Aptamers

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Answer added to:
19 What are the biomarkers for Mycobacterium Tuberculosis (TB) diagnosis?
By Shripal Dhewa · Birla Institute of Technology and Science Pilani

Harikrishnan Jayamohan · University of Utah

Biomarkers in breath - methyl phenylacetate, methyl p-anisate, methyl nicotinate, and o-phenylanisole. http://www.google.com/patents/WO2009045116A1?cl... [more]

Biomarkers in breath - methyl phenylacetate, methyl p-anisate, methyl nicotinate, and o-phenylanisole. http://www.google.com/patents/WO2009045116A1?cl=en

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Question:
New Why RNA aptamer?
In SELEX process for selection of aptamer, both DNA and RNA can be selected for various targets as reported in literature. The selection of RNA is mor... [more]

In SELEX process for selection of aptamer, both DNA and RNA can be selected for various targets as reported in literature. The selection of RNA is more complicated and there is the need to prepare a cDNA and use RT-PCR. Also RNA is significantly unstable and to work with it needs a lot of precautions. On the other side, the price of RNA is significantly higher than DNA oligonucleotide. Anybody know, while these problems are so serious, why for some targets, especially in cell-SELEX process, the selection of RNA aptamers are preferred?

By Masoud Mehrgardi

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5 Aptamers or oligonucleotides?
By Sebastian Vencken · Trinity College Dublin

Sebastian Vencken · Trinity College Dublin

Thanks all for the useful info. I'll go down the oligonucleotide strategy.

Thanks all for the useful info. I'll go down the oligonucleotide strategy.

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1 Ligand-besed targeted therapy of nanoparticle remains generally low in obesity, cancer and other diseases, Why?
By Md. Nazir Hossen · Hokkaido University

Arthur Nery · University of São Paulo

Probably the translation from bench to bedside is still on pre-clinical stages

Probably the translation from bench to bedside is still on pre-clinical stages

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2 What is the optimum quantity of the ssDNA library that should be added in PCR to carry out its amplification?
By Neetika Rani · Indian Institute of Toxicology Research

Arthur Nery · University of São Paulo

I used 2fmol, because the mass/strand of your library will be different from mine

I used 2fmol, because the mass/strand of your library will be different from mine

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1 Does anybody have information regarding exotic DNA/RNA structures and how to calculate the secondary structure?
By Naveen Kulkarni · Polyclone Bioservices

Arthur Nery · University of São Paulo

There are some very interesting tools to help you in most of the DNA/RNA companies, as IDT, AMBION and eventually try the mFold site. In those tools y... [more]

There are some very interesting tools to help you in most of the DNA/RNA companies, as IDT, AMBION and eventually try the mFold site. In those tools you can have not only the secondary structure but also the Gibbs free energy chart, and if I remember well, you can add all the modified nucleotides, you just have to check how to insert them into the sequence, e.g. ATCGTATCGACTCG<2fG>TAGTCAT

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1 What is the basis of selection of size of random sequence oligomers and sequence of their primer binding regions for Aptamer screening?
By Shripal Dhewa · Birla Institute of Technology and Science Pilani

Arthur Nery · University of São Paulo

The basis to define the lenght of the random sequence is based on the probability that you will be able to generate according to the number of nucleot... [more]

The basis to define the lenght of the random sequence is based on the probability that you will be able to generate according to the number of nucleotides presented in the region. For example, if you have 40 random basis region, you will have 4ˆ40 possibilities, or 2ˆ80 or 2ˆ10ˆ8, which we could simplify to 1024ˆ8 or 10ˆ3ˆ8 ending with 10ˆ24 possible sequences/structures, but here you have a problem, in order to cover all theses possibilities you would have to synthesise more than a mol of DNA/RNA! So, for most of cases you choose a random region that is possible to cover all the possibilities in a micro molar scale synthesis. For the primer binding regions a good start point is to follow the standards of good primer design, and then if you need insert any specific region you desire, as digestive enzymes sites or RNA polymerases initiation sites. I hope I could help! Keep in touch!

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1 Is it possible to design a pH sensitive aptamer, so that it has different conformation at different pH?
By Jyoti Roy · Purdue University

Pramod Yadava · Jawaharlal Nehru University

Like any biomolecular structure, aptamer structure also is dependent on physicochemical coinditions including pH. So most if not all aptamers would be... [more]

Like any biomolecular structure, aptamer structure also is dependent on physicochemical coinditions including pH. So most if not all aptamers would be pH sensitive in their interaction with cognate ligand. Pramod Yadava

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1 Fluorescence vs radio labeling?
By Jon Ashley · National University of Singapore

George Perdrizet · University of Chicago

Personally I prefer radio labeling... It is generally cleaner and more sensitive. It is also easy and cheap in the sense that RNA already naturally co... [more]

Personally I prefer radio labeling... It is generally cleaner and more sensitive. It is also easy and cheap in the sense that RNA already naturally contains phosphate. But of course, working with radioactivity can be somewhat of a hassle.... If you are not already working with radioactive protocols and fluorescence is sufficient for your purposes I would go with the flurophore.

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Open What software can be used for docking of proteins with DNA?
What software can be used for docking of proteins with DNA? I've heard that AutoDock can be used for docking proteins and RNA but does it work with DN... [more]

What software can be used for docking of proteins with DNA? I've heard that AutoDock can be used for docking proteins and RNA but does it work with DNA as well? And are there any other softwares?

By Priyamvada Jain · Indian Institute of Technology Guwahati

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Answer added to:
1 Synthesis of aptamer & SELEX method
By Yamak Mehta ·

Lisa Thurston · Base Pair Biotechnologies

We provide both aptamer development services and a catalog of available aptamers, more info can be found on our website at www.basepairbio.com and our... [more]

We provide both aptamer development services and a catalog of available aptamers, more info can be found on our website at www.basepairbio.com and our Founder has written a detailed market research report on aptamers available at BCC Research http://www.bccresearch.com/report/nucleic-acid-aptamers-bio071a.html

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3 Can anyone recommend a small molecule ligand or aptamer to specifically target nanoparticles towards astrocytes?
By Jayden Smith · University of Cambridge

Jayden Smith · University of Cambridge

Thanks Vitaliy; interesting paper, but kind of the reverse of what I was hoping to achieve (which is a targeting moiety on the nanoparticle, rather th... [more]

Thanks Vitaliy; interesting paper, but kind of the reverse of what I was hoping to achieve (which is a targeting moiety on the nanoparticle, rather than a recognition site anchored to the cell). And as you say, the attachment of the aptamer isn't necessarily cell specific.

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Question:
Open Any recommendation on Gel Shift / Super Shift experiments of transmembrane target protein using an aptamer as a probe?
I want to check the binding affinity of an aptamer to a transmembrane protein via GS experiments. My probe is the aptamer which should shift once I in... [more]

I want to check the binding affinity of an aptamer to a transmembrane protein via GS experiments. My probe is the aptamer which should shift once I incubate it with the proteic extract, but I'm having troubles to get the shifted band. There are plenty of things that could be going wrong, but my stakes are on: 1)the aptamer doesn't fold into its functional secondary structure --> Should I perform the incubation using the same conditions as when performing the SELEX? (i.e. salts concentration / temperature) 2) too much detergent used to solubilize the protein? It is the first time I work with aptamers so I don't really know what "care" they need: should they be reconstituted in TE? In water? in a solutions containing salts? How sensitive are they to changes on temperature? If anybody is working with aptamers and/or performing GS assays all comments are most welcome.

By Xenia Villalobos · University of Barcelona

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Answer added to:
3 Is there a better method to obtain/isolate small DNA fragments than by SELEX?
By Irshad Baig · Hanyang University

Frederic Ducongè · Commissariat à l'énergie atomique et aux énergies alternatives

What is your volume of PCR? Usually, you have to make at least one ml of PCR to be sure to detect something using UV shadowing. If you make few microL... [more]

What is your volume of PCR? Usually, you have to make at least one ml of PCR to be sure to detect something using UV shadowing. If you make few microL of PCR and make crush and soak from agarose gel using dye you do not have enough material to detect using UV spectroscopy, use a colorimetric analysis (for instance picogreen)

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5 Do aptamers serve the purpose of targeting effectively than other ligands like antibodies, small peptides etc?
By Arul Rabel · Sathyabama University

George Jackson · Base Pair Biotechnologies

Our website with considerable information on aptamers has moved to www.BasePairBio.com

Our website with considerable information on aptamers has moved to www.BasePairBio.com

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7 Can we raise/develop aptamers against fluoride ions/sodium fluoride salts?
By Shripal Dhewa · Birla Institute of Technology and Science Pilani

Shripal Dhewa · Birla Institute of Technology and Science Pilani

Thanks Joy a lot. I will send you a email for further discussion. Please be collaborated.

Thanks Joy a lot. I will send you a email for further discussion. Please be collaborated.

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Open Is there any body working on DNA/ RNA aptamer based diagnostics and therapeutics?
I want to work on aptamer based diagnostics, therapeutics etc. I want to collaborate with whoever is working is this field.

I want to work on aptamer based diagnostics, therapeutics etc. I want to collaborate with whoever is working is this field.

By Shripal Dhewa · Birla Institute of Technology and Science Pilani

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1 How to stabilize aptamer-liposomes in blood?
By Md. Nazir Hossen · Hokkaido University

Nilesh Rarokar · Rashtrasant Tukadoji Maharaj Nagpur University

u can use stabilizer which decreases the degradation of liposomes in blood ph i.e. of 7.4

u can use stabilizer which decreases the degradation of liposomes in blood ph i.e. of 7.4

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2 what is the crucial step in aptamer selection process?
By Zhaofeng Luo · University of Science and Technology of China

Zhaofeng Luo · University of Science and Technology of China

In my experiment, dimer in the no template control(NTC) can be seen about at 26 cycle, even use hot-start Taq. what about yours? how many cycles goin... [more]

In my experiment, dimer in the no template control(NTC) can be seen about at 26 cycle, even use hot-start Taq. what about yours? how many cycles going on? I cloned and sequence the NTC products, cannot understand why contaminated. So, optimize the PCR parameters is going on?

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1 hello,everyone
By Zhou Qingtong · University of Science and Technology of China

Zhaofeng Luo · University of Science and Technology of China

M-SELEX, CE-SELEX, cIEF-SELEX, etc. I hope that we can develop a more efficient method to produce the aptamers.

M-SELEX, CE-SELEX, cIEF-SELEX, etc. I hope that we can develop a more efficient method to produce the aptamers.

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About Aptamers

A place to discuss and share information and methods in the area of aptamer research and SELEX.

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Aptamers

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