What is the state of the art?

[SStell]

I am just wondering how far along or how advanced is our technology in regards to manipulating individual nucleotides and amino acids.

 

For a simple example:

can we make an AUC sequence in the lab? Can we multiply that? Can we drop a million of these sequences in a bucket of water? Can we do something similar with amino acids?

Just trying to see were we stand in the technology.

 

If someone can steer me towards the appropriate and accessible information that would be greatly appreciated. Thanks

[CharonY]

Synthesizing short DNA fragments even de novo is quite feasible today. Multiplying DNA using polymerase has been a standard technique for decades. I have no idea why you want to drop DNA into a bucket of water, but sure, you can. It won't do anything, but you can. Amino acids are just amino acids, you can synthesize artificial ones, though. Or do you mean proteins? It is a bit trickier as you need some form of expression system to create a proper protein efficiently. But still these are not new technologies. If you are curious what is commonly used take a look at the pretty much standard book of lab protocols: Molecular cloning (used to be Sambrook and Maniatis).

What you describe is also pretty much covered by the polymerase chain reaction and protein expression systems, which are surely covered by some wiki articles. They are simplified to the point were you have simple kits for these reactions, you could check companies such as Qiagen who produce sell them and read their manuals (some are surprisingly good).

[SStell]

Charon, you say dropping a bunch in a bucket of water won't do anything, well they may have once, and in order to figure out how that may have happened and be able to understand it one would need to be able to manipulate, regulate and duplicate exact species of short RNA sequences and short amino acid chains.

 

I guess my interest lies in whether anyone has tried every possible combination of short RNAs and very short proteins and if that data collecting strategy was even possible and if so what data has been collected concerning the possible reactions.

 

I would imagine using ATP, GTP,CTP and UTP or ADPs etc might activate a special reaction which is a one in a billion chance. They do that with massive numbers of subatomic particles at high densities, where highly unlikely things happen just enough times as to be able to be studied.

Are we using that approach with abiogenesis? Is it even possible at this time?

 

For a simple example: 1 liter of a 10 molar solution of the RNA sequence AGU plus 1 liter of a 10 molar solution of amino acid sequence Serine-Glutamine-Histidine plus 1 liter of a 10 molar solution of adenosine triphosphate, is this something that is possible at this time and if so has anyone done anything of this nature?

 

And most importantly would be what is our status in regards to analyzing a solution of this nature? Can we actually gather data of any use for study in this matter? Can we notice a one in a billion chance reaction that uses a 3 or 4 n-base chain with a 3 or 4 amino acid chain with a few nTPs and figure out the structure of the product or products? Or prove somewhat conclusively that no reactions occurred? Just trying to see the state of our ability to do something like this.

 

Analyzing the solution for chain length changes or sequence changes. Are there breakages, extensions, complimentary replications, hydrogen bondings, replacements, substitutions and every other possibility and what are the percentages of each if any?

Edited May 9, 2016 by SStell

[CharonY]

I am not sure what you wan to achieve, Could you specify? Or maybe spell out what you expect to happen? What do you hope to be able to measure? Also, I am not sure what the actual solubility limit is but a 10 molar solution of a trinucleotide would be about 15 kg/L.

Producing large amounts of these molecules is technically trivial, but expensive.

[SStell]

Charon, unless you think abiogenesis is unlikely, then small molecules such as short sequences of RNA and short sequences of amino acids and some energy source most likely from something like nTPs did something.

 

Isn't the role of science to figure out how things work? To discover new things in new ways?

 

Using incredibly large quantities at high densities of different combinations for different trials may illuminate some rare but real reactions between these short strands and to illuminate many new ideas as to how molecular evolution can happen. I thought I made that pretty clear in my last post.

 

I guess it boils down to can we make large quantities of exact short sequences of amino acids, RNAs, single nTPs and could we actually collect data on the rare and even bizarre reactions that might happen?

Using my previous example: Are there any RNA chains and or amino acid chains of 4 or 5 or 6 detected and at what percentages. What changed? Or are there absolutely no reactions observed. Do we have that ability?

 

I was interested in the state of our technical skill level as to our ability to analyze something like this and any information along these lines.

 

As I stated previously,"Analyzing the solution for chain length changes or sequence changes. Are there breakages, extensions, complimentary replications, hydrogen bondings, replacements, substitutions and every other possibility and what are the percentages of each if any?"

 

Are there patterns of reactions that have not been seen before? I thought that was what science was all about. Looking for things not seen before, making discoveries.

So I just wanted to know what the state of biochemical skills and analysis were at and ANY other information along these lines that anyone knew about. Thanks.

[CharonY]

I am not sure how any of this relates to abiogenesis as they are relatively complex molecules on the one hand but not complex enough for significant enzymatic actions on the other. And the point of science is not to conduct random trials, but create specific hypotheses and test them with carefully designed experiments. Throwing a truckload of of nucleotides or peptides into water and hoping that something might happen, despite our knowledge on their biochemical capabilities seems a bit.... random.

As I said, all the technical parts that you are referring to are old news. The issue is more about what you expect to happen wen you conduct an experiment as you describe.

Actual experiments that are carried out involve the analysis of potential functions of novel peptide(domains) by creating more or less random sequencing and select for those with catalytic capabilities, for example. But again, what you propose simply does not make sense, but are well within our technical capabilities since a few decades. I am pretty sure that no one wants to responsible for synthesizing kgs of nucleotides or peptides and dump them in a bucket, though.

 

Or let me ask again, what do you expect could possibly happen under circumstances you describe, based on what we know about nucleic acids and peptides?

Edited May 10, 2016 by CharonY

[SStell]

Charon, maybe I missed the discovery of how abiogenesis works.

 

You say "I am not sure how any of this relates to abiogenesis as they are relatively complex molecules to begin with."

 

Seeing that I have never seen the evidence that abiogenesis started with relatively complex molecules to begin with I sure would like to hear about them and how those 'complex' molecules would have formed. Wouldn't complex molecules have come about from less complex ones? And wouldn't these simpler molecules have had to come about fairly simply.

I was just working somewhere in the middle with sequences of 3, 4, 5, 6 etc.

 

I was also under the impression that we did not know exactly how abiogenesis worked and were actively trying to figure it out.

I guess I was way off. So please steer me towards this information if you would please.

 

What I had hoped to find out was what our present level of technology was and was any of what I asked about even possible. You say all of it is possible but it would just be a waste of time doing it seeing as we already know what these molecules can do. Well if that is in deed the case then I truly do look forward to reading about how abiogenesis has been shown to function. I truly thought it was still a mystery.

 

What I am still asking for is our state of chemical analysis techniques. If we did as I have proposed would we be able to analyze the resultant solutions and determine what new molecules were formed- if any. Could we even tell whether a 3 base segment bonded to another 3 base segment? Do we have the technology to analyze a solution with literally trillions and trillions of molecules interacting and some making different molecules and what those molecules were- if any? Or could we state that nothing at all happened.

 

But I do wish to skip all the preliminary lab work and get right to the heart of the matter. How does it work. Like I said, I thought it was still somewhat of a mystery. So I truly look forward to any research that can shed some light on this for me, thank you.

Edited May 10, 2016 by SStell

[CharonY]

No, the origins of abiogenesis are still unclear, but there have been hypotheses including e.g. peptide nucleic acids and other molecules being involved. My point being that all your proposed experiments would yield no insights into abiogenesis. To make it clear, yes, we can make a mix of nucleic acids with no poblems, and it is trivial to analyze the mix. The thing is, nothing is going to happen. They will not spontaneously form new molecules as a simple trinucleotides have no ability to catalyze that reaction (nor do tripeptides).

In order to understand what is needed I suggest you take a look at the following concepts: PCR, ribpozymes, catalytic peptides. Note that there is still a large gap between simple organic molecules (even with enzymatic functions) and how early life has formed.

[SStell]

Charon, why would a long chain of amino acids (a protein) catalyze a linking of nucleotides but a shorter one just isn't going to do that? You say there is a large gap between simple organics and life, but for some reason discount the study of THAT GAP.

 

I do thank you for the information you have provided and I also look forward to looking into the terms you provided me for further research.

 

I just find it a bit strange that you state there is a gap but are unwilling to entertain any ideas about studying that gap.

I find it extremely difficult that we can say conclusively that small sequences of RNA and small peptides with a chemical energy source absolutely cannot react to form any new molecules such as longer chains, shorter chains, whatever. Even as I mentioned a one in a billion or one in a trillion chance. That is a pretty conclusive statement you made regarding something that you admitted was a large gap in our understanding.

 

I gave you a very simple possible experiment and labeled it as such only to explain what I wanted to know about our technological skill level which matched the title of my thread.

I was not limiting the thoughts to just that simple concept. We could change temperatures, concentrations, toss in different metallic ions etc etc etc. I wanted to know if we could analyze the resultant solutions to determine if a one in a trillion reaction did occur and given the amounts I mentioned would be a considerable number. I think you said it would be easy to analyze that type of solution and that is what I wanted to know, so thanks.

 

We have already found that with repeated wet and dry cycles, radiation, other chemical additives, etc. DO cause things to happen. So I am a wee bit shocked at your conclusive declarative and absolute statements regarding experiments that apparently have not been done.

 

But again I thank you for your time and information.

Edited May 10, 2016 by SStell

[SStell]

""""The ribozymes are generally large molecules yet the shortest ribozyme is only UUU and it acts on CAAA. A two-base ribozyme may catalyze the formation of 3′,5′ phosphodiester linkages 36,000-fold faster (Reader JS, Joyce GF 2002 Nature [Lond] 420:841).""

So I guess my query was not as far fetched as some may think. But thanks anyhow.

[CharonY]

I was hoping that reading up on the topics would give you a hint why your idea is flawed. The basic issue is that you seem to assume that we no little or nothing about nucleic acid chemistry. Since you have not bothered to figure out the hypothesis of your experiments I will do that for you.

It is based on the assumption that a) a trinucleotide has catalytic function and that b) it will act on trinucleotides with the same sequence resulting in c) some replicative functions (otherwise there would be little link to your abiogenesis part). You further assume that d) this is a rare event and therefore may have not observed yet. Your actual question is only a tangent with regard to analytical feasibility, which I have answered a couple of times (yes, it is trivial).

 

The gap that you insist that exist but keep on missing is that for catalytic reactions we require functional domains. I.e. there is the requirement of some sort of structure, otherwise we would basically look at very basic chemical reactions of free residues. Three nucleotides are simply too short to form a simple loop, even if they were complementary, which is not even the case in the example you provided. The mini-ribozyme consists of 7-bp catalytic core that requires the binding of a metal to affect cleavage.

 

Now, why did I mention PCR? Well, in this reaction we actually mix nucleotides (free, and in form of primers) in reaction, on a daily basis. Typically a template-free sample is run as a negative control. Can you imagine what I am getting at?

[SStell]

If my assumption was that we knew very little of nucleic acid chemistry I certainly wouldn't be asking about it.

All I wanted to know is what is our present capability of producing mass amounts of specific sequences and mixing them and then analyzing solutions containing them. You answered that all for me. So thank you for your information, links and time.

 

I was hoping for a more fluid dialogue regarding abiogenesis with people interested but I needed a lot more information before I would be starting in such a discussion. Again, I was just asking for our present capabilities and I don't consider that 'speculation'. But somehow my inquiry into our present status was somehow deemed speculation and now my thread is in the speculation file. I do not consider asking about present technologies and techniques that could be used to study abiogenesis to be speculative in the least. But it makes no difference.

 

I did assume that our experimental attempts had been in a more or less top down structure. Starting with the complex present day catalysts and working our way down to smaller ones, I was just wondering whether what attempts had been made in the bottom up scenario. Starting with small chains and working our way up. But this will have to wait for another day.

 

Thanks again for your information, terms, links and time.