Introduction to Nucleic Acid Analysis

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en-us LUSNPJ7OP Nucleic Acid Analysis Introduction to Nucleic Acid Analysis /webroot/web/html/lsr/solutions/applications/genomics <p>Nucleic acid analysis generally involves isolation and characterization of the DNA or RNA sample of interest. Sample purification and quality assessment are important steps in experimental workflows since the quality of the recovered nucleic acid can affect the performance in downstream reactions. A wide range of techniques can be used to transform a sample which cannot be directly analyzed into one that fits the requirements of the analytical technique to be used.</p> Nucleic Acid Sample Preparation Method <p>DNA and RNA are nucleic acid molecules that are used to store and transmit genetic information inside a cell. The central dogma of molecular biology states that DNA is transcribed into RNA that is then translated into protein. While this is a simplistic look at gene and protein expression, it illustrates that DNA and RNA can provide important information about genomics, gene expression and cellular regulation for a sample of interest. In order to perform analysis on DNA and RNA, it is often necessary to first extract these molecules from cells or tissues.</p> <div style="text-align: center;"><img src="/webroot/web/images/lsr/solutions/applications/gene_expression/genomics/application_detail/gxa16_img1.gif" alt="" width="167" height="170" /></div> <p class="caption"><strong>Central dogma of molecular biology.</strong></p> <p>Several well established methods exist for extracting, purifying, and concentrating nucleic acids. Selecting the most appropriate nucleic acid isolation method depends on several factors including the starting sample material, the quantity, size and stability of the target nucleic acid, and the downstream application for the nucleic acid of interest. Following the purification step, it is often necessary to <a href="/evportal/destination/solutions?catID=LUSNQLDN">determine nucleic acid concentration, purity, and integrity</a> before proceeding with downstream applications.</p> <p><strong> Common Nucleic Acid Sample Preparation Methods</strong></p> <table class="pd_table pd_gridlines" border="0"> <tbody> <tr> <td align="left" valign="top">&nbsp;</td> <td align="left" valign="top"><strong>Cesium Chloride Gradients</strong></td> <td align="left" valign="top"><strong>Filter Column Purification</strong></td> <td align="left" valign="top"><strong>Gel Extraction</strong></td> <td align="left" valign="top"><strong>Guadinidium Isothiocyanate Phenol Chloroform Extraction - Ethanol Precipitation</strong></td> <td align="left" valign="top"><strong>Ion Exchange Resin</strong></td> <td align="left" valign="top"><strong>Phenol Chloroform Extraction - Ethanol Precipitation</strong></td> <td align="left" valign="top"><strong>Size Exclusion</strong></td> </tr> <tr class="pd_colorbackground"> <td align="left" valign="top"><strong>Recommended For</strong></td> <td align="left" valign="top">Plasmid DNA</td> <td align="left" valign="top">DNA and RNA &gt; 200bp</td> <td align="left" valign="top">DNA</td> <td align="left" valign="top">RNA</td> <td align="left" valign="top">DNA</td> <td align="left" valign="top">RNA</td> <td align="left" valign="top">DNA and RNA</td> </tr> <tr> <td align="left" valign="top"><strong>Pros</strong></td> <td align="left" valign="top">Highly pure DNA</td> <td align="left" valign="top">Fast and Easy</td> <td align="left" valign="top">Fast and Easy</td> <td align="left" valign="top">Scalable by volume: highly pure RNA</td> <td align="left" valign="top">Scalable by volume</td> <td align="left" valign="top">Scalable by volume: highly pure RNA</td> <td align="left" valign="top">Fast and Easy</td> </tr> <tr class="pd_colorbackground"> <td align="left" valign="top"><strong>Cons</strong></td> <td align="left" valign="top">Requires expensive instruments and removal of ethidium bromide and cesium chloride from isolated plasmid</td> <td align="left" valign="top">May not recover molecules &lt;200 bp</td> <td align="left" valign="top">Potentially low yield; agarose contamin-ation may inhibit downstream reactions</td> <td align="left" valign="top">Phenol is hazardous</td> <td align="left" valign="top">Residual resin may inhibit downstream reactions</td> <td align="left" valign="top">Phenol is hazardous</td> <td align="left" valign="top">Potentially low yield; imperfect size separation</td> </tr> </tbody> </table> <div class="top"><a href="#helptop">Back to Top</a></div> Nucleic Acid Electrophoresis <p>Gel electrophoresis can be used to effectively separate nucleic acids based on their size within agarose or polyacrylamide gels. <a href="/evportal/destination/solutions?catID=LUSNS52B7">You can successfuly separate nucleic acid fragments ranging in length from 20 base pairs to 20 kb by electrophoresis.</a> Size ladders containing a range of different-length DNA fragments are run with the sample of interest to identify the corresponding size bands in a gel. Agarose gels are ideal for the separation of DNA restriction digests, PCR products, and genomic DNA or RNA prior to Southern or northern blotting. Polyacrylamide gels can be used for what is known as polyacrylamide gel electrophoresis, or PAGE. Applications include oligonucleotide analysis, RNase protection assays, and northern blotting. Non-denaturing polyacrylamide gels are used to separate small double-stranded DNA (dsDNA) fragments, particularly PCR products. Denaturing polyacrylamide gels are used for separation of small RNA and single-stranded DNA (ssDNA) fragments. Gels can be hand cast in the lab, or precast gels can be purchased from commercial providers.</p> <div class="top"><a href="#helptop">Back to Top</a></div> General Considerations <p>Good laboratory technique is essential when working with nucleic acids to minimize nuclease contamination. One critical consideration when working with nucleic acid is to avoid nucleases in your solutions, consumables, and labware. Ready-to-use solutions and consumables that are nuclease-free, such as PCR-grade water, are readily available from commercial providers. Alternatively, for RNase removal, you can treat solutions with diethyl pyrocarbonate (DEPC), and then autoclave them. RNases on labware can also be inactivated by DEPC treatment, or by baking at 250&deg;C for 3 hr.</p> <p>When performing organic extractions with phenol, be aware that phenol causes burns and can be fatal if ingested. When working with phenol, use gloves and eye protection (laboratory glasses, shield, and safety goggles). Do not get on skin or clothing and avoid breathing vapor.</p> <div class="top"><a href="#helptop">Back to Top</a></div> 6018 High-Throughput Automated Extraction of RNA Using the Aurum Total RNA 96 Kit, Rev A 6018 /webroot/web/pdf/lsr/literature/Bulletin_6018.pdf Literature PDF Application_Notes /webroot/web/images/general/icons/icon_pdf.gif No High-Throughput Automated Extraction of RNA Using the Aurum Total RNA 96 Kit, Rev A 6018 6018, automation, C1000 thermal cycler, CFX96 real-time PCR detection system, HCV replicon, high throughput, HuH-7 cells, iQ supermix, iScript cDNA synthesis kit, isolation, polymerase chain reaction, purification, qPCR, realtime, real time, reverse transcription quantitative PCR, RNA isolation, RT-qPCR, 732-6800, 7326800, 170-8860, 1708860, 170-8891, 1708891, 184-1000, 1841000, 185-5096, 1855096 1810 InstaGene Matrix: Prepare DNA Templates for PCR With No Phenol/Chloroform Extractions and No Deproteinization Steps, Rev C 1810 /webroot/web/pdf/lsr/literature/Bulletin_1810.pdf Literature PDF Application_Notes /webroot/web/images/general/icons/icon_pdf.gif InstaGene Matrix: Prepare DNA Templates for PCR With No Phenol/Chloroform Extractions and No Deproteinization Steps, Rev C No InstaGene Matrix: Prepare DNA Templates for PCR With No Phenol/Chloroform Extractions and No Deproteinization Steps, Rev C 1810 bulletin 1810, lit1810, bulletin 1810, insta gene, instagene, dna cleanup, dna purification, contaminant removal, sample preparation, pcr, inhibitors, phenol/chloroform, phenol, chloroform, genomic, sample prep, 166-2001, 166-2001EDU, 1662001, 1662001EDU, 732-6030, 732-6030edu, 7326030, 7326030edu 2950 Comparison of PCR Kleen Spin Columns to Traditional Methods for Purification of PCR Products Prior to Sequencing, Rev A 2950 /webroot/web/pdf/lsr/literature/Bulletin_2950.pdf Literature PDF Application_Notes /webroot/web/images/general/icons/icon_pdf.gif No Comparison of PCR Kleen Spin Columns to Traditional Methods for Purification of PCR Products Prior to Sequencing, Rev A 2950 bulletin 2950, lit2950, spin column, spin columns, pcr kleen, dna, cleanup, pcr cleanup, sequencing, pcr products, purification, 732-6300, 732-6300EDU, 7326300, 7326300EDU 5990 2920 Aurum Total RNA Mini Kit Product Information Sheet, Rev B 2920 /webroot/web/pdf/lsr/literature/Bulletin_2920.pdf Literature PDF Product_Information_Sheets /webroot/web/images/general/icons/icon_pdf.gif No Aurum Total RNA Mini Kit Product Information Sheet, Rev B 2920 LIT2920, bulletin 2920, sample preparatioin 2919 Aurum Total RNA 96 Kit Product Information Sheet, Rev B 2919 /webroot/web/pdf/lsr/literature/Bulletin_2919.pdf Literature PDF Product_Information_Sheets /webroot/web/images/general/icons/icon_pdf.gif No Aurum Total RNA 96 Kit Product Information Sheet, Rev B 2919 sample preparation, bulletin 2919, LIT2919 5282 Aurum Total RNA Fatty and Fibrous Tissue Kit Flier, Rev A 5282 /webroot/web/pdf/lsr/literature/Bulletin_5282.pdf Literature PDF Brochures_and_Specifications /webroot/web/images/general/icons/icon_pdf.gif No Aurum Total RNA Fatty and Fibrous Tissue Kit Flier, Rev A 5282 7326830, aurum, rna, tissue, extraction, isolation, nucleic, acid, 732-6830, lit5282, sample preparation, prep, purification, 732-6830JA, 732-6870, 7326830, 7326830JA, 7326870 5736 iScript RT-qPCR Sample Preparation Reagent Flier, Rev A 5736 H /webroot/web/pdf/lsr/literature/Bulletin_5736.pdf Literature PDF Brochures_and_Specifications /webroot/web/images/general/icons/icon_pdf.gif No iScript RT-qPCR Sample Preparation Reagent Flier, Rev A 5736 high-throughput gene expression analysis, high throughput, protocol, protocols, quantitative PCR, quantitation, real time, real-time, realtime, RNA isolation, threshold cycle, 170-8898, 1708898, 170-8899, 170889 2277 2277 Quantum Prep Plasmid Miniprep Kit Product Information Sheet /webroot/web/pdf/lsr/literature/Bulletin_2277.pdf Literature PDF Product Information Sheets /webroot/web/images/general/icons/icon_pdf.gif No Quantum Prep Plasmid Miniprep Kit Product Information Sheet Life Science 2277 plasmid preparation, prep, LIT2277, nucleic acid purification, bulletin 2277 2664 Aurum Plasmid Mini Kit Product Information Sheet, Rev C 2664 /webroot/web/pdf/lsr/literature/Bulletin_2664C.pdf Literature PDF Product_Information_Sheets /webroot/web/images/general/icons/icon_pdf.gif No Aurum Plasmid Mini Kit Product Information Sheet, Rev C 2664 DNA purification, sample preparation, bulletin 2664, LIT2664 2074 InstaGene Matrix Product Information Sheet 2074 /webroot/web/pdf/lsr/literature/Bulletin_2074.pdf Literature PDF Manuals_and_Quick_Guides /webroot/web/images/general/icons/icon_pdf.gif No InstaGene Matrix Product Information Sheet 2074 bulletin 2074, lit2074, insta gene, instagene, nucleic acid purification, pcr, pcr inhibitors, sample preparation, sample prep, sample purification, chelex, sample prep, amplification, genomic, blood, tissue, phenol, chloroform, dna cleanup, dna purification, contaminant removal, sample preparation, phenol/chloroform, phenol, chloroform, 732-6030, 732-6030edu, 7326030, 7326030edu 2311 PCR Kleen Spin Columns Product Information Sheet, Rev D 2311 /webroot/web/pdf/lsr/literature/Bulletin_2311.pdf Literature PDF Product_Information_Sheets /webroot/web/images/general/icons/icon_pdf.gif PCR Kleen Spin Columns Product Information Sheet, Rev D No PCR Kleen Spin Columns Product Information Sheet, Rev D 2311 deoxyribonucleic acid, dna, spin column, exclusion chromatography, contaminant removal, prepacked, sample preparation, pcr kleen, dna, cleanup, sequencing, pcr products, purification, pcr-kleen, clean, clean up, impurity, impurity removal, lit2311, polymerase chain reaction, pre-packed, 2311, cleanup, primer dimers, pcr product, agarose, impurities, nucleic acid, prep, primer-dimer, purification, 732-6300, 732-6300EDU, 7326300, 7326300EDU 2320 Bio-Spin and Micro Bio-Spin Column Product Information Sheet, Rev A 2320 /webroot/web/pdf/lsr/literature/Bulletin_2320.pdf Literature PDF Product_Information_Sheets /webroot/web/images/general/icons/icon_pdf.gif No Bio-Spin and Micro Bio-Spin Column Product Information Sheet, Rev A 2320 bulletin 2320, spin columns, nucleic acid purification, sample preparation, prep, purification, terminator removal, desalt, probe cleanup, LIT2320, 732-6227, 732-6228, 732-6002, 732-6213, 732-6231, 732-6232, 732-6006, 732-6221, 732-6222, 732-6225, 732-6200, 732-6201, 732-6205, 732-6223, 732-6224, 732-6226, 732-6250, 732-6251, 732-6202, 732-6203, 732-6206, 7326227, 7326228, 7326002, 7326213, 7326231, 7326232, 7326006, 7326221, 7326222, 7326225, 7326200, 7326201, 7326205, 7326223, 7326224, 7326226, 7326250, 7326251, 7326202, 7326203, 7326206 RNA Isolation <p><a title="RNA Isolation Selection Guide" onclick="javascript:openAjaxOverlay('/webroot/web/html/lsr/products/nucleic_acid_sample_purification/category_overlay/global/na_rna_isloation_selection_guide.html' );" href="javascript:void(0);">RNA Isolation Selection Guide</a></p> Life Science Research/Products/Nucleic Acid Sample Preparation and Purification/RNA Isolation/Aurum Total RNA Mini Kit ->MT::eb91e411-d011-4032-95e0-cdb29691d4d3##Life Science Research/Products/Nucleic Acid Sample Preparation and Purification/RNA Isolation/Aurum Total RNA Fatty and Fibrous Tissue Kit ->MT::c70a51af-c424-4dc6-8ae4-d6a9f2fe81f6##Life Science Research/Products/Nucleic Acid Sample Preparation and Purification/RNA Isolation/Aurum Total RNA 96 Kit ->MT::49da5896-dfde-4292-8021-9df1d8b77fec##Life Science Research/Products/Nucleic Acid Sample Preparation and Purification/DNA Isolation/InstaGene Matrix ->MT::6c2be54f-6c95-43de-8ce3-e9aee8229eeb##Life Science Research/Products/Nucleic Acid Sample Preparation and Purification/RNA Isolation/PureZOL RNA Isolation Reagent ->MT::13ac63ab-4674-4e63-b0c2-095a704fab88## Life Science Research/Solutions/Applications/Genomics/Nucleic Acid Analysis/Nucleic Acid Electrophoresis ->MTS::LUSNS52B7##Life Science Research/Solutions/Technologies/PCR ->MTS::LUSNYI15##Life Science Research/Solutions/Technologies/qPCR|Real-Time PCR ->MTS::LUSO4W8UU## Eddie C What is Nucleic Acid Analysis? 12/21/11 02:36 PM 12/21/21 02:37 PM AE,AI,AL,AM,AR,AT,AU,AZ,BA,BD,BE,BF,BG,BH,BN,BO,BR,BW,CA,CH,CL,CM,CN,CO,CR,CY,CZ,DE,DK,DO,DZ,EC,EE,EG,EH,ER,ES,ET,FI,FM,FO,FR,GA,GE,GF,GH,GP,GR,GT,GU,HK,HN,HR,HT,HU,ID,IE,IL,IN,IS,IT,JM,JO,JP,KE,KH,KR,KW,KZ,LB,LI,LK,LT,LU,LV,MA,MD,MG,MK,ML,MO,MQ,MS,MT,MU,MX,MY,NG,NI,NL,NO,NP,NZ,OM,PA,PE,PF,PG,PH,PK,PL,PR,PS,PT,PW,PY,QA,RO,RS,RU,SA,SB,SE,SG,SI,SK,SN,ST,SV,TG,TH,TN,TO,TR,TT,TW,TZ,UA,UG,UK,US,UY,UZ,VA,VE,VU,XK,YE,ZA en LSR /LSR/Applications/Genomics N 0 /en-us/applications-technologies/url-title-missing?ID=LW7FBHE8Z Nucleic Acid Extraction and Purification /en-us/applications-technologies/applications-technologies/nucleic-acid-extraction-purification?ID=LUSNQLDN Nucleic Acid Electrophoresis /en-us/applications-technologies/applications-technologies/nucleic-acid-electrophoresis?ID=LUSNS52B7 Genomics /en-us/applications-technologies/applications-technologies/introduction-nucleic-acid-analysis?ID=LUSNI3MNI

Nucleic acid analysis generally involves isolation and characterization of the DNA or RNA sample of interest. Sample purification and quality assessment are important steps in experimental workflows since the quality of the recovered nucleic acid can affect the performance in downstream reactions. A wide range of techniques can be used to transform a sample which cannot be directly analyzed into one that fits the requirements of the analytical technique to be used.

 

Nucleic Acid Sample Preparation Method

DNA and RNA are nucleic acid molecules that are used to store and transmit genetic information inside a cell. The central dogma of molecular biology states that DNA is transcribed into RNA that is then translated into protein. While this is a simplistic look at gene and protein expression, it illustrates that DNA and RNA can provide important information about genomics, gene expression and cellular regulation for a sample of interest. In order to perform analysis on DNA and RNA, it is often necessary to first extract these molecules from cells or tissues.

Central dogma of molecular biology.

Several well established methods exist for extracting, purifying, and concentrating nucleic acids. Selecting the most appropriate nucleic acid isolation method depends on several factors including the starting sample material, the quantity, size and stability of the target nucleic acid, and the downstream application for the nucleic acid of interest. Following the purification step, it is often necessary to determine nucleic acid concentration, purity, and integrity before proceeding with downstream applications.

Common Nucleic Acid Sample Preparation Methods

  Cesium Chloride Gradients Filter Column Purification Gel Extraction Guadinidium Isothiocyanate Phenol Chloroform Extraction - Ethanol Precipitation Ion Exchange Resin Phenol Chloroform Extraction - Ethanol Precipitation Size Exclusion
Recommended For Plasmid DNA DNA and RNA > 200bp DNA RNA DNA RNA DNA and RNA
Pros Highly pure DNA Fast and Easy Fast and Easy Scalable by volume: highly pure RNA Scalable by volume Scalable by volume: highly pure RNA Fast and Easy
Cons Requires expensive instruments and removal of ethidium bromide and cesium chloride from isolated plasmid May not recover molecules <200 bp Potentially low yield; agarose contamin-ation may inhibit downstream reactions Phenol is hazardous Residual resin may inhibit downstream reactions Phenol is hazardous Potentially low yield; imperfect size separation
 

Nucleic Acid Electrophoresis

Gel electrophoresis can be used to effectively separate nucleic acids based on their size within agarose or polyacrylamide gels. You can successfuly separate nucleic acid fragments ranging in length from 20 base pairs to 20 kb by electrophoresis. Size ladders containing a range of different-length DNA fragments are run with the sample of interest to identify the corresponding size bands in a gel. Agarose gels are ideal for the separation of DNA restriction digests, PCR products, and genomic DNA or RNA prior to Southern or northern blotting. Polyacrylamide gels can be used for what is known as polyacrylamide gel electrophoresis, or PAGE. Applications include oligonucleotide analysis, RNase protection assays, and northern blotting. Non-denaturing polyacrylamide gels are used to separate small double-stranded DNA (dsDNA) fragments, particularly PCR products. Denaturing polyacrylamide gels are used for separation of small RNA and single-stranded DNA (ssDNA) fragments. Gels can be hand cast in the lab, or precast gels can be purchased from commercial providers.

 

General Considerations

Good laboratory technique is essential when working with nucleic acids to minimize nuclease contamination. One critical consideration when working with nucleic acid is to avoid nucleases in your solutions, consumables, and labware. Ready-to-use solutions and consumables that are nuclease-free, such as PCR-grade water, are readily available from commercial providers. Alternatively, for RNase removal, you can treat solutions with diethyl pyrocarbonate (DEPC), and then autoclave them. RNases on labware can also be inactivated by DEPC treatment, or by baking at 250°C for 3 hr.

When performing organic extractions with phenol, be aware that phenol causes burns and can be fatal if ingested. When working with phenol, use gloves and eye protection (laboratory glasses, shield, and safety goggles). Do not get on skin or clothing and avoid breathing vapor.

 

Related Content

 
Literature
Number Description Download
6018 High-Throughput Automated Extraction of RNA Using the Aurum Total RNA 96 Kit, Rev A Click to download
1810 InstaGene Matrix: Prepare DNA Templates for PCR With No Phenol/Chloroform Extractions and No Deproteinization Steps, Rev C Click to download
2950 Comparison of PCR Kleen Spin Columns to Traditional Methods for Purification of PCR Products Prior to Sequencing, Rev A Click to download
2920 Aurum Total RNA Mini Kit Product Information Sheet, Rev B Click to download
2919 Aurum Total RNA 96 Kit Product Information Sheet, Rev B Click to download
5282 Aurum Total RNA Fatty and Fibrous Tissue Kit Flier, Rev A Click to download
5736 iScript RT-qPCR Sample Preparation Reagent Flier, Rev A Click to download
2277 Quantum Prep Plasmid Miniprep Kit Product Information Sheet Click to download
2664 Aurum Plasmid Mini Kit Product Information Sheet, Rev C Click to download
2074 InstaGene Matrix Product Information Sheet Click to download
2311 PCR Kleen Spin Columns Product Information Sheet, Rev D Click to download
2320 Bio-Spin and Micro Bio-Spin Column Product Information Sheet, Rev A Click to download
 
 
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Sample purification and quality assessment are important steps in experimental workflows since the quality of the recovered nucleic acid can affect the performance in downstream reactions. A wide range of techniques can be used to transform a sample which cannot be directly analyzed into one that fits the requirements of the analytical technique to be used.</p> Nucleic Acid Sample Preparation Method <p>DNA and RNA are nucleic acid molecules that are used to store and transmit genetic information inside a cell. The central dogma of molecular biology states that DNA is transcribed into RNA that is then translated into protein. While this is a simplistic look at gene and protein expression, it illustrates that DNA and RNA can provide important information about genomics, gene expression and cellular regulation for a sample of interest. In order to perform analysis on DNA and RNA, it is often necessary to first extract these molecules from cells or tissues.</p> <div style="text-align: center;"><img src="/webroot/web/images/lsr/solutions/applications/gene_expression/genomics/application_detail/gxa16_img1.gif" alt="" width="167" height="170" /></div> <p class="caption"><strong>Central dogma of molecular biology.</strong></p> <p>Several well established methods exist for extracting, purifying, and concentrating nucleic acids. Selecting the most appropriate nucleic acid isolation method depends on several factors including the starting sample material, the quantity, size and stability of the target nucleic acid, and the downstream application for the nucleic acid of interest. Following the purification step, it is often necessary to <a href="/evportal/destination/solutions?catID=LUSNQLDN">determine nucleic acid concentration, purity, and integrity</a> before proceeding with downstream applications.</p> <p><strong> Common Nucleic Acid Sample Preparation Methods</strong></p> <table class="pd_table pd_gridlines" border="0"> <tbody> <tr> <td align="left" valign="top">&nbsp;</td> <td align="left" valign="top"><strong>Cesium Chloride Gradients</strong></td> <td align="left" valign="top"><strong>Filter Column Purification</strong></td> <td align="left" valign="top"><strong>Gel Extraction</strong></td> <td align="left" valign="top"><strong>Guadinidium Isothiocyanate Phenol Chloroform Extraction - Ethanol Precipitation</strong></td> <td align="left" valign="top"><strong>Ion Exchange Resin</strong></td> <td align="left" valign="top"><strong>Phenol Chloroform Extraction - Ethanol Precipitation</strong></td> <td align="left" valign="top"><strong>Size Exclusion</strong></td> </tr> <tr class="pd_colorbackground"> <td align="left" valign="top"><strong>Recommended For</strong></td> <td align="left" valign="top">Plasmid DNA</td> <td align="left" valign="top">DNA and RNA &gt; 200bp</td> <td align="left" valign="top">DNA</td> <td align="left" valign="top">RNA</td> <td align="left" valign="top">DNA</td> <td align="left" valign="top">RNA</td> <td align="left" valign="top">DNA and RNA</td> </tr> <tr> <td align="left" valign="top"><strong>Pros</strong></td> <td align="left" valign="top">Highly pure DNA</td> <td align="left" valign="top">Fast and Easy</td> <td align="left" valign="top">Fast and Easy</td> <td align="left" valign="top">Scalable by volume: highly pure RNA</td> <td align="left" valign="top">Scalable by volume</td> <td align="left" valign="top">Scalable by volume: highly pure RNA</td> <td align="left" valign="top">Fast and Easy</td> </tr> <tr class="pd_colorbackground"> <td align="left" valign="top"><strong>Cons</strong></td> <td align="left" valign="top">Requires expensive instruments and removal of ethidium bromide and cesium chloride from isolated plasmid</td> <td align="left" valign="top">May not recover molecules &lt;200 bp</td> <td align="left" valign="top">Potentially low yield; agarose contamin-ation may inhibit downstream reactions</td> <td align="left" valign="top">Phenol is hazardous</td> <td align="left" valign="top">Residual resin may inhibit downstream reactions</td> <td align="left" valign="top">Phenol is hazardous</td> <td align="left" valign="top">Potentially low yield; imperfect size separation</td> </tr> </tbody> </table> <div class="top"><a href="#helptop">Back to Top</a></div> Nucleic Acid Electrophoresis <p>Gel electrophoresis can be used to effectively separate nucleic acids based on their size within agarose or polyacrylamide gels. <a href="/evportal/destination/solutions?catID=LUSNS52B7">You can successfuly separate nucleic acid fragments ranging in length from 20 base pairs to 20 kb by electrophoresis.</a> Size ladders containing a range of different-length DNA fragments are run with the sample of interest to identify the corresponding size bands in a gel. Agarose gels are ideal for the separation of DNA restriction digests, PCR products, and genomic DNA or RNA prior to Southern or northern blotting. Polyacrylamide gels can be used for what is known as polyacrylamide gel electrophoresis, or PAGE. Applications include oligonucleotide analysis, RNase protection assays, and northern blotting. Non-denaturing polyacrylamide gels are used to separate small double-stranded DNA (dsDNA) fragments, particularly PCR products. Denaturing polyacrylamide gels are used for separation of small RNA and single-stranded DNA (ssDNA) fragments. Gels can be hand cast in the lab, or precast gels can be purchased from commercial providers.</p> <div class="top"><a href="#helptop">Back to Top</a></div> General Considerations <p>Good laboratory technique is essential when working with nucleic acids to minimize nuclease contamination. One critical consideration when working with nucleic acid is to avoid nucleases in your solutions, consumables, and labware. Ready-to-use solutions and consumables that are nuclease-free, such as PCR-grade water, are readily available from commercial providers. Alternatively, for RNase removal, you can treat solutions with diethyl pyrocarbonate (DEPC), and then autoclave them. RNases on labware can also be inactivated by DEPC treatment, or by baking at 250&deg;C for 3 hr.</p> <p>When performing organic extractions with phenol, be aware that phenol causes burns and can be fatal if ingested. When working with phenol, use gloves and eye protection (laboratory glasses, shield, and safety goggles). Do not get on skin or clothing and avoid breathing vapor.</p> <div class="top"><a href="#helptop">Back to Top</a></div> 6018 1810 2950 5990 2920 2919 5282 5736 2277 2664 2074 2311 2320 RNA Isolation <p><a title="RNA Isolation Selection Guide" onclick="javascript:openAjaxOverlay('/webroot/web/html/lsr/products/nucleic_acid_sample_purification/category_overlay/global/na_rna_isloation_selection_guide.html' );" href="javascript:void(0);">RNA Isolation Selection Guide</a></p> Life Science Research/Products/Nucleic Acid Sample Preparation and Purification/RNA Isolation/Aurum Total RNA Mini Kit ->MT::eb91e411-d011-4032-95e0-cdb29691d4d3##Life Science Research/Products/Nucleic Acid Sample Preparation and Purification/RNA Isolation/Aurum Total RNA Fatty and Fibrous Tissue Kit ->MT::c70a51af-c424-4dc6-8ae4-d6a9f2fe81f6##Life Science Research/Products/Nucleic Acid Sample Preparation and Purification/RNA Isolation/Aurum Total RNA 96 Kit ->MT::49da5896-dfde-4292-8021-9df1d8b77fec##Life Science Research/Products/Nucleic Acid Sample Preparation and Purification/DNA Isolation/InstaGene Matrix ->MT::6c2be54f-6c95-43de-8ce3-e9aee8229eeb##Life Science Research/Products/Nucleic Acid Sample Preparation and Purification/RNA Isolation/PureZOL RNA Isolation Reagent ->MT::13ac63ab-4674-4e63-b0c2-095a704fab88## Life Science Research/Solutions/Applications/Genomics/Nucleic Acid Analysis/Nucleic Acid Electrophoresis ->MTS::LUSNS52B7##Life Science Research/Solutions/Technologies/PCR ->MTS::LUSNYI15##Life Science Research/Solutions/Technologies/qPCR|Real-Time PCR ->MTS::LUSO4W8UU## Eddie C What is Nucleic Acid Analysis? 12/21/11 02:36 PM 12/21/21 02:37 PM AE,AI,AL,AM,AR,AT,AU,AZ,BA,BD,BE,BF,BG,BH,BN,BO,BR,BW,CA,CH,CL,CM,CN,CO,CR,CY,CZ,DE,DK,DO,DZ,EC,EE,EG,EH,ER,ES,ET,FI,FM,FO,FR,GA,GE,GF,GH,GP,GR,GT,GU,HK,HN,HR,HT,HU,ID,IE,IL,IN,IS,IT,JM,JO,JP,KE,KH,KR,KW,KZ,LB,LI,LK,LT,LU,LV,MA,MD,MG,MK,ML,MO,MQ,MS,MT,MU,MX,MY,NG,NI,NL,NO,NP,NZ,OM,PA,PE,PF,PG,PH,PK,PL,PR,PS,PT,PW,PY,QA,RO,RS,RU,SA,SB,SE,SG,SI,SK,SN,ST,SV,TG,TH,TN,TO,TR,TT,TW,TZ,UA,UG,UK,US,UY,UZ,VA,VE,VU,XK,YE,ZA en LSR /LSR/Applications/Genomics N 0
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