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Table 1 Oligonucleotides used in this study

From: A nucleotide-independent cyclic nitroxide label for monitoring segmental motions in nucleic acids

Name

Sequence (a)

Notes

CS

5′-dCdTdAdCdT*dG*dCdTdTdTdAdG-3′

DNA for cyclic ps attachment

CS_B

5′-dCdTdAdAdAdGdCdAdGdTdAdG-3′

Complementary to CS

S o (b,c,d)

5′-rCrCrCmUrCdUrArAdA*dC*rC-3′

RNA for cyclic ps attachment; directs ribozyme into the “open” complex

S c (b,c)

5′-rCrCrCrUrCdUrArAdA*dC*rC-3′

RNA for cyclic ps attachment; directs ribozyme into the “close” complex

S s (b,c,d)

5′-rCrCrCmUrCdUrArArAdC*rC-3′

RNA for single ps attachment; directs ribozyme into the “open” complex

IGS

5′-rGrGrUrUrUrGrGrArGrGrG-3′

Complimentary to S o , S c , or S s

  1. (a) Definition of symbols: *: phosphorothioate modification; r: 2′-OH; d: 2′-H; m: 2′-OCH3.
  2. (b) 2′-H substituted at position(s) adjacent to the phosphorothioate group(s) to prevent strand scission upon nitroxide labeling [17,19,22].
  3. (c) Bold position substituted to 2′-H to reduce ribozyme cleavage rate [19].
  4. (d) Italicized position substituted to 2′-OCH3 to remove a tertiary interaction with the ribozyme core [19].
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BMC Biophysics

ISSN: 2046-1682

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