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plausible prebiotic nucleotides

slo1
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4/27/2016 9:37:52 PM
Posted: 7 months ago
http://www.nature.com...

The current role of mononucleotides and RNA polymers in numerous cellular functions gave rise to the long-standing hypothesis that these molecules were involved early in the emergence of life: the RNA World hypothesis1. Supporting this hypothesis, model prebiotic reactions and analyses of carbonaceous meteorites provide evidence that the canonical nucleobases of RNA (adenine, guanine, cytosine, uracil) were likely present on the prebiotic Earth2, 3, 4. In addition, progress has been made towards finding abiotic routes to ribose and related sugars from simple molecules (for example, formaldehyde, glyoxylate), as well as mechanisms for ribose phosphorylation and ribose selection from complex sugar mixtures5, 6, 7, 8. Nevertheless, despite decades of effort, the chemical origin of nucleosides and nucleotides (that is, nucleobases glycosylated with ribose and phosphorylated ribose) remains an unsolved problem9, 10.

..............

Although we have not shown chiral nucleotide selection, in the current study we have demonstrated that the ^6;-anomer of MMP is enriched in supramolecular assemblies over the ^5;-anomer of MMP, and this selection leads to a detectable increase in the ratio of the ^6;-anomer over the ^5;-anomer of MMP in the entire solution (presumably due to anomerization and selective stabilization by the assembly). As a recent example of the ability of supramolecular polymers to promote local chiral resolution, Aida and co-workers demonstrated that racemic solutions of chiral macrocycles self-sort into homochiral supramolecular polymers42. It is therefore possible that supramolecular assemblies, formed by nucleotides with different sugars, including different anomers and enantiomers, could have been selectively enriched in individual supramolecular assemblies before polymerization. Current investigations of this possibility are actively being pursued in our laboratory.
slo1
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4/27/2016 9:47:18 PM
Posted: 7 months ago
Great study. I'm very supportive of investigating prebiotic nucleotides in quest for uncovering abiogenesis. In this case the process to make this possible pebiotic was relatively simple.

This one paragraph really sums it up.

Here, we show that glycosylation of melamine and BA by ribose-5-phosphate (R5P) occurs spontaneously in water to produce nucleotides in yields of up to 55% and 82%, respectively. When combined, the nucleotides form supramolecular assemblies with Watson"Crick-like base pairs, even within the crude reaction mixtures.

Here a summary article for dummies like me.
https://www.sciencedaily.com...
Mhykiel
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4/28/2016 2:17:17 AM
Posted: 7 months ago
At 4/27/2016 9:37:52 PM, slo1 wrote:
http://www.nature.com...

The current role of mononucleotides and RNA polymers in numerous cellular functions gave rise to the long-standing hypothesis that these molecules were involved early in the emergence of life: the RNA World hypothesis1. Supporting this hypothesis, model prebiotic reactions and analyses of carbonaceous meteorites provide evidence that the canonical nucleobases of RNA (adenine, guanine, cytosine, uracil) were likely present on the prebiotic Earth2, 3, 4. In addition, progress has been made towards finding abiotic routes to ribose and related sugars from simple molecules (for example, formaldehyde, glyoxylate), as well as mechanisms for ribose phosphorylation and ribose selection from complex sugar mixtures5, 6, 7, 8. Nevertheless, despite decades of effort, the chemical origin of nucleosides and nucleotides (that is, nucleobases glycosylated with ribose and phosphorylated ribose) remains an unsolved problem9, 10.


..............

Although we have not shown chiral nucleotide selection, in the current study we have demonstrated that the ^6;-anomer of MMP is enriched in supramolecular assemblies over the ^5;-anomer of MMP, and this selection leads to a detectable increase in the ratio of the ^6;-anomer over the ^5;-anomer of MMP in the entire solution (presumably due to anomerization and selective stabilization by the assembly). As a recent example of the ability of supramolecular polymers to promote local chiral resolution, Aida and co-workers demonstrated that racemic solutions of chiral macrocycles self-sort into homochiral supramolecular polymers42. It is therefore possible that supramolecular assemblies, formed by nucleotides with different sugars, including different anomers and enantiomers, could have been selectively enriched in individual supramolecular assemblies before polymerization. Current investigations of this possibility are actively being pursued in our laboratory.


Help me understand this.

So we assume that another paper about the spontaneous formation of pentose sugars in abiotic solutions is correct. And then say a lot of that happened in the Early oceans.

Then we don't use the actual nucleosides. Because that would be too difficult.

So we use Barbituric Acid and Melamine. They bind similar to Nucleotides. I think this is an important part that these 2 chemicals bind together.

Take the Acid and the pentose sugar and stir them together ((sadly I would like to know what direction they were stirred in)) But key here is stir for 24 hours, at 20 degrees C, in salt water of PH 9.

Then take the Melamine and dot he same but stir (possibly in the other direction) for 24 hours, at 65 degrees C, in salt water of PH 4-5. Then Dry to collect the residue

To control for hydrolysis mix the 2 together in FRESH water this time, lower the PH to 5 and the temperature to 5 degrees C.

The result is pretty cool. The Acid and Melamine bind together in disk like structures with the pentose sugar sprinkled on the outside. The Pentose sugars the ribose are not connected and do not support the disk. The disk is well structured and homogeneous.

This is to demonstrate that an RNA structure that is supported by a backbone of connected ribose, with nucleotides like Uracil, blah blah, can form naturally.

Yeah clearly this is a random natural process. I can imagine the Acid forming in some frozen salt ocean, and the Melamine formed on some salty puddle. It dries in the sun. Then it rains and washes the Melamine it a new puddle and the Acid mixture, must be high tide, washes into this new fresh water puddle. But it was a winter storm and the temperature plummets to near freezing.

Oh yeah but this is just one part of biological life. But it has a 6 months half life, so plenty of time to arrange itself into a long tape with imperfections that mirror the proteins needed to produce itself and a cell wall.

Thanks for the article Slo1 I do love a good science fiction.
slo1
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4/28/2016 12:23:30 PM
Posted: 7 months ago
At 4/28/2016 2:17:17 AM, Mhykiel wrote:
At 4/27/2016 9:37:52 PM, slo1 wrote:
http://www.nature.com...

The current role of mononucleotides and RNA polymers in numerous cellular functions gave rise to the long-standing hypothesis that these molecules were involved early in the emergence of life: the RNA World hypothesis1. Supporting this hypothesis, model prebiotic reactions and analyses of carbonaceous meteorites provide evidence that the canonical nucleobases of RNA (adenine, guanine, cytosine, uracil) were likely present on the prebiotic Earth2, 3, 4. In addition, progress has been made towards finding abiotic routes to ribose and related sugars from simple molecules (for example, formaldehyde, glyoxylate), as well as mechanisms for ribose phosphorylation and ribose selection from complex sugar mixtures5, 6, 7, 8. Nevertheless, despite decades of effort, the chemical origin of nucleosides and nucleotides (that is, nucleobases glycosylated with ribose and phosphorylated ribose) remains an unsolved problem9, 10.


..............

Although we have not shown chiral nucleotide selection, in the current study we have demonstrated that the ^6;-anomer of MMP is enriched in supramolecular assemblies over the ^5;-anomer of MMP, and this selection leads to a detectable increase in the ratio of the ^6;-anomer over the ^5;-anomer of MMP in the entire solution (presumably due to anomerization and selective stabilization by the assembly). As a recent example of the ability of supramolecular polymers to promote local chiral resolution, Aida and co-workers demonstrated that racemic solutions of chiral macrocycles self-sort into homochiral supramolecular polymers42. It is therefore possible that supramolecular assemblies, formed by nucleotides with different sugars, including different anomers and enantiomers, could have been selectively enriched in individual supramolecular assemblies before polymerization. Current investigations of this possibility are actively being pursued in our laboratory.


Help me understand this.

So we assume that another paper about the spontaneous formation of pentose sugars in abiotic solutions is correct. And then say a lot of that happened in the Early oceans.

No, there is no assumption. It is a study to look for a prebiotic alternative because, "the canonical nucleosides and nucleotides of RNA are thermodynamically disfavoured (but kinetically stable) in water29"

Also

"Base pairing is not exhibited by the canonical mononucleotides31, but such a property would have been advantageous for the prebiotic mutual selection
Then we don't use the actual nucleosides. Because that would be too difficult."

Yes it would be too difficult, also there is nothing that would indicate that there does not exist a precursor to RNA. In fact, it would be very unlikely there isn't. You can't create a barrier, just because you believe RNA would have to begin as RNA. Q: How do you eat an elephant? A: One bite at a time.

So we use Barbituric Acid and Melamine. They bind similar to Nucleotides. I think this is an important part that these 2 chemicals bind together.

Yes, the biggest challenge to this study is that the Barbituric Acid and Melamine are so reactive with each other that they have to bind with R5P before they meet to form the final RMA like polymer. They also interact with R5P at different temperatures. One was 20 C and other 65 C

Take the Acid and the pentose sugar and stir them together ((sadly I would like to know what direction they were stirred in)) But key here is stir for 24 hours, at 20 degrees C, in salt water of PH 9.

They didn't stir.
"Nucleotides spontaneously form when BA is mixed in water with one equivalent of R5P at 20R01;"C (without the need for drying)." The sample was examined after 24 hours in the solution.

Then take the Melamine and dot he same but stir (possibly in the other direction) for 24 hours, at 65 degrees C, in salt water of PH 4-5. Then Dry to collect the residue

To control for hydrolysis mix the 2 together in FRESH water this time, lower the PH to 5 and the temperature to 5 degrees C.

The result is pretty cool. The Acid and Melamine bind together in disk like structures with the pentose sugar sprinkled on the outside. The Pentose sugars the ribose are not connected and do not support the disk. The disk is well structured and homogeneous.

This is to demonstrate that an RNA structure that is supported by a backbone of connected ribose, with nucleotides like Uracil, blah blah, can form naturally.

Yeah clearly this is a random natural process. I can imagine the Acid forming in some frozen salt ocean, and the Melamine formed on some salty puddle. It dries in the sun. Then it rains and washes the Melamine it a new puddle and the Acid mixture, must be high tide, washes into this new fresh water puddle. But it was a winter storm and the temperature plummets to near freezing.

Oh yeah but this is just one part of biological life. But it has a 6 months half life, so plenty of time to arrange itself into a long tape with imperfections that mirror the proteins needed to produce itself and a cell wall.

Thanks for the article Slo1 I do love a good science fiction.

It is not science fiction. It is an investigation to uncover plausible prebiotics to RNA. Let's just imagine your senerio of puddles from tide formations and dropping temperatures happened. Nobody has even speculated how this combination could have evolved into RNA, which is even harder to imagine.

Simply, nobody is asking you to buy in any story. Nobody is stating that these are chemicals and processes that resulted in RNA. They are stating exactly what they stated in the paper.

As a recent example of the ability of supramolecular polymers to promote local chiral resolution, Aida and co-workers demonstrated that racemic solutions of chiral macrocycles self-sort into homochiral supramolecular polymers42. It is therefore possible that supramolecular assemblies, formed by nucleotides with different sugars, including different anomers and enantiomers, could have been selectively enriched in individual supramolecular assemblies before polymerization. Current investigations of this possibility are actively being pursued in our laboratory.

Oh yeah and it gives a pathway that does not require stirring, one of your biggest objections to producing the right chirality.
Mhykiel
Posts: 5,987
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4/28/2016 1:31:21 PM
Posted: 7 months ago
At 4/28/2016 12:23:30 PM, slo1 wrote:
At 4/28/2016 2:17:17 AM, Mhykiel wrote:
At 4/27/2016 9:37:52 PM, slo1 wrote:
http://www.nature.com...

The current role of mononucleotides and RNA polymers in numerous cellular functions gave rise to the long-standing hypothesis that these molecules were involved early in the emergence of life: the RNA World hypothesis1. Supporting this hypothesis, model prebiotic reactions and analyses of carbonaceous meteorites provide evidence that the canonical nucleobases of RNA (adenine, guanine, cytosine, uracil) were likely present on the prebiotic Earth2, 3, 4. In addition, progress has been made towards finding abiotic routes to ribose and related sugars from simple molecules (for example, formaldehyde, glyoxylate), as well as mechanisms for ribose phosphorylation and ribose selection from complex sugar mixtures5, 6, 7, 8. Nevertheless, despite decades of effort, the chemical origin of nucleosides and nucleotides (that is, nucleobases glycosylated with ribose and phosphorylated ribose) remains an unsolved problem9, 10.


..............

Although we have not shown chiral nucleotide selection, in the current study we have demonstrated that the ^6;-anomer of MMP is enriched in supramolecular assemblies over the ^5;-anomer of MMP, and this selection leads to a detectable increase in the ratio of the ^6;-anomer over the ^5;-anomer of MMP in the entire solution (presumably due to anomerization and selective stabilization by the assembly). As a recent example of the ability of supramolecular polymers to promote local chiral resolution, Aida and co-workers demonstrated that racemic solutions of chiral macrocycles self-sort into homochiral supramolecular polymers42. It is therefore possible that supramolecular assemblies, formed by nucleotides with different sugars, including different anomers and enantiomers, could have been selectively enriched in individual supramolecular assemblies before polymerization. Current investigations of this possibility are actively being pursued in our laboratory.


Help me understand this.

So we assume that another paper about the spontaneous formation of pentose sugars in abiotic solutions is correct. And then say a lot of that happened in the Early oceans.

No, there is no assumption. It is a study to look for a prebiotic alternative because, "the canonical nucleosides and nucleotides of RNA are thermodynamically disfavoured (but kinetically stable) in water29"

Also

"Base pairing is not exhibited by the canonical mononucleotides31, but such a property would have been advantageous for the prebiotic mutual selection
Then we don't use the actual nucleosides. Because that would be too difficult."

Yes it would be too difficult, also there is nothing that would indicate that there does not exist a precursor to RNA. In fact, it would be very unlikely there isn't. You can't create a barrier, just because you believe RNA would have to begin as RNA. Q: How do you eat an elephant? A: One bite at a time.


I haven't addressed that other paper. Just saying they are using that one experiment as a pluasible solution to having pentose sugars in the water. In a big enough quantity to keep up with hydrolysis of the ribose.

So we use Barbituric Acid and Melamine. They bind similar to Nucleotides. I think this is an important part that these 2 chemicals bind together.

Yes, the biggest challenge to this study is that the Barbituric Acid and Melamine are so reactive with each other that they have to bind with R5P before they meet to form the final RMA like polymer. They also interact with R5P at different temperatures. One was 20 C and other 65 C

Take the Acid and the pentose sugar and stir them together ((sadly I would like to know what direction they were stirred in)) But key here is stir for 24 hours, at 20 degrees C, in salt water of PH 9.

They didn't stir.

They did stir says so in the sections discussing how the synthesized both elements seperately with the d ribose.

"Nucleotides spontaneously form when BA is mixed in water with one equivalent of R5P at 20R01;"C (without the need for drying)." The sample was examined after 24 hours in the solution.

Then take the Melamine and dot he same but stir (possibly in the other direction) for 24 hours, at 65 degrees C, in salt water of PH 4-5. Then Dry to collect the residue

To control for hydrolysis mix the 2 together in FRESH water this time, lower the PH to 5 and the temperature to 5 degrees C.

The result is pretty cool. The Acid and Melamine bind together in disk like structures with the pentose sugar sprinkled on the outside. The Pentose sugars the ribose are not connected and do not support the disk. The disk is well structured and homogeneous.

This is to demonstrate that an RNA structure that is supported by a backbone of connected ribose, with nucleotides like Uracil, blah blah, can form naturally.

Yeah clearly this is a random natural process. I can imagine the Acid forming in some frozen salt ocean, and the Melamine formed on some salty puddle. It dries in the sun. Then it rains and washes the Melamine it a new puddle and the Acid mixture, must be high tide, washes into this new fresh water puddle. But it was a winter storm and the temperature plummets to near freezing.

Oh yeah but this is just one part of biological life. But it has a 6 months half life, so plenty of time to arrange itself into a long tape with imperfections that mirror the proteins needed to produce itself and a cell wall.

Thanks for the article Slo1 I do love a good science fiction.

It is not science fiction. It is an investigation to uncover plausible prebiotics to RNA. Let's just imagine your senerio of puddles from tide formations and dropping temperatures happened. Nobody has even speculated how this combination could have evolved into RNA, which is even harder to imagine.

Simply, nobody is asking you to buy in any story. Nobody is stating that these are chemicals and processes that resulted in RNA. They are stating exactly what they stated in the paper.

So you don't think this is a pluasible precursor scenario to the natural creation of RNA?


As a recent example of the ability of supramolecular polymers to promote local chiral resolution, Aida and co-workers demonstrated that racemic solutions of chiral macrocycles self-sort into homochiral supramolecular polymers42. It is therefore possible that supramolecular assemblies, formed by nucleotides with different sugars, including different anomers and enantiomers, could have been selectively enriched in individual supramolecular assemblies before polymerization. Current investigations of this possibility are actively being pursued in our laboratory.

Oh yeah and it gives a pathway that does not require stirring, one of your biggest objections to producing the right chirality.

They did stir for 24 hours. Kenetic stability refers to such physical vectors of chemistry

To produce biological life takes the same rapid changes in enviroment and strict tolerances that manufacturing does.
slo1
Posts: 4,308
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4/28/2016 1:44:05 PM
Posted: 7 months ago
At 4/28/2016 1:31:21 PM, Mhykiel wrote:
At 4/28/2016 12:23:30 PM, slo1 wrote:
At 4/28/2016 2:17:17 AM, Mhykiel wrote:
At 4/27/2016 9:37:52 PM, slo1 wrote:
http://www.nature.com...

The current role of mononucleotides and RNA polymers in numerous cellular functions gave rise to the long-standing hypothesis that these molecules were involved early in the emergence of life: the RNA World hypothesis1. Supporting this hypothesis, model prebiotic reactions and analyses of carbonaceous meteorites provide evidence that the canonical nucleobases of RNA (adenine, guanine, cytosine, uracil) were likely present on the prebiotic Earth2, 3, 4. In addition, progress has been made towards finding abiotic routes to ribose and related sugars from simple molecules (for example, formaldehyde, glyoxylate), as well as mechanisms for ribose phosphorylation and ribose selection from complex sugar mixtures5, 6, 7, 8. Nevertheless, despite decades of effort, the chemical origin of nucleosides and nucleotides (that is, nucleobases glycosylated with ribose and phosphorylated ribose) remains an unsolved problem9, 10.


..............

Although we have not shown chiral nucleotide selection, in the current study we have demonstrated that the ^6;-anomer of MMP is enriched in supramolecular assemblies over the ^5;-anomer of MMP, and this selection leads to a detectable increase in the ratio of the ^6;-anomer over the ^5;-anomer of MMP in the entire solution (presumably due to anomerization and selective stabilization by the assembly). As a recent example of the ability of supramolecular polymers to promote local chiral resolution, Aida and co-workers demonstrated that racemic solutions of chiral macrocycles self-sort into homochiral supramolecular polymers42. It is therefore possible that supramolecular assemblies, formed by nucleotides with different sugars, including different anomers and enantiomers, could have been selectively enriched in individual supramolecular assemblies before polymerization. Current investigations of this possibility are actively being pursued in our laboratory.


Help me understand this.

So we assume that another paper about the spontaneous formation of pentose sugars in abiotic solutions is correct. And then say a lot of that happened in the Early oceans.

No, there is no assumption. It is a study to look for a prebiotic alternative because, "the canonical nucleosides and nucleotides of RNA are thermodynamically disfavoured (but kinetically stable) in water29"

Also

"Base pairing is not exhibited by the canonical mononucleotides31, but such a property would have been advantageous for the prebiotic mutual selection
Then we don't use the actual nucleosides. Because that would be too difficult."

Yes it would be too difficult, also there is nothing that would indicate that there does not exist a precursor to RNA. In fact, it would be very unlikely there isn't. You can't create a barrier, just because you believe RNA would have to begin as RNA. Q: How do you eat an elephant? A: One bite at a time.


I haven't addressed that other paper. Just saying they are using that one experiment as a pluasible solution to having pentose sugars in the water. In a big enough quantity to keep up with hydrolysis of the ribose.

So we use Barbituric Acid and Melamine. They bind similar to Nucleotides. I think this is an important part that these 2 chemicals bind together.

Yes, the biggest challenge to this study is that the Barbituric Acid and Melamine are so reactive with each other that they have to bind with R5P before they meet to form the final RMA like polymer. They also interact with R5P at different temperatures. One was 20 C and other 65 C

Take the Acid and the pentose sugar and stir them together ((sadly I would like to know what direction they were stirred in)) But key here is stir for 24 hours, at 20 degrees C, in salt water of PH 9.

They didn't stir.

They did stir says so in the sections discussing how the synthesized both elements seperately with the d ribose.

"Nucleotides spontaneously form when BA is mixed in water with one equivalent of R5P at 20R01;"C (without the need for drying)." The sample was examined after 24 hours in the solution.

Then take the Melamine and dot he same but stir (possibly in the other direction) for 24 hours, at 65 degrees C, in salt water of PH 4-5. Then Dry to collect the residue

To control for hydrolysis mix the 2 together in FRESH water this time, lower the PH to 5 and the temperature to 5 degrees C.

The result is pretty cool. The Acid and Melamine bind together in disk like structures with the pentose sugar sprinkled on the outside. The Pentose sugars the ribose are not connected and do not support the disk. The disk is well structured and homogeneous.

This is to demonstrate that an RNA structure that is supported by a backbone of connected ribose, with nucleotides like Uracil, blah blah, can form naturally.

Yeah clearly this is a random natural process. I can imagine the Acid forming in some frozen salt ocean, and the Melamine formed on some salty puddle. It dries in the sun. Then it rains and washes the Melamine it a new puddle and the Acid mixture, must be high tide, washes into this new fresh water puddle. But it was a winter storm and the temperature plummets to near freezing.

Oh yeah but this is just one part of biological life. But it has a 6 months half life, so plenty of time to arrange itself into a long tape with imperfections that mirror the proteins needed to produce itself and a cell wall.

Thanks for the article Slo1 I do love a good science fiction.

It is not science fiction. It is an investigation to uncover plausible prebiotics to RNA. Let's just imagine your senerio of puddles from tide formations and dropping temperatures happened. Nobody has even speculated how this combination could have evolved into RNA, which is even harder to imagine.

Simply, nobody is asking you to buy in any story. Nobody is stating that these are chemicals and processes that resulted in RNA. They are stating exactly what they stated in the paper.

So you don't think this is a pluasible precursor scenario to the natural creation of RNA?


As a recent example of the ability of supramolecular polymers to promote local chiral resolution, Aida and co-workers demonstrated that racemic solutions of chiral macrocycles self-sort into homochiral supramolecular polymers42. It is therefore possible that supramolecular assemblies, formed by nucleotides with different sugars, including different anomers and enantiomers, could have been selectively enriched in individual supramolecular assemblies before polymerization. Current investigations of this possibility are actively being pursued in our laboratory.

Oh yeah and it gives a pathway that does not require stirring, one of your biggest objections to producing the right chirality.

They did stir for 24 hours. Kenetic stability refers to such physical vectors of chemistry

To produce biological life takes the same rapid changes in enviroment and strict tolerances that manufacturing does.

Good catch. I missed the stirring. I'll write one of the author's to see if stirring direction was a variable, however since the structure is not a helix with backbone, I assume direction was not important.
Mhykiel
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4/28/2016 1:50:55 PM
Posted: 7 months ago
Don't get me wrong I think it's an extraordinary experiment. Not so much in the results but the attention to detail and thoroughness of the scientists involved.

I think they even hoped to see the ribose connect around the hexad supramolecules to form somekind of backbone like found in RNA.

And this will no doubt be a springboard for other RNA world research.

But abiogenesis to me is impluasible leaning towards impossible. I see no research to convince me otherwise.

Slo1 when does it become a scientist is going to find evidence whether abiogenesis is true or not? When does the 1 in ten million chance stop being revered to as pluasible?

Is it when scientist control for so many variables like kenetic vector, uv, temparature. Jumping from one specific amount to another in a chain more reminiscent of an assembly line than nature? For me that's what it looks like.
Mhykiel
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4/28/2016 3:45:41 PM
Posted: 7 months ago
At 4/28/2016 1:44:05 PM, slo1 wrote:
At 4/28/2016 1:31:21 PM, Mhykiel wrote:
At 4/28/2016 12:23:30 PM, slo1 wrote:
At 4/28/2016 2:17:17 AM, Mhykiel wrote:
At 4/27/2016 9:37:52 PM, slo1 wrote:
http://www.nature.com...

The current role of mononucleotides and RNA polymers in numerous cellular functions gave rise to the long-standing hypothesis that these molecules were involved early in the emergence of life: the RNA World hypothesis1. Supporting this hypothesis, model prebiotic reactions and analyses of carbonaceous meteorites provide evidence that the canonical nucleobases of RNA (adenine, guanine, cytosine, uracil) were likely present on the prebiotic Earth2, 3, 4. In addition, progress has been made towards finding abiotic routes to ribose and related sugars from simple molecules (for example, formaldehyde, glyoxylate), as well as mechanisms for ribose phosphorylation and ribose selection from complex sugar mixtures5, 6, 7, 8. Nevertheless, despite decades of effort, the chemical origin of nucleosides and nucleotides (that is, nucleobases glycosylated with ribose and phosphorylated ribose) remains an unsolved problem9, 10.


..............

Although we have not shown chiral nucleotide selection, in the current study we have demonstrated that the ^6;-anomer of MMP is enriched in supramolecular assemblies over the ^5;-anomer of MMP, and this selection leads to a detectable increase in the ratio of the ^6;-anomer over the ^5;-anomer of MMP in the entire solution (presumably due to anomerization and selective stabilization by the assembly). As a recent example of the ability of supramolecular polymers to promote local chiral resolution, Aida and co-workers demonstrated that racemic solutions of chiral macrocycles self-sort into homochiral supramolecular polymers42. It is therefore possi

So we assume that another paper about the spontaneous formation of pentose sugars in abiotic solutions is correct. And then say a lot of that happened in the Early oceans.

No, there is no assumption. It is a study to look for a prebiotic alternative because, "the canonical nucleosides and nucleotides of RNA are thermodynamically disfavoured (but kinetically stable) in water29"

Also

"Base pairing is not exhibited by the canonical mononucleotides31, but such a property would have been advantageous for the prebiotic mutual selection
Then we don't use the actual nucleosides. Because that would be too difficult."

Yes it would be too difficult, also there is nothing that would indicate that there does not exist a precursor to RNA. In fact, it would be very unlikely there isn't. You can't create a barrier, just because you believe RNA would have to begin as RNA. Q: How do you eat an elephant? A: One bite at a time.


I haven't addressed that other paper. Just saying they are using that one experiment as a pluasible solution to having pentose sugars in the water. In a big enough quantity to keep up with hydrolysis of the ribose.

So we use Barbituric Acid and Melamine. They bind similar to Nucleotides. I think this is an important part that these 2 chemicals bind together.

Yes, the biggest challenge to this study is that the Barbituric Acid and Melamine are so reactive with each other that they have to bind with R5P before they meet to form the final RMA like polymer. They also interact with R5P at different temperatures. One was 20 C and other 65 C

Take the Acid and the pentose sugar and stir them together ((sadly I would like to know what direction they were stirred in)) But key here is stir for 24 hours, at 20 degrees C, in salt water of PH 9.

They didn't stir.

They did stir says so in the sections discussing how the synthesized both elements seperately with the d ribose.

"Nucleotides spontaneously form when BA is mixed in water with one equivalent of R5P at 20R01;"C (without the need for drying)." The sample was examined after 24 hours in the solution.

Then take the Melamine and dot he same but stir (possibly in the other direction) for 24 hours, at 65 degrees C, in salt water of PH 4-5. Then Dry to collect the residue

To control for hydrolysis mix the 2 together in FRESH water this time, lower the PH to 5 and the temperature to 5 degrees C.

The result is pretty cool. The Acid and Melamine bind together in disk like structures with the pentose sugar sprinkled on the outside. The Pentose sugars the ribose are not connected and do not support the disk. The disk is well structured and homogeneous.

This is to demonstrate that an RNA structure that is supported by a backbone of connected ribose, with nucleotides like Uracil, blah blah, can form naturally.

Yeah clearly this is a random natural process. I can imagine the Acid forming in some frozen salt ocean, and the Melamine formed on some salty puddle. It dries in the sun. Then it rains and washes the Melamine it a new puddle and the Acid mixture, must be high tide, washes into this new fresh water puddle. But it was a winter storm and the temperature plummets to near freezing.

Oh yeah but this is just one part of biological life. But it has a 6 months half life, so plenty of time to arrange itself into a long tape with imperfections that mirror the proteins needed to produce itself and a cell wall.

Thanks for the article Slo1 I do love a good science fiction.

It is not science fiction. It is an investigation to uncover plausible prebiotics to RNA. Let's just imagine your senerio of puddles from tide formations and dropping temperatures happened. Nobody has even speculated how this combination could have evolved into RNA, which is even harder to imagine.

Simply, nobody is asking you to buy in any story. Nobody is stating that these are chemicals and processes that resulted in RNA. They are stating exactly what they stated in the paper.

So you don't think this is a pluasible precursor scenario to the natural creation of RNA?


As a recent example of the ability of supramolecular polymers to promote local chiral resolution, Aida and co-workers demonstrated that racemic solutions of chiral macrocycles self-sort into homochiral supramolecular polymers42. It is therefore possible that supramolecular assemblies, formed by nucleotides with different sugars, including different anomers and enantiomers, could have been selectively enriched in individual supramolecular assemblies before polymerization. Current investigations of this possibility are actively being pursued in our laboratory.

Oh yeah and it gives a pathway that does not require stirring, one of your biggest objections to producing the right chirality.

They did stir for 24 hours. Kenetic stability refers to such physical vectors of chemistry

To produce biological life takes the same rapid changes in enviroment and strict tolerances that manufacturing does.

Good catch. I missed the stirring. I'll write one of the author's to see if stirring direction was a variable, however since the structure is not a helix with backbone, I assume direction was not important.

Chirality was discussed in regards to the formation of the hexads. I could probably figure out the direction of stiring.

When I get time I'll cite the relevant pasages talking about the anomerization of the mixture
Dragon_of_Christ
Posts: 1,293
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4/28/2016 4:00:00 PM
Posted: 7 months ago
At 4/28/2016 12:23:30 PM, slo1 wrote:
At 4/28/2016 2:17:17 AM, Mhykiel wrote:
At 4/27/2016 9:37:52 PM, slo1 wrote:
http://www.nature.com...

The current role of mononucleotides and RNA polymers in numerous cellular functions gave rise to the long-standing hypothesis that these molecules were involved early in the emergence of life: the RNA World hypothesis1. Supporting this hypothesis, model prebiotic reactions and analyses of carbonaceous meteorites provide evidence that the canonical nucleobases of RNA (adenine, guanine, cytosine, uracil) were likely present on the prebiotic Earth2, 3, 4. In addition, progress has been made towards finding abiotic routes to ribose and related sugars from simple molecules (for example, formaldehyde, glyoxylate), as well as mechanisms for ribose phosphorylation and ribose selection from complex sugar mixtures5, 6, 7, 8. Nevertheless, despite decades of effort, the chemical origin of nucleosides and nucleotides (that is, nucleobases glycosylated with ribose and phosphorylated ribose) remains an unsolved problem9, 10.


..............

Although we have not shown chiral nucleotide selection, in the current study we have demonstrated that the ^6;-anomer of MMP is enriched in supramolecular assemblies over the ^5;-anomer of MMP, and this selection leads to a detectable increase in the ratio of the ^6;-anomer over the ^5;-anomer of MMP in the entire solution (presumably due to anomerization and selective stabilization by the assembly). As a recent example of the ability of supramolecular polymers to promote local chiral resolution, Aida and co-workers demonstrated that racemic solutions of chiral macrocycles self-sort into homochiral supramolecular polymers42. It is therefore possible that supramolecular assemblies, formed by nucleotides with different sugars, including different anomers and enantiomers, could have been selectively enriched in individual supramolecular assemblies before polymerization. Current investigations of this possibility are actively being pursued in our laboratory.


Help me understand this.

So we assume that another paper about the spontaneous formation of pentose sugars in abiotic solutions is correct. And then say a lot of that happened in the Early oceans.

No, there is no assumption. It is a study to look for a prebiotic alternative because, "the canonical nucleosides and nucleotides of RNA are thermodynamically disfavoured (but kinetically stable) in water29"

Also

"Base pairing is not exhibited by the canonical mononucleotides31, but such a property would have been advantageous for the prebiotic mutual selection
Then we don't use the actual nucleosides. Because that would be too difficult."

Yes it would be too difficult, also there is nothing that would indicate that there does not exist a precursor to RNA. In fact, it would be very unlikely there isn't. You can't create a barrier, just because you believe RNA would have to begin as RNA. Q: How do you eat an elephant? A: One bite at a time.

So we use Barbituric Acid and Melamine. They bind similar to Nucleotides. I think this is an important part that these 2 chemicals bind together.

Yes, the biggest challenge to this study is that the Barbituric Acid and Melamine are so reactive with each other that they have to bind with R5P before they meet to form the final RMA like polymer. They also interact with R5P at different temperatures. One was 20 C and other 65 C

Take the Acid and the pentose sugar and stir them together ((sadly I would like to know what direction they were stirred in)) But key here is stir for 24 hours, at 20 degrees C, in salt water of PH 9.

They didn't stir.
"Nucleotides spontaneously form when BA is mixed in water with one equivalent of R5P at 20R01;"C (without the need for drying)." The sample was examined after 24 hours in the solution.

Then take the Melamine and dot he same but stir (possibly in the other direction) for 24 hours, at 65 degrees C, in salt water of PH 4-5. Then Dry to collect the residue

To control for hydrolysis mix the 2 together in FRESH water this time, lower the PH to 5 and the temperature to 5 degrees C.

The result is pretty cool. The Acid and Melamine bind together in disk like structures with the pentose sugar sprinkled on the outside. The Pentose sugars the ribose are not connected and do not support the disk. The disk is well structured and homogeneous.

This is to demonstrate that an RNA structure that is supported by a backbone of connected ribose, with nucleotides like Uracil, blah blah, can form naturally.

Yeah clearly this is a random natural process. I can imagine the Acid forming in some frozen salt ocean, and the Melamine formed on some salty puddle. It dries in the sun. Then it rains and washes the Melamine it a new puddle and the Acid mixture, must be high tide, washes into this new fresh water puddle. But it was a winter storm and the temperature plummets to near freezing.

Oh yeah but this is just one part of biological life. But it has a 6 months half life, so plenty of time to arrange itself into a long tape with imperfections that mirror the proteins needed to produce itself and a cell wall.

Thanks for the article Slo1 I do love a good science fiction.

It is not science fiction. It is an investigation to uncover plausible prebiotics to RNA. Let's just imagine your senerio of puddles from tide formations and dropping temperatures happened. Nobody has even speculated how this combination could have evolved into RNA, which is even harder to imagine.

Simply, nobody is asking you to buy in any story. Nobody is stating that these are chemicals and processes that resulted in RNA. They are stating exactly what they stated in the paper.

As a recent example of the ability of supramolecular polymers to promote local chiral resolution, Aida and co-workers demonstrated that racemic solutions of chiral macrocycles self-sort into homochiral supramolecular polymers42. It is therefore possible that supramolecular assemblies, formed by nucleotides with different sugars, including different anomers and enantiomers, could have been selectively enriched in individual supramolecular assemblies before polymerization. Current investigations of this possibility are actively being pursued in our laboratory.

Oh yeah and it gives a pathway that does not require stirring, one of your biggest objections to producing the right chirality.

"plausable"
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Mhykiel
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5/2/2016 12:55:34 AM
Posted: 7 months ago
At 4/28/2016 3:45:41 PM, Mhykiel wrote:
At 4/28/2016 1:44:05 PM, slo1 wrote:
At 4/28/2016 1:31:21 PM, Mhykiel wrote:
At 4/28/2016 12:23:30 PM, slo1 wrote:
At 4/28/2016 2:17:17 AM, Mhykiel wrote:
At 4/27/2016 9:37:52 PM, slo1 wrote:
http://www.nature.com...

Chirality was discussed in regards to the formation of the hexads. I could probably figure out the direction of stiring.

When I get time I'll cite the relevant pasages talking about the anomerization of the mixture

After more carefully reading the article, I see chirality was not a big indication of anomer structure. The used temperature and PH to find equilibrium of A and B anomers.

They found when mixed together the Hexads would form and incourage change of A to B anomers.
Axonly
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6/15/2016 2:09:16 AM
Posted: 5 months ago
At 4/27/2016 9:47:18 PM, slo1 wrote:
Great study. I'm very supportive of investigating prebiotic nucleotides in quest for uncovering abiogenesis. In this case the process to make this possible pebiotic was relatively simple.

This one paragraph really sums it up.

Here, we show that glycosylation of melamine and BA by ribose-5-phosphate (R5P) occurs spontaneously in water to produce nucleotides in yields of up to 55% and 82%, respectively. When combined, the nucleotides form supramolecular assemblies with Watson"Crick-like base pairs, even within the crude reaction mixtures.

Here a summary article for dummies like me.
https://www.sciencedaily.com...

This is extremely interesting! It could lead to revolutionary understandings of lifes origins.
Meh!