DYNAMIC EQUILIBRIA MAY PROVIDE A PREBIOTIC
ROUTE TO INCREASING COMPLEXITY.
M. R. Tirumalai1, M. Paci1, A. Marathe1, D Chavan1, and G. E. Fox1,
1Biology and Biochemistry, University of Houston, Houston, TX 77204-5001. Corresponding author: [email protected]
Abstract
To understand the extent to which complexity can emerge in an RNA World and how it might be
effected by peptides or amino acids, we are pursuing a novel experimental approach based on
dynamic combinatorial chemistry (DCC)[1,2]. It is hypothesized that when subject to a persistent
equilibrium of ligation and cleavage, RNAs will naturally increase in complexity while gaining
resistance to degradation over time. It will be of immense interest to see if this equilibrium or the
pathways towards increasing complexity are strongly affected by the presence of amino acids or
peptides. To obtain such equilibrium, we are using a two enzyme system. The cleavage enzyme is
Benzonase [3], which is the commercial name for an extracellular endonuclease secreted by Serratia
marcescens. This enzyme cleaves RNA, including circular forms, to produce products with a 3’
hydroxyl and 5’ phosphate. This is ideal for ligation by T4 RNA ligase [4], which requires these exact
ends and utilizes ATP as a source of energy. In order to monitor population changes, samples are
extracted from the reactions mix and millions of individual RNAs sequences are determined using
RNA-seq technology on an Illumina NextSeq 500 system [5].
A mutually compatible buffer system established
•  An equilibrium experiment over 180 minutes was conducted using a defined
sequence 20-mer as the starting RNA.
•  Gel analysis suggested that the RNA was initially ligated, as expected as large
products were seen.
ATP Concentration (uM)
•  These persisted for 120 minutes after which their quantity began to diminish,
presumably because the benzonase was still active while the ligase likely began to
run out of ATP.
7.00
Oligo+Ligase+Benzonase+ATP
6.00
Oligo+Ligase+ATP
5.00
ATP only in buffer
•  Reaction mixtures processed using the
NEXTflex™ Small RNA-Seq Kit v3 (Illumina®
Compatible) (Catalog #5132-05).
4.00
3.00
•  This kit utilizes patent-pending adapters with
randomized ends to greatly reduce sequence bias in small RNA sequencing library construction.
2.00
1.00
0.00
0
30
60
120
180 240 300
Time (minutes)
360
420
480
•  Samples were run on a NextSeq 500 system at the University of Houston.
•  Does the ligase prefer circularizing the oligo more than linear ligation?
•  Is this why while we see the larger bands on the gel, we don’t see sequences larger than 40 bases from
samples at 60, 90, 120, 150, and 180 min from the sequenced data sets?
•  The results to date have made it clear that in the absence of an error prone replicase, the manner in
which an RNA sequence space can be explored is more limited.
•  We have successfully created a dynamic equilibrium between ligation and degradation.
•  Under present conditions the rate of exploration of sequence space is slower than we desire because of cyclization of much of the
RNA.
Acknowledgement: This project/ publication was made
possible through the support of a grant from the John
Templeton Foundation. The opinions expressed in this
publication are those of the author(s) and do not
necessarily reflect the views of the John Templeton
Foundation.
Near Term and Future Plans:
References:
•  We are exploring means of decreasing the rate of cyclization or increasing its rate of removal by decreasing T4 ligase
[2] Tuerk C. and Gold L. (1990) Science, 249, 505-510.
concentrations.
•  A long term study, especially with a random sequence (oligo) will be undertaken to determine if products of particular sequence
begin to accumulate.
[1] Benner S. A. et al (1996) Acta Chem. Scand, 50(3), 243-248.
[3] Olszewski M. and Filipkowski P. (2009) Postepy Biochem 55,
21-24.
[4] Tessier D. C. et al (1986) Anal Biochem 158, 171-178.
[5] http://support.illumina.com/downloads/nextseq-500-userguide-15046563.html