Synthesis of Specifically Modified Oligonucleotides for Application in Structural and Functional Analysis of RNA

Table 1

Sequences of synthesized linker-modified RNA oligonucleotides. The bold letters (U/A) mark the position of the modification (see Figure 2).

Name	Length	Sequence	Mod.	Dye
A1L1	25 nts	UGG CAA GCU CGC AGU CGG CAC CGC C	5	Cy5
A1L2	25 nts	UGG CAA GCU CGC AGU CGG CAC CGC C	6	Cy5, ATTO 647N
A1L3	25 nts	UGG CAA GCU CGC AGU CGG CAC CGC C	7	Cy5
A2L1	25 nts	UGG CAA GCU CGC AGU CGG CAC CGC C	5	Cy5
A2L2	25 nts	UGG CAA GCU CGC AGU CGG CAC CGC C	6	Cy5, ATTO 647N
A2L3	25 nts	UGG CAA GCU CGC AGU CGG CAC CGC C	7	Cy5
D1L1	25 nts	GGC GGU GCC GAC UGC GAG CUU GCC A	5	Alexa 488
D1L2	25 nts	GGC GGU GCC GAC UGC GAG CUU GCC A	6	Alexa 488
D1L3	25 nts	GGC GGU GCC GAC UGC GAG CUU GCC A	7	Alexa 488
L2-TEST	8 nts	GGA AUU CC	6	—
2-L3-A	8 nts	GGA AUU CC	7	ATTO 647N
8-L1-A	8 nts	UUA GUA CU	8	—
2-L3-A	8 nts	GGA AAU CC	10	ATTO 647N
RNA-25	32 nts	CCC CAC GUC AAG GCG UGG UGG CCG AAG GUC GG	6	Cy5
RNA-26	32 nts	CCG ACC UUC GGC CAC CUG ACA GUC CUG UGG GG	6	Alexa 488
4U-Ther.	60 nts	GGC GGU GCC GAC UGC GAG CUU GCC AUG UUG AAC UUU UGA AUA GUG AUU CAG GAG GUU AAU	6	Alexa 488
4U-Ther.	60 nts	GGC GGU GCC GAC UGC GAG CUU GCC AUG UUG AAC UUU UGA AUA GUG AUU CAG GAG GUU AAU	6	Alexa 488
4U-Ther.	60 nts	GGC GGU GCC GAC UGC GAG CUU GCC AUG UUG AAC UUU UGA AUA GUG AUU CAG GAG GUU AAU	6	Alexa 488
4U-Ther.	60 nts	GGC GGU GCC GAC UGC GAG CUU GCC AUG UUG AAC UUU UGA AUA GUG AUU CAG GAG GUU AAU	6	Alexa 488
4U-Ther.	60 nts	GGC GGU GCC GAC UGC GAG CUU GCC AUG UUG AAC UUU UGA AUA GUG AUU CAG GAG GUU AAU	6	Alexa 488