POLYNUCLEOTIDE SECONDARY STRUCTURE

1 - 25 . (canceled)

26 . A method for producing highly expressing mRNA, comprising:

(a) determining a flexibility value for each nucleotide within a population of synonymous RNA;

(b) determining a SHAPE reactivity for each RNA corresponding to the primary sequence and chemistry of the nucleotides based on the combined flexibility values of the nucleotides;

(c) selecting a RNA from the population having a SHAPE reactivity of less than 1.0; and

(d) synthesizing highly expressing mRNA based on the primary sequence and chemistry of the nucleotides of the selected RNA having a SHAPE reactivity of less than 1.0.

27 . The method of claim 26 , wherein the highly expressing mRNA is determined to be highly expressing relative to a corresponding wild type chemically unmodified RNA and the highly expressing mRNA produces more protein than the wild type RNA.

28 . The method of claim 27 , wherein the highly expressing mRNA produces at least 10% more protein than the wild type RNA.

29 . The method of claim 26 , wherein the highly expressing mRNA has a SHAPE reactivity of less than 0.8.

30 . The method of claim 26 , wherein the primary sequence of the RNA has a low U content, wherein less than 24% of the nucleotides are U.

31 . The method of claim 26 , wherein the primary sequence of the RNA is thermodynamically stable.

32 . The method of claim 31 , wherein at least some of the nucleotides have a 5-methoxy-uridine chemical modification.

33 . The method of claim 26 , wherein the primary sequence of the RNA is thermodynamically unstable.

34 . The method of claim 33 , wherein at least some of the nucleotides have a N1-methyl-pseudouridine or pseudouridine chemical modification.

35 . The method of claim 26 , wherein the highly expressing mRNA has a mRNA minimum free energy (MFE) value within a top 0.1% of low MFE as defined computationally of synonymous variants.

36 . The method of claim 26 , wherein the highly expressing mRNA has secondary structure capability and wherein greater than 50% of the mRNA forms secondary structure at 37° C. as defined by UV-melting analysis.

37 . The method of claim 26 , wherein the highly expressing mRNA has secondary structure capability and wherein greater than 70% of the thermostable mRNA forms secondary structure at 37° C. as defined by UV-melting analysis.

38 . The method of claim 26 , wherein the highly expressing mRNA has secondary structure capability and wherein greater than 90% of the thermostable mRNA forms secondary structure at 37° C. as defined by UV-melting analysis.

39 - 61 . (canceled)

62 . A method of synthesizing a thermostable mRNA, comprising:

(a) binding a first polynucleotide comprising a flexible region comprising a first set of nucleotides having a primary sequence and including a 5′ untranslated region (UTR), wherein the first set of nucleotides encoding the 5′ UTR have a first flexibility value based on folding conformation propensity of the primary sequence and thermodynamic stability of nucleotide chemistry, wherein the first polynucleotide is conjugated to a solid support, and a second polynucleotide comprising a thermostable region comprising a second set of nucleotides having a primary sequence and including at least a portion of an open reading frame (ORF), wherein the second set of nucleotides encoding the ORF have a second flexibility value;

(b) ligating the 3′-terminus of the first polynucleotide to the 5′-terminus of the second polynucleotide under suitable conditions, wherein the suitable conditions comprise a DNA Ligase, thereby producing a first ligation product;

(c) ligating the 5′ terminus of a third polynucleotide comprising a 3′-UTR to the 3′-terminus of the first ligation product under suitable conditions, wherein the suitable conditions comprise an RNA Ligase, thereby producing a second ligation product; and

(d) releasing the second ligation product from the solid support,

thereby producing the thermostable mRNA.

63 - 64 . (canceled)