCR. RNA-based assays are essential for detecting RNA viruses, measuring gene expression, and analyzing transcriptional responses.

The choice between total RNA and poly(A) RNA for target preparation can affect microarray hybridization results. A comparison of nucleic acid targets prepared from total RNA or poly(A) RNA for DNA oligonucleotide microarray hybridization found that poly(A) affinity purification could be omitted for routine messenger RNA expression analysis. However, structurally exceptional RNA species such as histone mRNAs that lack poly(A) tails were identified by comparing targets derived from both preparation methods.

RNA sequencing provides a comprehensive view of the transcriptome, revealing which genes are expressed and at what levels. RNA sequencing of the epidermis in aged versus young mice following barrier disruption demonstrated that aging alters transcriptional responses to environmental challenges. These findings have implications for understanding disease processes and developing diagnostic approaches based on gene expression signatures.

Reverse Transcription and Its Role in Diagnostics

Reverse transcription is the process by which RNA is converted into complementary DNA. This process is essential for RNA-based amplification because DNA polymerase cannot use RNA as a template. Reverse transcriptase enzymes synthesize a DNA strand complementary to the RNA template, producing a hybrid molecule that can then be amplified by PCR.

The efficiency of reverse transcription affects the sensitivity and accuracy of RNA-based assays. Factors that influence reverse transcription efficiency include RNA quality, primer design, enzyme activity, and reaction conditions. RNA degradation during sample collection, transport, or storage can reduce the amount of detectable target and lead to false-negative results.

The genesis of ancestral haplotypes involves RNA modifications and reverse transcription-mediated polymorphisms, highlighting the biological importance of reverse transcription beyond its diagnostic applications. Understanding the mechanisms of reverse transcription helps diagnostic professionals optimize assay conditions and interpret results.

Hybridization and Probe Design Considerations

DNA/DNA versus RNA/DNA Duplex Stability

Hybridization is the process by which complementary nucleic acid strands anneal to form double-stranded structures. This process underlies probe-based detection methods, microarray analysis, and many amplification techniques. The stability of hybrid duplexes depends on the nucleic acid composition, sequence, and reaction conditions.

The impact of point mutations on the hybridization affinity of surface-bound DNA/DNA and RNA/DNA oligonucleotide duplexes has been systematically investigated. Single base mismatches and base bulges affect hybridization affinity differently depending on their position within the oligonucleotide, with the largest effects observed in the middle of the strand. RNA/DNA purine-purine mismatches were found to be more discriminating than corresponding DNA/DNA mismatches, which has implications for probe design and mismatch discrimination.

These findings are relevant for diagnostic assay design. When developing probes for RNA targets, the hybridization properties of RNA/DNA duplexes must be considered. When designing assays that must discriminate between closely related sequences, the position and type of mismatches should be optimized for maximum discrimination.

Secondary Structure and Assay Performance

RNA molecules can form complex secondary structures through intramolecular base pairing. These structures can interfere with primer binding, probe hybridization, and reverse transcription. Secondary structure prediction tools can help identify regions of RNA that are accessible for primer and probe binding.

The ATPase-dependent duplex nucleic acid unwinding by SARS-CoV-2 nsP13 demonstrates that helicase enzymes can unwind double-stranded nucleic acids, a process that may be relevant for accessing RNA targets in diagnostic assays. Understanding the structural features of nucleic acids helps diagnostic professionals design assays that overcome secondary structure barriers.

For diagnostic laboratories, the practical implication is that RNA assays may require optimization of reaction conditions to disrupt secondary structures. Increasing reaction temperature, adding denaturants, or designing primers to avoid structured regions can improve assay performance.

Sample Processing and Quality Considerations

RNA Integrity and Stability

RNA is more susceptible to degradation than DNA due to the presence of the 2-hydroxyl group in ribose. Ribonucleases are ubiquitous enzymes that rapidly degrade RNA, requiring careful handling procedures in the laboratory. RNA samples must be stored at appropriate temperatures, protected from ribonuclease contamination, and processed promptly.

The nucleolar changes in bovine nucleotransferred embryos illustrate the dynamic nature of RNA-containing structures during development. These observations highlight the importance of understanding RNA biology when interpreting diagnostic results.

For diagnostic laboratories, RNA integrity should be assessed before performing RNA-based assays. Methods for assessing RNA quality include spectrophotometric analysis, gel electrophoresis, and microfluidic analysis. Degraded RNA samples may produce unreliable results and should be flagged for quality review.

DNA Stability and Storage

DNA is generally more stable than RNA and can be stored for longer periods under appropriate conditions. However, DNA can still be damaged by nucleases, oxidative stress, and repeated freeze-thaw cycles. Proper sample collection, storage, and processing procedures are essential for maintaining DNA quality.

The UV-induced DNA damage and DNA repair in ribosomal genes chromatin demonstrates that DNA is subject to environmental damage that can affect its integrity. Diagnostic laboratories should implement quality control measures to ensure that DNA samples are suitable for analysis.

Sample Collection and Transport

The choice between DNA and RNA testing affects sample collection and transport requirements. DNA samples can often be collected using simpler methods and transported at ambient temperatures for short periods. RNA samples typically require immediate stabilization, cold-chain transport, or the use of preservative solutions that inactivate ribonucleases.

The Laboratory Quality Management System Handbook from the World Health Organization provides guidance on quality management practices for diagnostic laboratories. These practices include specimen collection, handling, transport, and storage procedures that ensure reliable test results.

Assay Design and Workflow Decisions

Selecting the Appropriate Nucleic Acid Target

The choice between DNA and RNA targets depends on the diagnostic question being addressed. DNA targets are appropriate for detecting the presence of organisms, identifying genetic mutations, and determining genetic identity. RNA targets are appropriate for measuring gene expression, detecting RNA viruses, and assessing transcriptional activity.

For pathogen detection, the choice between DNA and RNA targets depends on the genome composition of the target organism. DNA-based assays are suitable for bacteria, DNA viruses, and parasites. RNA-based assays are required for RNA viruses and for detecting active transcription of DNA pathogens.

The development of a rapid and cost-effective allele-specific PCR assay targeting the 18S rRNA gene for differential detection of Sarcocystis species demonstrates how ribosomal RNA genes can serve as diagnostic targets. The 18S rRNA gene contains conserved and variable regions that enable species identification, and the assay was designed to differentiate between species without the need for sequencing.

Primer and Probe Design for DNA versus RNA

Primer and probe design principles differ between DNA and RNA targets. For DNA targets, primers are designed to anneal to complementary sequences in double-stranded DNA. For RNA targets, primers are designed to anneal to the RNA sequence, and the reverse transcription step must be considered.

The base composition of primers and probes must reflect the target nucleic acid. Primers for RNA targets contain uracil instead of thymine in the positions complementary to adenine. This difference must be accounted for during primer synthesis and quality control.

The impact of point mutations on hybridization affinity has implications for primer and probe design. Mismatches in the middle of the oligonucleotide have the largest effect on hybridization affinity, so primers and probes should be designed to avoid mismatches in these critical positions.

Amplification Strategies

Different amplification strategies are used for DNA and RNA targets. PCR amplifies DNA directly using thermostable DNA polymerase. RT-PCR includes a reverse transcription step before amplification. Quantitative PCR measures the amount of amplified product in real time, enabling quantification of the initial target concentration.

The choice of amplification strategy affects assay sensitivity, specificity, and throughput. DNA-based assays are generally simpler and more robust than RNA-based assays. RNA-based assays provide additional information about gene expression but require more complex workflows.

The Bioanalytical Method Validation Guidance from the U.S. Food and Drug Administration provides guidance on validating analytical methods, including those used for nucleic acid detection. Validation ensures that assays perform reliably and produce accurate results.

Quality Control and Assurance

Controls for DNA and RNA Assays

Quality control is essential for reliable diagnostic testing. Positive controls contain known amounts of the target nucleic acid and confirm that the assay is working correctly. Negative controls contain no target nucleic acid and detect contamination. Internal controls monitor the efficiency of nucleic acid extraction and amplification.

For RNA-based assays, additional controls are needed to monitor the reverse transcription step. Reverse transcription controls ensure that RNA is being converted to complementary DNA efficiently. These controls are essential for detecting inhibition or failure of the reverse transcription reaction.

The Laboratory Quality Management System Handbook provides guidance on quality control practices for diagnostic laboratories. These practices include the use of controls, calibration of equipment, and participation in external quality assessment programs.

Preventing Contamination

Nucleic acid contamination is a major concern in diagnostic laboratories. Amplicon contamination from previous amplification reactions can cause false-positive results. Sample-to-sample contamination can occur during nucleic acid extraction or processing.

Prevention strategies include physical separation of pre-amplification and post-amplification areas, use of dedicated equipment and reagents, and implementation of decontamination procedures. The Laboratory Biosafety Manual from the World Health Organization provides guidance on biosafety practices that reduce the risk of contamination and exposure to biological hazards.

Validation and Verification

Assay validation demonstrates that a test performs as intended for its intended use. Validation includes assessment of sensitivity, specificity, accuracy, precision, and reproducibility. Verification confirms that an established assay performs correctly in a specific laboratory setting.

The Assay Guidance Manual from the National Center for Advancing Translational Sciences provides guidance on assay development and validation. This resource covers assay design, optimization, and validation considerations for various assay formats.

Common Failure Patterns and Troubleshooting

RNA Degradation

RNA degradation is a common cause of failed RNA-based assays. Symptoms include low or absent amplification, inconsistent results between replicates, and poor correlation with expected values. Causes include ribonuclease contamination, improper storage, and delays in processing.

Prevention strategies include using ribonuclease-free reagents and consumables, processing samples promptly, and storing RNA at appropriate temperatures. If RNA degradation is suspected, RNA integrity should be assessed before repeating the assay.

Reverse Transcription Inhibition

Reverse transcription can be inhibited by various substances present in clinical samples. Hemoglobin, heparin, and other compounds can interfere with reverse transcriptase activity. Symptoms include reduced amplification efficiency and false-negative results.

Troubleshooting strategies include optimizing nucleic acid extraction to remove inhibitors, diluting samples, and using internal controls to detect inhibition. If inhibition is suspected, the extraction procedure should be reviewed and modified as needed.

Primer Dimer Formation

Primer dimers are artifacts formed when primers anneal to each other instead of the target sequence. They can reduce amplification efficiency and interfere with result interpretation. Symptoms include unexpected amplification products and high background signals.

Prevention strategies include optimizing primer design, adjusting primer concentrations, and using hot-start polymerases. If primer dimers are observed, the assay conditions should be reviewed and modified.

Secondary Structure Interference

RNA secondary structures can interfere with primer binding, reverse transcription, and amplification. Symptoms include reduced amplification efficiency and inconsistent results. Prevention strategies include designing primers to avoid structured regions, increasing reaction temperatures, and using additives that disrupt secondary structures.

Interpretation Limitations

DNA Presence versus Viability

DNA-based detection cannot distinguish between viable and non-viable organisms. DNA can persist in the environment or in clinical samples after organisms have been killed. This limitation is particularly relevant for monitoring treatment response or assessing environmental contamination.

RNA-based detection can provide information about active transcription, which is more closely associated with viability. However, RNA can also persist for some time after cell death, and the relationship between RNA detection and viability depends on the specific organism and context.

Gene Expression Variability

RNA levels reflect gene expression at a specific point in time and can vary substantially between individuals, tissues, and conditions. The aged and young mice differentially respond to tape-stripping in epidermal gene expression demonstrates that gene expression responses can differ based on physiological state.

When interpreting RNA-based test results, diagnostic professionals should consider the biological variability of gene expression. Reference ranges and clinical decision thresholds should be established based on appropriate populations and validated for the intended use.

Technical Variability

Nucleic acid testing is subject to technical variability from multiple sources. Sample collection, nucleic acid extraction, reverse transcription, amplification, and detection each contribute to overall variability. Standardized procedures and quality control measures help reduce technical variability.

The comparison of nucleic acid targets prepared from total RNA or poly(A) RNA demonstrated that different target preparation methods can produce slightly different results. Understanding the sources of technical variability helps diagnostic professionals interpret results appropriately.

Safety and Regulatory Context

Biosafety Considerations

Handling clinical samples and nucleic acids requires appropriate biosafety practices. The Laboratory Biosafety Manual from the World Health Organization provides guidance on biosafety levels, containment practices, and personal protective equipment.

Diagnostic laboratories should implement biosafety procedures that protect laboratory workers and prevent environmental contamination. These procedures include proper handling of clinical samples, decontamination of work surfaces, and safe disposal of biological waste.

Regulatory Requirements

Diagnostic tests are subject to regulatory requirements that ensure their safety and effectiveness. The Bioanalytical Method Validation Guidance from the U.S. Food and Drug Administration provides guidance on validating bioanalytical methods used in regulatory studies.

Laboratories performing diagnostic testing should comply with applicable regulatory requirements, including quality management standards, proficiency testing, and reporting obligations. The Laboratory Quality Management System Handbook provides guidance on implementing quality management systems in diagnostic laboratories.

Professional Escalation Criteria

Diagnostic professionals should escalate unusual or unexpected results to appropriate supervisors or clinical personnel. Escalation criteria include results that are inconsistent with clinical presentation, results that suggest contamination or assay failure, and results that require clinical interpretation.

When results are ambiguous or conflicting, repeat testing, alternative testing methods, or consultation with specialists may be appropriate. The NCBI Literature Resources provide access to scientific literature that can support interpretation of complex results.

Records and Documentation

Maintaining Accurate Records

Accurate records are essential for diagnostic testing. Records should document sample collection, nucleic acid extraction, assay performance, quality control results, and final results. Records should be complete, accurate, and traceable.

The Laboratory Quality Management System Handbook provides guidance on documentation practices for diagnostic laboratories. These practices include record keeping, document control, and data management.

Quality Control Records

Quality control records document the performance of controls and the acceptability of assay runs. These records are essential for identifying trends, troubleshooting problems, and demonstrating the reliability of test results.

Quality control records should include the identity of controls, expected and observed values, and actions taken when control results are unacceptable. Regular review of quality control records can identify emerging problems before they affect patient results.

Proficiency Testing

Proficiency testing involves analyzing unknown samples provided by an external organization and comparing results with those of other laboratories. Participation in proficiency testing programs helps laboratories assess their performance and identify areas for improvement.

The Laboratory Quality Management System Handbook recommends participation in external quality assessment programs as part of a comprehensive quality management system.

Frequently Asked Questions

Is RNA a protein?

RNA is not a protein. RNA is a nucleic acid composed of nucleotide subunits, while proteins are composed of amino acid subunits. RNA and proteins are both essential biomolecules, but they have different chemical structures, synthesis pathways, and biological functions. RNA participates in gene expression by carrying genetic information and catalyzing biochemical reactions, while proteins perform a wide range of structural and functional roles in cells.

Is RNA a single strand of DNA?

RNA is not a single strand of DNA. Although both are nucleic acids, RNA and DNA differ in their sugar components, nitrogenous bases, and biological functions. RNA contains ribose sugar and uracil instead of thymine, while DNA contains deoxyribose sugar and thymine. RNA is typically single-stranded, while DNA is typically double-stranded. These structural differences give RNA and DNA distinct functional roles in cells.

Does uracil replace adenine in RNA?

Uracil does not replace adenine in RNA. Uracil replaces thymine in RNA. Both DNA and RNA contain adenine, but DNA contains thymine while RNA contains uracil. The base pairing rules are consistent: adenine pairs with thymine in DNA and with uracil in RNA. Guanine pairs with cytosine in both DNA and RNA.

Why is RNA less stable than DNA?

RNA is less stable than DNA because of the presence of a hydroxyl group at the 2-carbon position of ribose sugar. This hydroxyl group makes RNA more susceptible to alkaline hydrolysis and enzymatic degradation by ribonucleases. DNA lacks this hydroxyl group, making it more chemically stable. The reduced stability of RNA has practical implications for sample handling, storage, and assay design in diagnostic laboratories.

What is the difference between PCR and RT-PCR?

PCR amplifies DNA directly using thermostable DNA polymerase. RT-PCR includes an additional reverse transcription step that converts RNA into complementary DNA before amplification. RT-PCR is used to detect RNA targets, such as RNA viruses or gene expression products. The reverse transcription step adds complexity to the assay but enables detection of RNA molecules that cannot be amplified directly by PCR.

Why do RNA-based assays require more careful sample handling?

RNA-based assays require more careful sample handling because RNA is susceptible to degradation by ribonucleases, which are ubiquitous enzymes present in biological samples and the environment. RNA samples must be processed promptly, stored at appropriate temperatures, and protected from ribonuclease contamination. DNA is more stable and can tolerate less stringent handling conditions.

Can DNA-based tests detect RNA viruses?

DNA-based tests cannot directly detect RNA viruses because DNA polymerase cannot use RNA as a template. Detection of RNA viruses requires reverse transcription to convert viral RNA into complementary DNA before amplification. This process is the basis of RT-PCR, which is the standard method for detecting RNA viruses such as influenza and SARS-CoV-2.

How do secondary structures affect RNA assays?

RNA molecules can fold into complex secondary structures through intramolecular base pairing. These structures can interfere with primer binding, probe hybridization, and reverse transcription, reducing assay efficiency and reliability. Assay design should account for RNA secondary structures by selecting target regions that are accessible and optimizing reaction conditions to disrupt structured regions.

Related Diagnostic Guides

• Digital Droplet PCR for Absolute Quantification of Feline Enteric Coronavirus RNA in Fecal Samples: Diagnostic Utility and Prognostic Implications
• How to Calculate the Amount of RNA for Reverse Transcription
• Reverse Transcription PCR: Principles and Protocol for cDNA Synthesis
• Reverse Transcription Quantitative PCR (RT-qPCR): Principles and Workflow
• Template Quality Control for PCR and qPCR: Assessing DNA and RNA Integrity

References and Further Reading

• Laboratory Quality Management System Handbook. World Health Organization.
• Laboratory Biosafety Manual. World Health Organization.
• Assay Guidance Manual. National Center for Advancing Translational Sciences.
• Bioanalytical Method Validation Guidance. U.S. Food and Drug Administration.
• NCBI Literature Resources. National Center for Biotechnology Information.
• Structure-function comparisons of (p)ppApp vs (p)ppGpp for Escherichia coli RNA polymerase binding sites and for rrnB P1 promoter regulatory responses in vitro.. Biochimica et biophysica acta. Gene regulatory mechanisms, 2018.
• Comparison of nucleic acid targets prepared from total RNA or poly(A) RNA for DNA oligonucleotide microarray hybridization.. Analytical biochemistry, 2007.
• Impact of point-mutations on the hybridization affinity of surface-bound DNA/DNA and RNA/DNA oligonucleotide-duplexes: comparison of single base mismatches and base bulges.. BMC biotechnology, 2008.
• Aged and young mice differentially respond to tape-stripping in epidermal gene expression.. Experimental dermatology, 2022.
• The plant circadian clock influences rhizosphere community structure and function.. The ISME journal, 2018.
• Genesis of ancestral haplotypes: RNA modifications and reverse transcription-mediated polymorphisms.. Human immunology, 2011.
• Nucleolar changes in bovine nucleotransferred embryos.. Biology of reproduction, 2002.
• Utilizing metagenomic next-generation sequencing for diagnosis and lung microbiome probing of pediatric pneumonia through bronchoalveolar lavage fluid in pediatric intensive care unit: results from a large real-world cohort.. Frontiers in cellular and infection microbiology, 2023.
• Development of a rapid and cost-effective Allele-Specific PCR assay targeting the 18S rRNA gene for differential detection of Sarcocystis species in Cattle and Water Buffalo, and phylogenetic analysis of macrocyst-forming species in cattle in Iran.. 2026.
• Sabulicella flocculans sp. nov., a Floc-Forming Bacterium of the Genus Sabulicella Isolated from Activated Sludge.. 2026.
• Identification of a single-stranded DNA virus associated with citrus chlorotic dwarf disease, a new member in the family Geminiviridae.. Virology, 2012.
• ATPase-dependent duplex nucleic acid unwinding by SARS-CoV-2 nsP13 relies on facile binding and translocation along single-stranded nucleic acid. Journal of Biological Chemistry, 2025.
• UV-induced DNA damage and DNA repair in ribosomal genes chromatin. Methods in Molecular Biology, 2012.
• A computer simulation model for analysis of conformation of nuclear chromatin and of the transcription process. Biosystems, 1975.
• LDA vs. QDA for FT-MIR prostate cancer tissue classification. Chemometrics and Intelligent Laboratory Systems, 2017.

This article is educational and does not replace validated laboratory procedures, institutional biosafety review, manufacturer instructions, or professional interpretation.