Nucleic acid methods

For protein methods, see Protein methods.

Nucleic acid methods are the techniques used to study nucleic acids: DNA and RNA.

Purification

• DNA extraction
• Phenol–chloroform extraction
• Minicolumn purification
• RNA extraction
• Boom method
• Synchronous coefficient of drag alteration (SCODA) DNA purification

Quantification

• Abundance in weight: spectroscopic nucleic acid quantitation
• Absolute abundance in number: real-time polymerase chain reaction (quantitative PCR)
• High-throughput relative abundance: DNA microarray
• High-throughput absolute abundance: serial analysis of gene expression (SAGE)
• Size: gel electrophoresis

Synthesis

• De novo: oligonucleotide synthesis
• Amplification: polymerase chain reaction (PCR), loop-mediated isothermal amplification (LAMP), transcription-mediated amplification (TMA)

Kinetics

• Multi-parametric surface plasmon resonance^[1][2]
• Dual-polarization interferometry^[3]
• Quartz crystal microbalance with dissipation monitoring (QCM-D)^[4]

Gene function

• RNA interference^[5]

Other

• Bisulfite sequencing
• DNA sequencing
• Expression cloning
• Fluorescence in situ hybridization
• Lab-on-a-chip
• Comparison of nucleic acid simulation software
• Northern blot
• Nuclear run-on assay
• Radioactivity in the life sciences
• Southern blot
• Differential centrifugation (sucrose gradient)
• Toeprinting assay
• Several bioinformatics methods, as seen in list of RNA structure prediction software

See also

• CSH Protocols
• Current Protocols

References

1. Tang, Wei; Hu, Shichao; Wang, Huaming; Zhao, Yan; Li, Na; Liu, Feng (23 September 2014). "A universal molecular translator for non-nucleic acid targets that enables dynamic DNA assemblies and logic operations". Chem. Commun. 50 (92): 14352–14355. doi:10.1039/C4CC07041K. PMID 25295484.
2. Ihalainen, Petri; Pettersson, Fredrik; Pesonen, Markus; Viitala, Tapani; Määttänen, Anni; Österbacka, Ronald; Peltonen, Jouko (7 March 2014). "An impedimetric study of DNA hybridization on paper-supported inkjet-printed gold electrodes". Nanotechnology. 25 (9): 094009. Bibcode:2014Nanot..25i4009I. doi:10.1088/0957-4484/25/9/094009. PMID 24522116. S2CID 206070778.
3. Berney, H.; Oliver, K. (2005). "Dual polarization interferometry size and density characterisation of DNA immobilisation and hybridisation". Biosensors and Bioelectronics. 21 (4): 618–626. doi:10.1016/j.bios.2004.12.024. PMID 16202875.
4. Dixon, Matthew C. (July 2008). "Quartz Crystal Microbalance with Dissipation Monitoring: Enabling Real-Time Characterization of Biological Materials and Their Interactions". Journal of Biomolecular Techniques. 19 (3): 151–158. PMC 2563918. PMID 19137101.
5. Hannon, Gregory J. (July 2002). "RNA interference". Nature. 418 (6894): 244–251. Bibcode:2002Natur.418..244H. doi:10.1038/418244a. ISSN 1476-4687. PMID 12110901. S2CID 4426281.

External links

• Protocols for Recombinant DNA Isolation, Cloning, and Sequencing