Scope and Criteria for Consideration

NAR provides rapid publication of papers on physical, chemical, biochemical and biological aspects of nucleic acids and proteins involved in nucleic acid metabolism and/or interactions. All manuscripts must present some novel development and meet the general criteria of originality, timeliness, significance and scientific excellence.

From 2025, NAR will be published online only.

Papers which are considered to be a better fit in another related journal are offered a direct transfer to the most relevant journal in the wider NAR or OUP portfolios.

The Journal publishes the following types of papers:

Standard research articles
Methods articles
Critical Reviews and Perspectives
Database articles
Web Server articles

Standard Research Articles

Standard research articles are published both in print and online in the following subject categories:

Chemical Biology and Nucleic Acid Chemistry
Computational Biology
Data Resources and Analyses
Gene Regulation, Chromatin and Epigenetics
Genome Integrity, Repair and Replication
Genomics
Molecular and Structural Biology
Nucleic Acid Enzymes
Nucleic Acid Therapeutics
RNA and RNA-protein complexes
Synthetic Biology and Bioengineering

Approaches and topics of particular current interest to the journal (including nucleic acid therapeutics, RNA base modifications, subnuclear structures, gene editing, single cell gene expression studies, visualization of molecular assemblages, and single molecule studies) are described within the category descriptions below; many of these topics are appropriate for more than one category.

Methods Articles

General Requirements and Instructions:

Nucleic Acids Research publishes “METHODS” manuscripts that detail methodological developments of highest originality and usefulness within the core subject areas of NAR. Broad METHODS category sub-headings, with core area descriptions and manuscript examples, can be found in the NAR Methods subject categories. METHODS are counted for citation by ISI and Medline, searchable through all services including PubMed and the general NAR search page, and indexed in the NAR Methods Collections, under the various area sub-headings. Queries regarding submission of METHODS papers are encouraged and may be directed to Dr. Alan R. Kimmel ([email protected]) and/or Dr. Georg Sczakiel ([email protected]), or, if they are primarily computational (see below), to Dr. M. Madan Babu ([email protected]).

METHODS papers are prepared in exactly the same format as standard research papers and are subject to the same quality criteria  for review and requirements regarding availability of materials, computational executables, and/or source codes. Computational and other methods papers should be presented for a broad readership, with their significance easily understood by biologists.

METHODS papers should report novel techniques, highly significant advances in existing techniques, and/or novel utility or advantage to an extended, rather than a specialist, audience. Submitted METHODS manuscripts should be the first report of utility and application. Submissions will not be considered if the method has already been applied and published, even if technical details had not been fully elaborated. By extension, we also discourage submissions that are intended to further evaluate assertions made in a previous methods publication.

Novel utility should be made clear at the outset and advantage to existing techniques demonstrated at a comparative, benchmarked level and proven effective at a genome-wide scale with experimental, rather than simulated or reconstructed, data. We encourage focus on rapidly evolving technologies, in areas such as genome editing, environmental/microbiome/metagenome analyses,  single-cell/spatial sequencing (see computational analyses below), RNA modifications, nucleic acid/protein complexes, epigenetics, nanotechnology, phase condensation (e.g. nuclear and RNA granules), and multi-omics. Simple extended or optimized applications of existing mature technologies (e.g. diagnostic applications of established techniques, mutation/pathogen detection without comparative improvement to quantification/sensitivity, computational methods that serve as alternative tools without demonstrating significant comparative advantage) or comparative studies of published procedures, without significant novel conclusions are discouraged. Methods that include nucleic acids-based steps but that are primarily useful for areas outside the scope of NAR (e.g. molecular pathology, tumor monitoring, plant or animal biotechnology, and biomarker or sensor technology) are generally not appropriate.

While we recognize that step-by-step specifics and optimizations can greatly improve experimental reproducibility, NAR METHODS does not consider manuscripts that delineate laboratory protocols, per se. Relevant protocol manuscripts can be directed to Biology Methods and Protocols. Further, at acceptance, authors of an NAR METHODS publication are specifically encouraged to consider a detailed protocol version for submission to Biology Methods and Protocols.

Computational Methods and Analyses of Single-Cell/Spatial and other Omics Sequencing:

NAR publishes METHODS that provide mechanistic insight into biological processes through computational analyses of high-throughput nucleic acid data. New computational methods should include substantial innovative algorithms, routines, metrics, programs, and software implementations for bioinformatic analyses of nucleic acid sequences, structures, interactions, manipulations, annotations, design, or assemblies, mining, and interpretations of large genetic and genomic data sets. Novelty should be at both the conceptual and algorithmic levels, rather than exhibit modest variation of standard approaches (such as machine learning, graph partitioning, neural networks, community detection, deep learning, auto-coder, etc.), even if good predictive power is displayed. Computational manuscripts in NAR are intended for biologists as users and should be fully understandable by non-specialists, with avoidance of poorly explained dense jargon.

New methods should demonstrate superior performance through comparative testing to existing alternatives with fair benchmarking. Approaches that are comparably effective to published alternatives are generally not appropriate. For comparative analyses, alternative program parameters should be optimized and not simply rely on default pre-sets; similarly, databases selected for comparative testing should have broad coverage. We recognize that benchmarking can be selective and have its own set of unintended biases, especially with heavy reliance on simulated data. Should benchmark testing of alternatives show significantly reduced performance (e.g. precision/recall values) compared to that published, the authors must reference the contradictory results and attempt to resolve the discrepancies. Validations should not be limited to simulated data sets or re-constructions but require comparative benchmarking using actual experimental evidence; indeed, simulations on the whole should be minimized. Extreme care and documentation must also be taken with the choice and use of training data. Potential performance biases, which can result when training and testing data sets are functionally identical, especially during comparative benchmarking to untrained programs, must be addressed experimentally.

Results should be interpreted in the context of biological relevance and not just show improvement in statistical parameters or technical performance. Manuscripts should demonstrate practical utility with respect to real biological or biotechnological applications and detail specific and significant issues in nucleic acid biology that cannot be accomplished by other approaches. Manuscripts, which assert that their approach can uniquely derive novel observations through probing defined experimental data sets, must similarly and fairly test alternatives using the same data and demonstrate that other strategies are unable to draw similar conclusions. Ideally, predictive conclusions should be supported by experimental evidence; collaborations between bioinformatic and research groups are very much encouraged.

Updates and extensions of published programs are generally not appropriate. Computational "pipelines" that apply existing tools or papers that describe combinations of standard computational applications are also discouraged. For some of these, the NAR Database or the NAR Web Server issue may instead be considered; for these, please contact directly the NAR Database Editor Dr. Daniel Rigden ([email protected]) or the NAR Web Server Editor Dr. Dominik Seelow ([email protected]).

NAR considers METHODS papers in two formats:

NAR METHODS: These manuscripts detail methodological developments of highest originality and usefulness to the wide research of the NUCLEIC ACID community and are reviewed primarily to that end. These manuscripts are not intended as vehicles to report significant new experimental or mechanistic conclusions. Their inclusion is not prohibited, but data must be sufficient to support such findings.

Novel Method within a Standard Research paper: Research papers that include innovative methodologies, should be submitted as Standard Research, with indication that a novel method is included. While the method is evaluated as per criteria above, its relative novelty does not usually impact publication decision. Accepted manuscripts in this category are listed in the Table of Contents under the standard subject category, and are additionally annotated with the +M novel methods designation. They are also listed within the NAR METHODS collections.

Alternative Journals for Methods Submissions:

We recognize that many excellent methodological studies of nucleic acids may not fit NAR METHODS guidelines for highest originality, global utility, or NAR core interests. These might include comparative studies of published procedures, extended/adapted studies to specific organism classes, information technology, approaches that rely primarily on simulated data or that lack global experimental support, medical diagnostic applications (e.g. therapeutic sequencing), and complex vector or genome assembly engineering, in the absence of fundamentally novel principles. In such cases where the content of a submitted manuscript is deemed inappropriate, regardless of experimental quality, NAR METHODS may offer authors direct transfer of a submitted manuscript for consideration by a related journal in the Oxford University Press catalog (including journals in the NAR portfolio: NAR Cancer, NAR Genomics and Bioinformatics, NAR Molecular Medicine); direct submission to these journals is also very encouraged.

Critical Reviews and Perspectives

This Section is dedicated to reviews relevant to the journal’s core area of interest in DNA/RNA function and the structure and interactions of proteins involved in nucleic acid interactions. A typical Critical Reviews and Perspectives occupies about 15 printed pages, with ~4-10 display items and ~100-150 references, but shorter and more focused contributions are also welcome. Articles should appeal to a diverse audience of specialists and non-specialists and should provide critical analyses, a synthesis of ideas, and new insights. Critical Reviews and Perspectives authors should have a strong track record of publication within the field covered by the article and their expertise should be reflected by critical discussion of strengths and weaknesses of current experimental methods and findings and by discussion of strategies for evaluating the rigor of published research. Controversies in a field and future directions should be addressed. While offering a balanced perspective, authors should feel free to offer their own opinions as experts. Prospective authors are strongly encouraged examine exemplary review articles (Example1, Example2, Example3) to gain a sense of format, style, and scientific goals for a NAR Critical Review and Perspective.

Articles that uncritically catalog work or that do not benefit from expertise in a subject area are not appropriate.

Although many Critical Reviews and Perspectives are by invitation, the journal also welcomes unsolicited proposals. For unsolicited contributions, a presubmission enquiry should be sent to Drs. David Corey ([email protected]) and David Rusling ([email protected]).

Database articles

In January of each year, the journal devotes a special online issue to biological databases. For an article to be considered, a presubmission query must be sent to Dr. Daniel Rigden by July 1 of the preceding year (Email: [email protected]). Special Database issue submission instructions. Papers appear online only but print copies of the Database issue are available for purchase.

Web Server articles

In July of each year, the Journal devotes an entire online issue to web-based software resources of value to the biological community. For an article to be considered, authors must upload a one-page summary at https://nar.bihealth.de/ to check the suitability of their proposed submission by 20 December at the latest. Special Web Server issue submission instructions. Papers appear online only but print copies of the Web Server issue are available for purchase.

Standard Research Articles

Specific criteria apply in each subject category as outlined below:

Chemical Biology and Nucleic Acid Chemistry

NAR encourages submission of papers describing the engineering, synthesis, delivery and application of novel nucleic acids, nucleic acid binding proteins, or their derivatives. Examples of such studies might include:

• Novel syntheses or modifications of nucleic acids or nucleic acid binding proteins that lead to a desired, beneficial effect in a biological application.
• Novel methods of delivery of nucleic acids or nucleic acid binding proteins, that involve new mechanisms or that demonstrate significantly improved effectiveness, especially in whole organisms.
• Cellular and in vivo targeting applications of nucleic acids or their derivatives (such as antisense, siRNA or aptamers) or nucleic acid binding proteins, where there is a strong emphasis on understanding their mechanism of action.
• Design or selection of nucleic acids, or nucleic acid binding proteins, that leads to a novel ligand binding or catalytic activity, a unique regulatory function, or the ability to selectively modify gene function. Studies that reveal novel principles of biomolecular engineering are particularly encouraged.
• Studies that facilitate (i) the creation of novel materials and devices via the manipulation of individual nucleic acid-based oligomers and polymers (i.e. nanotechnology and nanomaterial development), (ii) genome engineering, and/or (iii) the creation of novel genetic and cellular circuits or systems.
• Creation of new biological systems. Studies that reveal novel principles of rewriting and reconfiguring natural systems to understand the origins of life are also encouraged.
• Novel approaches for gene editing, including novel strategies to engineer gene targeting scaffolds, or novel combinations or fusions of these scaffolds with functional or catalytic domains that enhance or alter their functions. Studies correlating the activity of such systems in living cells to clearly measured genetic outcomes (recombination, end-joining, mutagenesis, off-target activities) are also encouraged. We particularly welcome papers that describe novel strategies and applications to drive ex vivo or in vivo genome modifications in primary (patient-derived) cells and tissues for therapeutic purpose.  Papers describing extension of existing gene targeting approaches to alternative cell lines or additional model organisms, or that examine routine variants or homologues of previously studied gene targeting systems, are usually redirected to a more specialized journal.
• Use of an expanded DNA alphabet or an expanded genetic code (either through the expansion of the DNA alphabet to include unnatural base pairs or by the use of suppressor tRNA approaches) to create nucleic acid and protein modifications that result in unique biological activities and phenotypes in living cells and organisms.

Of particular interest to the journal are submissions in all areas related to the development of nucleic acid therapeutics. Reports must include rigorous controls and statistical analysis. Advanced in mechanistic understanding should be stressed. Studies describing clinical results will be considered, but only if studies address key questions related to drug mechanism of action, distribution, or pharmacokinetics. Studies relating to cellular uptake, delivery, and oligonucleotide chemistry are particularly encouraged.

Chemical synthesis of novel nucleoside or nucleotide analogues will not be considered unless there is a significant and demonstrated useful application relating to oligonucleotide or nucleic acid structure or function. Papers that describe molecules that are primarily intended for use as in vitro sensors are more appropriate for the Methods category.

Experiments that include the use of synthetic oligonucleotides of any type must report both their exact sequences and exact chemical modifications at any position, as well as a source for acquisition of these reagents and/or precise methods for their creation.  This information can be provided either in the main text or in supplementary information.

Knockdown experiments with duplex RNAs or antisense oligonucleotides should follow published guidelines.

For related criteria, see Synthetic Biology and Bioengineering.

Computational Biology

Manuscripts may be considered if they fall into one of two categories:

1. Description of a new algorithm that represents a substantial improvement over current methodology, and that has direct biological relevance. It should be bench-marked on gold-standard datasets and ideally, be supported by experimental validation where applicable. The performance of such algorithms must be compared with current methods and the relevant statistics (e.g., sensitivity, selectivity, etc.) of the performance must be indicated. Limitations of the method and general directions for future improvement should be reported. Incremental improvements or obvious modifications of existing algorithms will not be considered.
2. Primarily describe the use of existing computational methods to generate significant, novel biological information and insight. Limitations of the approach and issues that may affect the conclusions drawn must be explicitly stated. Purely descriptive 'data mining' studies, (e.g., those that computationally predict biomarkers from disease expression datasets or those that simply compile or catalogue microRNAs from published datasets without providing significant biological or mechanistic insight) are discouraged.

In either case, the manuscript must be written so as to be understandable to biologists. It should ideally report insights pertaining directly to nucleic acids, or to cellular processes that involve nucleic acids. Extensive use of equations should be avoided in the main text and any detailed mathematics should be presented as supplementary material.

Availability of algorithms and code: If the manuscript describes new software tools or the implementation of novel algorithms the software must be freely available to users at the time of submission (either as executable versions for multiple, common platforms or as source code). Availability must be clearly stated in the article. Authors must ensure that the software is available for a full TWO YEARS following publication, preferably through a download link on a stable URL. Authors are strongly encouraged to make their source code available through an open source license (see OpenSource for examples).

Manuscripts that describe computational methods that primarily focus on protein multi-sequence alignment algorithms, prediction of protein folds or structures, or prediction of protein-protein binding sites or affinities will not be considered by NAR (with the possible exception of papers prepared specifically for the annual NAR special issues on Web Servers or Databases, as described above)

Manuscripts describing results from molecular dynamics simulations will be considered only if they provide valuable new insights into biological questions related to nucleic acids. Theoretical results must be put into perspective with available structural and/or biological data, although it is not always essential for them to be accompanied by experimentation. However, theoretical interpretations or speculative ideas should be experimentally testable and, if not backed up by experimental results, should constitute only a small part of the manuscript. Constraints or limitations of the simulation method or theoretical approach used should be identified and discussed. Manuscripts must be written so as to be intelligible to as wide an audience as possible and should avoid jargon and undefined terms.

Data Resources and Analyses

The Data Resource and Analyses category is designed to highlight papers documenting and interpreting substantive amounts of new biological data. To be considered for publication at NAR, these manuscripts should usually report a major informational database/dataset/data resource and provide new biological insights that can be derived from an analysis of the dataset(s). Significant examples of experimental and/or theoretical validation, in addition to the dataset itself, are expected to be included and described in sufficient detail to allow replication and further examination by interested investigators (e.g. trends that are consistent on a genomic scale with the reported findings).

Data Resources should be made available via web services or as standalone repositories to be downloaded for local use.

Data Resources should be compared to resources already available. Analyses and performance should be bench-marked against state-of-the-art methods and datasets already available. If a specific analysis is presented on a restricted range of examples as a proof of concept, it should be further validated on a larger scale, using the genome/transcriptome etc. data available.

Examples of such resources include (1) collections of whole genome sequencing, transcriptomic or epigenomic data that shed light on significant biological or pathological processes, (2) the output of substantive functional, genetic, biochemical or phenotypic screens, (3) sequence data corresponding to novel, comparative analyses of the genomes and/or transcriptomes of multiple organisms or experimental samples e.g. single cells, tissues, key model organisms, etc.) or (4) comprehensive, clearly novel meta-analyses of existing datasets. In the case of analyses of previously published datasets, the study should clearly state and support the new conceptual and/or biological insights arising from the analysis that are experimentally testable. Analysis and data resource of disease conditions might be considered but such studies should provide new mechanistic insights and the reported findings should be of interest and within the scope of the journal.

Manuscripts describing data resources and analyses that are specific to or derived from a single model system or organism should offer a substantive, unambiguous indication of its general interest and utility for a wide community of research investigators. Data resources that are limited to detailed studies of a narrowly employed organism are often more appropriate for a journal specifically focused on applications employing that model system.

Papers proposing biomarkers or collection of existing datasets will not be considered. Instead, we encourage authors to look at the criteria for the Database and/or Web Server articles.

Gene Regulation, Chromatin and Epigenetics

For consideration, papers should provide new insights into generally applicable principles or mechanisms that extend beyond a single gene, or present new information about the mechanisms underlying the regulation of genes involved in the synthesis, maturation, or degradation of nucleic acids. Findings must demonstrate relevance to the physiological or cellular context in which the process occurs.

The Journal specifically encourages manuscripts that:

• Identify novel structural or dynamic features of chromatin and demonstrate their biological significance.
• Provide novel insights into the functions of elements or factors that mediate long-range interactions such as insulators and enhancers.
• Present new mechanisms underlying the functions of promoters, terminators, silencers, RNA polymerases, transcription factors and other DNA binding proteins.
• Report significant new information about histone and DNA modifying enzymes and chromatin remodelling factors.
• Provide novel insights into mechanisms through which covalent modification of DNA or chromatin proteins impinge on gene expression.
• Probe the interfaces between transcription, chromatin and RNA processing (including splicing, post-transcriptional processing and regulation of transcribed RNAs).
• Provide mechanistic insights into how large or small non-coding RNAs influence chromatin structure and function and/or gene regulation.
• Use single cell approaches and mathematical modelling to reveal new gene regulatory mechanisms.

Papers that primarily report the application of genome-wide approaches to the analysis of gene expression or regulation should provide new biological or mechanistic insights with detailed follow-up investigation; otherwise, they may be more appropriate for the Data Resources and Analyses category.

Genome Integrity, Repair and Replication

The Journal encourages manuscripts focusing on systems for maintenance of genome integrity through direct surveillance of or interaction with nucleic acids. In particular we encourage manuscripts that:

• Report novel mechanisms for sensing and responding to DNA damage, including relevant checkpoints.
• Characterise the structural biology of DNA replication complexes, damage sensors and repair enzymes.
• Study the molecular mechanisms of mitosis and/or meiosis with focus on the key transactions involving DNA and chromatin and the relevant checkpoints.
• Study the mechanisms of mutagenesis and genetic instability in prokaryotes and eukaryotes.
• Use novel experimental approaches or models.

Papers may use physical, genetic, genomic, developmental, biochemical, or cell biological approaches. Papers using physical techniques without biological relevance are unlikely to be considered.

Genomics

The Journal encourages the submission of manuscripts that:

• Report the DNA sequences of complete genomes, large chromosomes or extensive gene families accompanied by bioinformatic analyses that shed significant new light on basic questions regarding genome structure and function. Papers should include complementary experimental data with relevance to genomic organisation, transcription, RNA processing, expression, genetic inheritance or other novel biology. These data may also correspond to molecular, biochemical or other equally informative analyses that support sequence-based functional annotation. Exceptions to this requirement might be made for analyses, including comparative studies, of entire genomes or large/dynamic gene families that display unusual features or provide especially novel or significant insights, including comparative studies. Reports that merely summarize information from DNA sequence database annotations, or that focus primarily on topics outside of the core subject areas of the Journal, are discouraged.
• Report application of whole genomic approaches to the analysis of gene regulation (e.g. RNA sequencing/array and proteomic technologies, ChIP-Seq or computational methods). Such manuscripts must provide novel insights into a nucleic acid-based process and provide experimental evidence to validate hypotheses generated using genome-wide approaches. ChIP-seq studies should go beyond the analysis of a single factor associating with DNA/chromatin and basic downstream bioinformatic characterisation. Correlative studies or purely descriptive accounts of microarray or sequence data will not be considered. Extensive new sequence datasets or comparative (data mining) studies that do not include experimental validation of biological relevance are more suitable for the Data Resources and Analyses category.
• Describe experimental and theoretical studies that address how the architectural organization of genomes and RNomes determine and regulate biological function. This may include studies that examine the biology and function of nuclear condensates and subnuclear structures and complexes, and/or those that describe new methods (computational and experimental) to address these questions on a cellular scale.

Nucleic acid sequences must be deposited in a databank with a release date no later than the date of publication (see General Policies).

Molecular and Structural Biology

The Journal encourages the submission of manuscripts that focus primarily on the folding, behavior, interactions, and/or structures of biological molecules and molecular assemblages that are comprised of nucleic acids and/or proteins that interact with nucleic acids in the course of their molecular, cellular and biological functions.  This category is intended for studies of highly generalizable aspects of molecular behaviors and structures. 

Studies containing such analyses, that are part of a broader description of how such molecules and molecular assemblages function within fundamental biological processes and systems (specifically, “Gene Regulation, Chromatin and Epigenetics”, “Genome Integrity, Repair and Regulation”, “Nucleic Acid Enzymes” or “RNA and RNA-protein complexes”) should instead be directed to those individual biological categories.

Examples of papers that are appropriate for this category, rather than a biological category, include those that are focused upon and describe:

• New insights into the basis of sequence- and structure-specific molecular recognition between nucleic acid targets, proteins, and/or small molecules, where such studies have clear biological and physiological relevance. 
• New insights into molecular trafficking within and between cells, including nuclear or organellar transport, and/or nucleic acid intracellular modification.
• Characterisation of molecular folding, including studies that report the thermodynamic and/or kinetic basis for folding events, where there is a clear and important question or hypothesis relevant to cellular processes.
• Studies of the molecular processes and factors that regulate or impact cellular mitosis, meiosis, and division. Such studies should offer significant molecular and mechanistic details of pathways, molecular interactions and checkpoints involving the nucleic acid of the cell, for instance mechanisms of DNA damage surveillance and repair and the corresponding maintenance of genomic integrity.
• Novel studies of molecular processing and packaging in viruses that report fundamental features that extend beyond individual cellular or viral systems. Such studies should clearly extend to a broad range of viral families or elucidate more general principles in molecular biology.
• Novel studies of molecular interactions and pathways involved in genetic conflicts at the cellular level, such as phage restriction, toxin-antitoxin systems, invasive elements, etc.
• Manuscripts that focus on the description of molecular structures (that are not otherwise appropriate for publication in a corresponding biological category). Such studies should offer novel, generalizable insights into molecular folds and function. Manuscripts that utilize database and bioinformatics approaches must be firmly related to experimental observations. Papers that describe new biophysical and structural methods, but do not contain significantly novel findings relating to an important biological problem, are more appropriate for the Methods category.

Nucleic Acid Enzymes

The Journal invites manuscripts that present in-depth studies on enzymes interacting with nucleic acids, including both natural and engineered nucleic acid structures that function as enzymes, such as ribozymes and DNAzymes. We are interested in a variety of systems, notably those involved in DNA replication, RNA synthesis, DNA and RNA editing, translation, DNA repair, transposition, recombination, cleavage, restriction and modification.

We particularly value studies that reveal new aspects of the composition, structure, or functioning of molecular machines and large complexes involved in nucleic acid enzymology. This includes research on how these enzyme complexes are organized and change over time. Studies using high-resolution cryo-EM to explore the mechanisms of these molecular machines are of great interest. We also strongly encourage studies that apply single molecule techniques like optical and magnetic tweezers, atomic force microscopy, and FRET pair analyses. We welcome studies focused on the function and mechanism of isolated biological macromolecules, either alone or in combination with other solution-based assays.

Submissions introducing new methods, both computational and experimental, for investigating these topics are also welcome. Research that uses or builds upon existing data will be considered if it addresses a significant and novel biological question relevant to nucleic acid biology or chemistry and offers new biological insights.

Nucleic Acid Therapeutics

NAR encourages submissions of paper related to the discovery, and development of Nucleic Acid Therapeutics. This section complements the section on Chemical Biology and Nucleic Acid Chemistry and submission should meet the technical guidelines at the end of that section. Examples of such studies might include.

•  All studies related to the discovery and development of therapeutic strategies using synthetic oligonucleotides, small molecules that bind DNA or RNA, mRNA therapy, CRISPR therapy, and gene therapy broadly.
•  Studies that investigate molecular or biological mechanism of actions.
•  We welcome studies that report Methods enabling development and practical application of therapeutic strategies. Methods include screening assays, production-scale synthesis, analytical methods, pharmacology, and pharmacokinetics. Methods contributions should conform to the guidelines outlined for contribution to NAR Methods.
•  Reports of data from clinical trials will be considered, but they should emphasize findings related to the mechanism of drug action and broadly interesting lessons from the trial.
•  Research related to n=1 therapies, with an emphasis on research that shares broadly useful lessons.
•  Critical Reviews and Perspectives related to nucleic acid therapeutics. In particular, we welcome Perspectives that summarize the history and outlook of newly approved therapeutics or thoughtful analysis of therapeutic strategies that have been less successful. See detailed guidelines for Critical Reviews and Perspectives.

 All contributions should be based on rigorous mechanistic data linking the proposed lead compound or drug to a particular molecular target, either in the submission or in a prior paper. Authors should highlight evidence for “on-target” effects and address alternative explanations for their observations. 

RNA and RNA-protein complexes

For consideration, papers should provide new insights into generally applicable molecular principles that govern RNA metabolism or present new information about the synthesis, maturation, or turnover of RNA in prokaryotic and eukaryotic cells. Findings must have implications that extend beyond a single transcript or RNA binding protein and include experimental evidence supporting general biological and functional relevance such as mutagenesis data.

The Journal specifically encourages manuscripts that:

• Report new structural features, assembly pathways or biological functions of ribosomes, spliceosomes, or other large ribonucleoprotein complexes. Studies that provide new insights into mechanisms of translation, splicing, or other RNA-based processes are also welcome. 
• Shed new light on the mechanisms and regulation of constitutive or alternative processing of pre-messenger RNAs including splicing, polyadenylation and editing.
• Describe new insights into the composition, formation, dynamics and functions of biological condensates. Studies that shed light on the roles of liquid-liquid phase separation in living cells are especially welcome.
• Describe novel aspects of the biogenesis, cellular roles or mechanisms underlying regulation of or by non-coding RNAs including microRNAs, small interfering RNAs, piwi-associated RNAs and long non-coding RNAs.
• Provide new insights into the molecular determinants of RNA half-lives, constitutive and regulated turnover mechanisms, and surveillance pathways that eliminate aberrant transcripts.
• Provide new information about the structure and dynamics of RNA enzymes (ribozymes) or RNAs that contribute to catalysis such as spliceosomal snRNAs or the ribosomal peptidyl transferase center.
• Elucidate the relationship between structure and function of RNA binding proteins or enzymes that function in any aspect of RNA metabolism.
• Describe novel methods for the detection and analysis of RNA modifications or reveal the impact of base modifications on RNA structure and/or function.
• Report novel experimental, computational or technical approaches leading to new insights into RNA folding or RNA recognition and complex formation in RNPs.
• Report novel approaches leading to new understandings of RNA folding or RNA recognition and complex formation in RNPs.

Manuscripts that report the results of sequencing RNA populations (transcriptome analyses) or other genome-wide approaches or identifying and classifying RNAs, including those carrying a particular base modification, may be more appropriate for the Data Resources and Analyses category. Such studies are acceptable only if they include follow-up experiments that provide mechanistic insight into physiological or functional relevance.

Manuscripts that primarily report the application of knockdown experiments with duplex RNAs or antisense oligonucleotides should follow published guidelines.

If a manuscript reports development of an RNA-based therapeutic, rigorous controls and statistical analysis must be included. Advances in mechanistic understanding should be stressed. Studies describing clinical results will be considered, but only if results related to the drug's mechanism of action, distribution, or pharmacokinetics are reported. Studies relating to cellular uptake, delivery, and chemistry of oligonucleotides are particularly encouraged.

Synthetic Biology and Bioengineering

NAR encourages submission of papers describing the modification and/or redesign of genetic information in living cells and organisms, deliberate genetic recoding of biological pathways and decision points to alter biological behaviours and responses, or the generation of organisms harbouring synthetic genetic circuits or dramatically modified and/or fully synthetic genomes.

The main text of all submissions in this category must be written in a manner that is easily understood by non-specialists and readers comprising a broad spectrum of molecular and cellular biologists. The main text in all submissions must be largely, if not entirely, free of specialised jargon and mathematical derivations that will only be understood by specialists working directly in the field of the submission. More detailed information required for specialists working in areas related to the manuscript's precise focus can be provided in the supplemental information.

Examples of such studies might include:

• The creation of novel genetic pathways and/or regulatory elements in living cells including biological computing circuits and/or information storage. Such papers must be written in a manner that is easily understood by molecular and cellular biologists without extensive experience in synthetic biology, rather than relying on jargon related to computational algorithms and/or electronic circuitry. Manuscripts that focus primarily on the development and description of new functional genetic elements or DNA computing devices, without demonstration of a broader biological application and corresponding physiological phenotypes, will usually be redirected to a journal with a more specific focus on core principles of synthetic biology.

• The creation of new nanomaterials involving nucleic acids (e.g., DNA and/or RNA origami etc.), and nanomachines that are based on or acting on nucleic acids and that display an obvious biological or physiological applications. Studies that focus primarily on the physical behavior and structure of such constructs, without demonstration of corresponding biological or physiological application will usually be redirected to a journal with a more specific focus on core principles of molecular engineering.  Descriptions of the generation and application of aptamers for molecular diagnostics, detection and/or as antagonists of molecular function (i.e. for purposes similar to antibodies) will generally be redirected towards biotechnology journals with a focus on the development of molecular targeting reagents. Descriptions of 'DNA computing devices' will generally be redirected to a computational sciences journal.

• The creation of new biological parts, systems and synthetic organisms. Studies that reveal novel principles of rewriting and rebuilding the natural systems to understand the origins of life are encouraged.

For related criteria, see Chemical Biology and Nucleic Acid Chemistry.

Newly designed or engineered constructs and genetic ‘parts' described in this category. should be made publicly available, most usually by registration and deposition of constructs and vectors in ADDGENE. Additional forms of standardization such as use of the BioBrick standard and its Registry of Standard Biological Parts, is encouraged when appropriate.

 

Other journals in the NAR portfolio

We recognize that many excellent studies of nucleic acids may not fit within NAR’s strict criteria for publishing the highest originality and global utility. In such cases where the content of a submitted manuscript is deemed inappropriate, regardless of experimental quality, NAR may offer authors a direct transfer of a submitted manuscript for consideration by a related journal in the Oxford University Press Collection; direct submission to these journals is also encouraged.

Authors may be offered a transfer to one of the following alternative journals:

NAR Genomics and Bioinformatics: NAR recognizes the increasing importance for genome/genetic analyses. Manuscripts that do not fall within NAR guidelines (e.g. therapeutic sequencing, medical diagnostics, information technology) may be directed to NAR Genomics and Bioinformatics (NARGAB). Enquiries may be sent to the editorial office at [email protected]; pre-submission inquiries of a scientific nature may also be directed to the Editor-in-Chief, Dr. Cedric Notredame: [email protected].

NAR Cancer: NAR Cancer publishes original research and Critical Reviews and Perspectives at the intersection of nucleic acids research and cancer, including computational biology and data resources, DNA damage sensing and repair, gene regulation and chromatin, genomics, methods, nucleic acid-based therapeutics, and structural biology. Enquiries may be sent to the editorial office at [email protected]; pre-submission inquiries of a scientific nature may also be directed to the Editor-in-Chief, Dr. William S. Dynan: [email protected].

NAR Molecular Medicine: NAR Molecular Medicine publishes original research and critical reviews at the intersection of nucleic acid biology, therapeutics, and the molecular mechanisms of disease. The journal considers paper within this broad scope from all areas of clinical medicine, pathology, molecular and cellular biology, structure-activity investigations related to disease, computation and drug discovery. Enquiries may be sent to the editorial office at [email protected]; pre-submission inquiries of a scientific nature may also be directed to the Editor-in-Chief, Dr. Maria Spies: [email protected].

Related journals in OUP's portfolio

Synthetic Biology: NAR will only consider new vectors and assemblies if they are based on fundamentally novel principles. However complex vector engineering, while not technically novel, can have enormous value. More information can be found at Synthetic Biology. Enquiries may be sent to the editorial office at [email protected]; pre-submission inquiries of a scientific nature may be addressed to the  Editor-in-Chief, Dr. Jean Peccoud at the same address.

Biology Methods and Protocols: NAR Methods does not consider manuscripts that delineate laboratory protocols per se, however novel. Nonetheless, there are situations where step-by-step specifics greatly improve experimental reproducibility. To this, relevant protocol manuscripts can be directed to Biology Methods and Protocols (Editor-In-Chief, Andrzej Stasiak) a journal that focuses on broad biological methods. Enquiries  may be sent to the editorial office at [email protected]. Authors of NAR Methods publications are also encouraged to submit a detailed protocol version to Biology Methods and Protocols.

Bioinformatics Advances is a broad scope, fully open access journal publishing across all areas of computational biology including databases and webservers. The journal covers bioinformatics methods, such as algorithms, statistics, databases and software as well as biological contributions for which the application of advanced computational methods is an essential factor. The major focus of the journal is on the molecular and cellular levels of biology. Bioinformatics Advances is published in collaboration with the International Society for Computational Biology (ISCB). More information can be found at Bioinformatics Advances, and the editorial office can be contacted at [email protected].

DNA Research publishes research articles with original findings of substantial importance in broad aspects of DNA- and genome-related fields. As genome data provide us with the most fundamental basis for a variety of research and applications derived thereof, the journal is willing to accept articles investigating genomes of various organisms to enrich the collection of useful genome data resources. In addition, DNA Research publishes comprehensive review articles, surveying research progresses in the fields of interest to encourage readers to challenge unsolved important problems. Visit DNA Research for more details and the editorial office can be contacted at [email protected].

Oxford Open Neuroscience is a broad scope, fully open access journal publishing the widest interpretation of neuroscience, including cellular and molecular neuroscience, neural development, neurogenetics, systems and behavioural neuroscience, through to computational neuroscience, and cognitive neuroscience. The journal aims to represent the entire neuroscience community and is run by a representative group of Senior Editors who are active scientists and subject specialists. More about the journal can be found at Oxford Open Neuroscience. Pre-submission inquiries may be sent to the editorial office at [email protected].

In addition to these transfer opportunities, NAR sends transfers to other journals on related topics published by Oxford University Press. All transfers are sent according to the choice of the authors. Reviewer reports and the original decision letter are included in the transfer, but the reviewer identities are not shared. 

Transferred manuscripts may be sent out for additional peer review, and a decision will be made on the manuscript based on the feedback from all reviewers and the judgment of the editorial team.