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Nucleic Acids Research Methods

Each of the collections on this page is a category-specific archive of Methods published in NAR from 1999 to the present.

Click here for more information about NAR Methods, including how to cite Methods Online papers.

cell biology

Cell Biology

This category presents methods using nucleic acids to study cellular biological processes, such as intra- and inter-cellular transport, apoptosis, subcellular localization, etc. and for structural and biochemical studies of nucleic acid-containing organelles and macromolecular, nucleoprotein particles. View all

chromatin - epigenetics

Chromatin and Epigenetics

This category presents techniques for analyzing DNA and chromatin organization and its constituents by ChIP (chromatin immunoprecipitation) and nucleosome and transcription factor mapping. Methods will also address the regulation, recognition and genetic transmission of protein and DNA secondary modifications. View all

computational methods

Computational Methods

Computational Methods include useful new programs, routines, metrics and algorithms with applications to Bioinformatics. This can include new sequence manipulations, annotations, assemblies, but also new methods of computational analysis that facilitate data interpretation. View all

cell transformation and DNA transfer

DNA-Mediated Cell Transformation and Nucleic Acids Transfer

This category describes novel methods for introducing and maintaining DNA, RNA and oligonucleotides in cells and transgenic animals. This may involve mechanisms for increasing efficiencies of transformation/transfection, novel selection schemes, and use of integrating versus extrachromosomal vectors. View all

genomics

Genomics

This category presents new strategies for genome scale analyses including positional or whole genome cloning, chromosonal mapping and synteny characterisation, Genome-Wide Association Studies (GWAS), and large scale sequencing and assembly. Strategies may involve molecular biology methods and emerging new technologies. View all

deep sequencing

Massively Parallel (Deep) Sequencing

We encourage submission of all manuscripts directed toward generating and analyzing high throughout sequencing (HTS) data using 454/pyrosequencing, Solexa/Illumina, ABI SOLiD, Ion Torrent, Helicos, Pacific Bioscience and other relevant systems and approaches. New platforms, including single molecule analyses, tested and proven on a global-scale are also of interest. Areas would include all categories of DNA-seq, RNA-seq, ChIP-seq, Clin-seq, RIP-seq, exome-seq, etc. as well as, novel bioinformatic applications for sequence assembly of short reads, exon-exon boundary mapping, protein-nucleic acid interactions, et al. Manuscripts, which rely on HTS analyses, but offer important novel insight into aspects of genome organization, transcription, RNA processing, or other biological pathways and processes, may be submitted to the 'Genomics' research category.

Comparative studies of various platforms are generally not appropriate unless they provide unique biological insight. Statistical, read-assembly, normalisation, and clustering approaches must offer significant advantage in sensitivity, discrimination, or resolution to those in common use and be proven comparatively at a genome-wide level. We discourage submission of computational "pipelines" that use existing tools unless significant novelty is demonstrated; papers describing combinations of standard computational applications are also not appropriate. Novel utility must be made clear at the outset and be easily accessible to non-specialists. All SEQ data must be submitted to Array Express or Gene Expression Omnibus, and compliance should follow MINSEQE guidelines (http://www.fged.org/projects/minseqe/). View all

microarray

Microarray Technology

This category represents only wholly novel strategies for generating or evaluating data using microarray and related technologies. Comparative studies of various platforms are not appropriate unless they provide unique biological insight. New statistical and normalisation approaches must offer significant advantage in sensitivity, discrimination, or resolution and must be proven comparatively at a genome-wide level; papers describing combinations of standard computational applications are not appropriate. Papers reporting novel modes of nucleic acid immobilisation require validation by genome-wide analyses. All microarray data must conform to MIAME guidelines and be submitted to GEO or Array Express. View all

miscellaneous

Miscellaneous/Other

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mutagenesis

Mutagenesis

This category presents widely useful new or highly optimized methods for random, site-specific, or high-throughput mutagenesis. Techniques may involve chemical or enzymatic processes and be applied or screened in vivo or in vitro. View all

new restriction enzymes

New Restriction Enzymes

This category includes descriptions of new restriction enzymes that recognize novel sequences or cleave at new positions within known recognition sites (neoschizomers). Sequence specific methylases, etc. that interfere with restriction enzyme function and recognition will also be considered. View all

nucleic acid amplification

Nucleic Acid Amplification

This category presents in vivo and in vitro methods for generation of identical synthetic copies of RNA and DNA. These methods may operate at micro or macro scales and at various or uniform temperatures. The method may address a specific new strategy for nucleic acid amplification or a new application or significant enhancement of previously described protocols. View all

nucleic acid enzymology

Nucleic Acid Enzymology

This category presents methods for characterizing enzymes involved in nucleic acid biochemistry. Processes may focus on enzymes that act directly on DNA or RNA, or on proteins that interact with such species. Nucleic acids with inherent enzymatic activity are of particular interest, as are multi-protein complexes. View all

nucleic acid modification

Nucleic Acid Modification

This category presents chemical and biophysical methods for identifying specific modifications as well as biological approaches for assaying functional modifications of DNA and RNA and their consequences in vivo. View all

Nucleic Acid Structure

Nucleic Acid Structure

This category presents methods to analyze nucleic acid structure either indirectly (e.g. by chemical probing, using electrophoresis) or directly (e.g. using fluorescence, NMR or crystallography). Specific methods to prepare nucleic acid samples for structural analyses are also described. View all

DNA characterisation

Physical and Biochemical Characterisation of DNA

This category includes all new or highly significant improved methods for DNA purification from various sources (e.g. ancient DNA, DNA from widely used hosts), DNA quantification, DNA structural analyses (by enzymatic, gel electrophoresis, mass-spectrometry, hybridization), and DNA sequencing. View all

polymorphism/mutation detection

Polymorphism/Mutation Detection

This category describes new methods for detecting mutations or polymorphic sites. The method may address general principle of the polymorphism or mutation detection. Alternatively, widely useful methods may be developed for the detection of specific types of mutations or polymorphisms (e.g. tri-nucleotide repeats). These mutations or polymorphisms must however be widespread and not limited to a specific gene. View all

protein- nucleic acid interaction

Protein-Nucleic Acid Interaction

This category describes methods for the analysis of protein-nucleic acid interactions including footprinting, interference, cross-linking, fluorescence techniques, one- and tri-hybrid strategies, in vivo methods and analysis of mutants. View all

protein-protein interaction

Protein-Protein Interaction

This category describes methods using nucleic acids for the analysis of protein-protein interactions or methods specifically suited for the analysis of interactions between proteins involved in nucleic acid function. This includes, but is not limited to, two-hybrid system, surface display, arrays, generation of mutant libraries. View all

recombinant DNA expression

Recombinant DNA Expression

This category describes methods for the expression of recombinant DNA in vitro or in various hosts. Expression of the DNA can be at the protein or RNA level and involved regulated or constitutive expression. An extension of these techniques may involve transgenic animals for ectopic expression, tissue specific expression, mutant rescue or involve gene therapy. View all

recombination

Recombination

This category describes methods making use of homologous, site specific or random recombination including their use in mutagenesis. View all



repair

Repair

This category describes widely applicable methods to analyze the repair of damaged nucleic acids including, but not limited to, general assays for specific enzymes, detection of specific damages, generation of specific templates for repair assays. View all

replication

Replication

This category describes methods for the analysis of nucleic acid replications including, but not limited to, the analysis of specific enzymes, the development of widely applicable model system and the description of new assay. View all

ribosomes and protein translation

Ribosomes and Protein Translation

This category presents methods for analyzing protein translational machinery in vivo and in vitro. Focus would include issues involving ribosomes, rRNA, tRNA, translation, protein synthesis, initiation factors, elongation factors, termination factors, and nucleoli. New and improved methods for protein translation or component purification will also be considered. View all

RNA characterisation

RNA Characterisation and Manipulation

This category presents all methods to analyze RNA including, but not limited to, RNA production, enzymatic treatment of RNA, RNA sequencing and probing, strategies involving ribozymes, biophysical methods for the characterization of RNA. View all

Synthetic Biology and Assembly Cloning

Synthetic Biology and Assembly Cloning

This category includes novel approaches for generating and joining Nucleic Acid fragments. Fragments may be produced chemically, from RNA templates, from DNA with specific attributes (genome location, repetitive nature, viral, polymorphic), or for whole genes or whole genomes. Procedures could include applications for large fragment (whole genome) assembly or be specific to recombineering, subcloning, or library construction. These latter applications or relevant vectors may be presented only if based on novel principles worthy of own publication on their own. View all

targeted gene modification

Targeted Gene Modification

Articles in this category describe the creation and delivery of sequence-specific DNA targeting platforms (such as CRISPRs, TALENs, ZFNs, homing endonucleases, or peptide-nucleic acid conjugates) to deliver catalytic functions (such as nuclease, integrase, or transposase activities) or other molecule functions (such as transcriptional activators and repressors or chromatin modifiers) to individual loci within biological genomes, for the purpose of inducing site-specific gene disruptions, insertions, or modifications. Methods can include the development and application of novel combinations and architectures for gene targeting molecular systems, new methods for packaging and/or delivery into living cells, tissues or organisms, and new methods for characterization and validation of their activity, specificity and effect.
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inhibition of gene function

Targeted Inhibition of Gene Function

This category covers new developments using RNA and oligonucleotide strategies for specific inhibition of gene function. Examples include antisense, ribozymes, triplex and RNAi. View all



monitoring gene expression

Transcriptome Mapping - Monitoring Gene Expression

This category incorporates new techniques for detecting expression of specific genes or for following the simultaneous expression of many or all genes under specific physiological or developmental conditions. Many whole cell approaches are either now well optimized (hybridization, cDNA libraries, subtracted hybridization, SAGE, RDA, DDRT-PCR, CAGE, microarrays) or are being rapidly supplanted by more dynamic methods (RNAseq). Technical variations must be significant and proven to have unequivocal comparative advantage (e.g. in sensitivity, reproducibility). New methods for in situ detection or subcellular localization are encouraged. View all

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