The abiotic synthesis of nucleosides, nucleotides and RNA in hydrothermal systems

Douglas E. LaRowe, Andy W. Dale and Pierre Regnier

Department of Earth Science - Geochemistry, Utrecht University, PO Box 80.021, 3508 TA, Utrecht, Netherlands, (larowe@geo.uu.nl, Phone: +31 30 253 3990, www.geo.uu.nl)

The abiotic synthesis of nucleosides, nucleotides and RNA in hydrothermal systems

7. Concluding remarks

hydrothermal systems.

1. Abstract

Recent calculations have shown that the abiotic synthesis of nucleobases, ribose and

deoxyribose from formaldehyde (CH ₂ O) and hydrogen cyanide (HCN) under hydrothermal conditions are thermodynamically favored [1]. Yet, to form the nucleosides, and ultimately by the addition of phosphate, nucleotides, that constitute RNA, a thermodynamic drive

(negative Gibbs energy) must also be available for the condensation reactions among these fundamental building blocks. In this study, the energy required for these reactions and the polymerization of RNA at high temperatures and pressures has been quantified Results reveal that none of these reactions are thermodynamically favored under the low concentrations of nucleobases, ribose and deoxyribose that would likely exist on the

early Earth. A concentrating step of the building block molecules, likely driven by the

steep thermal gradients that exist in some hydrothermal systems, is required to overcome this energetic limitation. Building on work by Baaske et al. [2], who calculate that

nucleotides can be concentrated in hydrothermal environments through a combination of convection and thermal diffusion in narrow pore spaces, we show that nucleobases, ribose, and phosphate can be concentrated under hydrothermal conditions to sufficiently high

concentrations to overcome the condensation energy barrier. Calculations of this kind strongly support the notion that hydrothermal systems played a fundamental role in the origin of life.

[1] LaRowe, D.E. and Regnier, P. (2008) Orig. Life Evol. Bios., DOI 10.1007/s11084-008-9137-2 [2] Baaske, P. et al.

(2007) PNAS 104, 9346-9351.

2. Glossary

Nucleobase - partially aromatic heterocyclic compound, e.g., adenine Ribose ^- 5-carbon carbohydrate

Nucleoside - nucleobase + ribose, e.g., adenosine

Nucleotide - nucleobase + ribose + phosphate, e.g., AMP ^2- RNA - polymer of nucleotides

3. Condensation Reactions

4. Concentrating Biomolecules

The Soret effect

5. Quantifying Concentration

Although the condensation reactions among phosphate, nucleobases, and ribose that form nucleosides, nucleotides and RNA are not thermodynamically favored unless high concentrations of these reactants persist, the combined force of thermally-driven convection and the non-equilibrium Soret effect can work in concert to concentrate these biomolcules. The thermal gradient required for these phenomena to act in concert can be achieved in hydrothermal pores. These results support that notion that fundamental biomolecules, if not life itself, originated in hydrothermal systems. Acknowledgements This work is supported by the by the Netherlands Organization for Scientific

Research (NWO) grant number 815.01.008. We are indebted to Philipp Baske and Dieter Braun for providing the COMSOL Multiphysics files that were modified to produce the concentration factor plots.

O

OH OH

H H

H H

HO H

N

N N H N

NH₂

Figures 3a-d show activities of adenosine and AMP ^2- that are in equilibrium with variable activites of adenine and ribose (Figs. 3a & b) and phosphate and adenosine (Figs. 3c & d) at 25 ^o C and 250 ^o C and 500 bars. Large activities (~1) of each of the reactant compounds

are required for appraciable activities (~10 ^-3 ) of the condensed, product molecules to coexist.

N

N N N

NH₂

O

OH OH

H H

H H

O P -O

O- O

-6 -4 -2 0 2

-6 -4 -2 0 2

log a

_ribose

lo g a

adenine

log a

_adenosine

25^oC 500 bars -7

-5 -3

-6 -4 -2 0 2

-6 -4 -2 0 2

log a

_ribose

lo g a

adenine

log a

_adenosine

250^oC 500 bars -7

-5 -3

-6 -4 -2 0 2

-6 -4 -2 0 2

log a

_adenosine

lo g a

HPO

log a _AMP

25^oC 500 bars -7

-5 -3

2-

42-

-6 -4 -2 0 2

-6 -4 -2 0 2

log a

_adenosine

lo g a

HPO

log a _AMP

250^oC 500 bars -7

-5 -3

2-

42-

1 2 3 4 5 6

0 50 100 150 200 250 300 350

G

r

(K ca l m ol

-1

)

TEMPERATURE,

^o

C

0

500 bars

PSAT

Dickson et al. (2000) PNAS

These plots were made using thermodynamic data taken from LaRowe and Helgeson (2006) using the the SUPCRT software package (Johnson et al., 1992).

N

N N N

NH₂

O

OH OH

H H

H H

HO

Because it is unlikely that ribose, adenine and phosphate existed at concentrations on the priobiotic earth high enough for significant reactions among them to occur, a concentration mechanism for them is required. The mechanism preposed below

(after Baaske et al., 2007) combines thermodiffusion (the Soret effect) with convection in a hydrothermal pore system.

co nc en tr at io n i

x

₁

x

₂

4a

T

_cold

co nc en tr at io n i

x

₁

x

₂

T

_hot

The Soret effect, or thermodifffusion, is a 4b

non-equilibrium phenomenon in which a concentration gradient is established in response to a sustained temperature

gradient. In Fig. 4a, the concentration of i is constant throughout an isothermal

solution. However, when a thermal gradient is imposed on the solution,

species i is concentrated onone side of the system.

T

₁

T

₂

Thermal

gradient + ^Convective _flow

T

₁

T

₂

a a

b b

Hydrothermal Pore

b a

Low High

= Concentration factor

a

b

Consider a temperature gradient in a hydrothermal pore:

A hydrothermal pore of length a and width b characterized by a thermal gradient, T , that is open at the top and closed at the bottom can concentrate biomolecules

through a combination of the Soret effect and convection.. In this scenario, the bulk fluid, conatining a small concentration of a biomolecule, enters the pore and due to the thermal gradient, thermodiffusion and convection act in concert to concentrate the biomolecule in a subcompartment of the system:

Ñ

Fig. 6a - Adenine

The concentration factors reported here were calculated using the COMSOL Multiphysics finite element code for hydrothermal pores corresponding to the following specifications:

2 O H ) 1 (

] RNA [

NT ® + -

å i n i n n

-10 -8 -6 -4 -2 0 2 4

0 50 100 150 200 250

G r (Kcal mol-1 )

TEMPERATURE, ^oC

10²

NT / [RNA]_n

10³ 10⁴

-2.4 -2.2 -2 -1.8 -1.6 -1.4

0 50 100 150 200 250

G r (Kcal mol-1 )

TEMPERATURE, ^oC

log a = -3 log a_adenosine= 0 log a = 0_HPO

4 2-

AMP^2-

-2.6 -2.4 -2.2 -2 -1.8 -1.6

0 50 100 150 200 250

G r (Kcal mol-1 )

TEMPERATURE, ^oC

log a_adenosine= -3 log a_adenine= 0 log a_ribose= 0

0.2 0.4 0.6 0.8 1.0 1.2

1.4 x 10

⁴

100 200 300 400 500 600 700 800 900

200 400 600 800 1000 1200 1400 1600

1 3 5 9

7

0.5 1.0 1.5 2.0 2.5

500 1000 1500 2000 2500 3000

Adenine Ribose Adenosine AMP ^2-

3a. 3c.

3d.

3b.

2 O H ) 1 (

] RNA [

NT ® + -

å i n i n n

Figure 3e depicts the standard molal Gibbs energy of reaction required to polymerize nucleotides (NT) into RNA using the amino acid polymerization model established in Dick, LaRowe and Helgeson (2006).

3e.

∆ Width: 140 µm

Length: 7mm Ratio: 50

Mesh: 644 elements

Temperature gradient: 30 K (linear) Left side temperature: 323 K

Equation systems considered:

Incompressible Navier-Stokes Heat Transfer

Mass & Thermal Diffusion

6. Model Results: Concentration factors

The figures shown below display the concentration factors for phosphate, adenine, ribose, adenosine and AMP ^2- in the model pore described in Section 5a.

pore scale

Fig. 6b - Ribose I

3.0 x 10 ⁷

Fig. 6c -Ribose II

pore scale pore pore zoom scale

Fig. 6d - Adenosine Fig. 6e - Phosphate Fig. 6e - AMP ^2-

It can be seen in Figs. 6a-e that each of the molecules considered in this study can be concentrated many times their bulk solution

concentration due to the combined effects of thermodiffusion and

convection. However, the scale to which they can be concentrated is very sensitive to the values of the mass diffusion coefficients used. For instance, a nearly seven order of

magnitude difference in concentration factor for ribose can be seen in Figs.

6b & c The value of the mass diffusion coefficient is altered

by a factor of 10 (10 ^-9 vs.10 ^-10 m ² s ^-1 , respectively).

pore zoom scale scale

scale pore

pore pore

Figures 6f-h depict the energetic consequences of concentrating the molecules considered in this study as a function of temperature. It

can be seen in Figs. 6f & g that the Gibbs energy of the reactions written above these panels is negative for activities of the reactants equal to 1. Similarly, the polymerization of RNA, shown in Fig. 6h, becomes favorable as the temperature

increases and as the concentration of nucleotides increases by only a couple of orders of magnitude.

Fig. 6f Fig. 6g Fig. 6h

∆ ∆ ∆

adenine + ribose = adenosine + H

₂

O adenosine + HPO

₄^2-

= AMP

^2-

+ H

₂

O

model

hydrothermal

pore: