Table 1.

Comparison of biophysical properties of various 3WJ cores

Family	Name	Sequence 5′-3′	Assembly of 3WJ-RNA Core		Assembly of 3WJ- pRNA with three pRNA monomers		Tm(°C)
			Native Gel	8M Urea Denaturing Gel	Native Gel	8M Urea Denaturing Gel	TMS Buffer
A	16s H34-H35-H38	a) GGG GAC GAC GUC b) CGA GCG CAA CCC CC c) GUC GUC AGC UCG	Weak	No	Yes	No	45.3 ± 6.7
	23s H75-H76- H79	a) GAG GAC ACC GA b) GGC UCU CAC UC c) UCG CUG AGC C	No	No	No	No	33.3 ± 0.6
B	23s H83-H84- H85	a) AGC AAA AGA U b) CCC GGC GAA GAG UG c) AUC UCA GCC GGG	No	No	No	No	53.7 ± 0.6
C	5S rRNA	a) CCC GGU UCG CCG CCA b) CCC ACC AGC GUU CCG GG c) AGG CGG CCA UAG CGG UGG G	Very Strong	Very Strong	Yes	Yes	54.3 ± 3.1
	G- Riboswitch (Type I)	a) GGA CAU AUA AUC GCG UG b) AUG UCC GAC UAU GUC C c) CAC GCA AGU UUC UAC CGG GCA	Medium	No	Yes	No	46.0 ± 3.5
	TPP Riboswitch (Type II)	a) GCG ACU CGG GGU GCC CUU C b) GAA GGC UGA GAA AUA CCC GUA UCA CCU GAU CUG G c) CCA GCG UAG GGA AGU CGC	Strong	No	Yes	No	52.0 ± 4.4
	M-box Riboswitch (Type II)	a) GAC GCC AAU GGG UCA ACA GAA AUC AUC G b) AGG UGA UUU UUA AUG CAG CU c) ACG CUG CUG CCC AAA AAU GUC	Strong	No	Yes	No	45.3 ± 5.5
	Hammerhead ribozyme	a) CUG UCA CCG GAU b) GGA CGA AAC AG c) UUC CGG UCU GAU GAG UCC	No	No	No	No	49.7 ± 1.5
	Alu SRP	a) GGG CCG GGC GCG GU b) UCG GGA GGC UC c) GGC GCG CGC CUG UAG UCC CAG C	No	No	No	No	45.3 ± 4.6
Unknown	HCV	a) UCA UGG UGU UCC GGA AAG CGC b) GUG AUG AGC CGA UCG UCA GA c) UCU GGU GAU ACC GAG A	No	No	No	No	49.7 ± 1.5
	pRNA	a) UUG CCA UGU GUA UGU GGG b) CCC ACA UAC UUU GUU GAU CC c) GGA UCA AUC AUG GCA A	Very Strong	Very Strong	Yes	Yes	58.0 ± 0.5

Note: The sequences of the 3WJ cores were obtained from References ^{35,39,41–43}. Families A, B and C are based on Lescoute and Westhof classification ³⁹. Other 14 3WJ cores that were not practical for thorough investigations are listed in Supplementary Table 2.