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 ^[1]
• 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 ^{[2] [3]}
• Dual-polarization interferometry ^[4]
• Quartz crystal microbalance with dissipation monitoring (QCM-D) ^[5]

Gene function

• RNA interference ^[6]

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. Rana, Ajay K. (2025). "Challenging biological samples and strategies for DNA extraction" . Journal of Investigative Medicine. 73 (6): 443–459. doi:10.1177/10815589251327503. PMID   40033560.
2. 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.
3. 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.
4. 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.
5. 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.
6. 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