Nucleic acid methods explained

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

External links

• Protocols for Recombinant DNA Isolation, Cloning, and Sequencing

Notes and References

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