Inverse RNA Folding Workflow to Design and Test Ribozymes that Include Pseudoknots

Kayedkhordeh, Mohammad; Yamagami, Ryota; Bevilacqua, Philip C.; Mathews, David H.

doi:10.1007/978-1-0716-0716-9_8

Cited by 2 publications

(2 citation statements)

References 42 publications

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“…Eterna designs were originally evaluated computationally as to whether the sequence is predicted to fold with the lowest free energy to the target structure. This can be achieved whether or not the NED is relatively low. ,, Therefore, we expected that many of the designs would not provide low NED, despite performing well by minimum free energy folding. We compared the lowest NED for our solutions using P–Z to the lowest NED using Eterna player RNA sequences (Figure S4).…”

Section: Resultsmentioning

confidence: 99%

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DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters

Pham,

Miffin,

Sun

et al. 2023

ACS Synth. Biol.

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We show that in silico design of DNA secondary structures is improved by extending the base pairing alphabet beyond A−T and G−C to include the pair between 2-amino-8-(1′-β-D-2′deoxyribofuranosyl)-imidazo-[1,2-a]-1,3,5-triazin-(8H)-4-one and 6amino-3-(1′-β-D-2′-deoxyribofuranosyl)-5-nitro-(1H)-pyridin-2-one, abbreviated as P and Z. To obtain the thermodynamic parameters needed to include P−Z pairs in the designs, we performed 47 optical melting experiments and combined the results with previous work to fit free energy and enthalpy nearest neighbor folding parameters for P−Z pairs and G−Z wobble pairs. We find G−Z pairs have stability comparable to that of A−T pairs and should therefore be included as base pairs in structure prediction and design algorithms. Additionally, we extrapolated the set of loop, terminal mismatch, and dangling end parameters to include the P and Z nucleotides. These parameters were incorporated into the RNAstructure software package for secondary structure prediction and analysis. Using the RNAstructure Design program, we solved 99 of the 100 design problems posed by Eterna using the ACGT alphabet or supplementing it with P−Z pairs. Extending the alphabet reduced the propensity of sequences to fold into off-target structures, as evaluated by the normalized ensemble defect (NED). The NED values were improved relative to those from the Eterna example solutions in 91 of 99 cases in which Eterna-player solutions were provided. P−Z-containing designs had average NED values of 0.040, significantly below the 0.074 of standard-DNA-only designs, and inclusion of the P−Z pairs decreased the time needed to converge on a design. This work provides a sample pipeline for inclusion of any expanded alphabet nucleotides into prediction and design workflows.

show abstract

Section: Resultsmentioning

confidence: 99%

“…This can be achieved whether or not the NED is relatively low. 13 , 44 , 45 Therefore, we expected that many of the designs would not provide low NED, despite performing well by minimum free energy folding. We compared the lowest NED for our solutions using P–Z to the lowest NED using Eterna player RNA sequences ( Figure S4 ).…”

Section: Resultsmentioning

confidence: 99%

DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters

Pham,

Miffin,

Sun

et al. 2023

ACS Synth. Biol.

Self Cite

View full text Add to dashboard Cite

show abstract

DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters

Pham,

Miffin,

Sun

et al. 2023

Preprint

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We show that in silico design of DNA secondary structures is improved by extending the base pairing alphabet beyond A-T and G-C to include the pair between 2-amino-8-(1'-β-D-2'-deoxyribofuranosyl)-imidazo-[1,2-a]-1,3,5-triazin-(8H)-4-one and 6-amino-3-(1'-β-D-2'-deoxyribofuranosyl)-5-nitro-(1H)-pyridin-2-one, simply P and Z. To obtain the thermodynamic parameters needed to include P-Z pairs in the designs, we performed 47 optical melting experiments and combined the results with previous work to fit a new set of free energy and enthalpy nearest neighbor folding parameters for P-Z pairs and G-Z wobble pairs. We find that G-Z pairs have stability comparable to A-T pairs and therefore should be considered quantitatively by structure prediction and design algorithms. Additionally, we extrapolated the set of loop, terminal mismatch, and dangling end parameters to include P and Z nucleotides. These parameters were incorporated into the RNAstructure software package for secondary structure prediction and analysis. Using the RNAstructure Design program, we solved 99 of the 100 design problems posed by Eterna using the ACGT alphabet or supplementing with P-Z pairs. Extending the alphabet reduced the propensity of sequences to fold into off-target structures, as evaluated by the normalized ensemble defect (NED). The NED values were improved relative to those from the Eterna example solutions in 91 of 99 cases where Eterna-player solutions were provided. P-Z-containing designs had average NED values of 0.040, significantly below the 0.074 of standard-DNA-only designs, and inclusion of the P-Z pairs decreased the time needed to converge on a design. This work provides a sample pipeline for inclusion of any expanded alphabet nucleotides into prediction and design workflows.

show abstract

Inverse RNA Folding Workflow to Design and Test Ribozymes that Include Pseudoknots

Cited by 2 publications

References 42 publications

DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters

DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters

DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters

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