Distinction of Individual Lanthanide Ions with a DNAzyme Beacon Array

Abstract

Developing chemical probes to distinguish each lanthanide ion is a long-standing challenge. Aside from its analytical applications, solving this problem will also enhance our knowledge in metal ligand design. Using in vitro selection, we previously reported four RNA-cleaving DNAzymes, each with a different activity trend cross the lanthanide series. We herein performed another eight in vitro selection experiments using each and every lanthanide from La 3+ to Tb 3+ but excluding the radioactive Pm 3+ . A new DNAzyme named Gd2b was identified and characterized. By labeling this DNAzyme with a fluorophore/quencher pair to create a catalytic beacon, a detection limit of 14 nM Gd 3+ was achieved. With the same beacon design, all the five lanthanide-specific DNAzymes were used together to form a sensor array. Each lanthanide ion produces a unique response pattern with these five sensors, allowing a pattern-recognition-based linear discriminant analysis (LDA) algorithm to be applied, where separation was achieved between lanthanides and nonlanthanides, light and heavy lanthanides, and for the most part, each lanthanide. These lanthanidespecific DNA molecules are useful for understanding lanthanide coordination chemistry, designing hybrid materials, and developing related analytical probes.

A Selective Na+ Aptamer Dissected by Sensitized Tb3+ Luminescence

“…By using specific metal ions during selection, many DNAzymes have been obtained with high specificityf or Na + , [13,14] Pb 2 + , [15,16] Zn 2 + , [17] Cu 2 + , [18,19] UO 2 2 + , [20] Cd 2 + , [21] Hg 2 + , [22] and trivalentl anthanides. [23][24][25][26][27] In principle, the metal specificity is associated with am etal-binding site, however it is quite challenging to extract aptamer motifs from DNAzymes.…”

Global Folding of a Na+‐Specific DNAzyme Studied by FRET

“…Sometimes, excellent metal specificity can be achieved . For example, DNAzymes requiring divalent Ca 2+ , Pb 2+ , UO 2 2+ , Cd 2+ , and Cu 2+ , and trivalent lanthanides, have been reported. Recently, monovalent Ag +[17] and Na +[18–22] were also selectively recognized by DNAzymes.…”

The Two Classic Pb2+‐Selective DNAzymes Are Related: Rational Evolution for Understanding Metal Selectivity

“…In 1994, the first DNAzyme namedG R5 was reported,w hich specifically requires Pb 2 + for its RNA cleavage activity.T hree years later,the 8-17 DNAzyme was isolated. [8][9][10][11][12][13][14][15][16][17] DNAzyme and the related 17E DNAzyme are also most active with Pb 2 + , although other divalent metals can work as well. GR5 and 17E have the same substrates equence, and their catalytic loopsi n the enzyme strandsa lso have af ew similar and conserved nucleotides.…”

“…To test this hypothesis, we performed systematic rational evolution experiments to gradually mutate GR5 toward1 7 E. By using the activity ratio in the presence of Pb 2 + and Mg 2 + for defining these two DNAzymes, the critical nucleotide was identified to be T 12 in 17E for metal specificity. In addition, G 9 in GR5i sap ositionn ot found in most 17E or [8][9][10][11][12][13][14][15][16][17]and G 9 needs to be added to rescue GR5 activity if T 12 becomes ac ytosine. This study highlightst he links between these two classic and widely used DNAzymes, and offers new insight into the sequence-activity relationshipr elated to metal selectivity.…”

“…[1] With excellent stability, high catalytic efficiency,programmability,and ease of modification, DNAzymes have been explored for various applications such as metal sensing,a ntiviral activity,a nd nanotechnology. [2] So far,RNA-cleaving DNAzymes have been studied mostexten-sively,a nd they often require metal ions for activity.D NAzymes requiring ad iverse range of metal ions have been reported to date, such as Pb 2 + , [3] Zn 2 + , [4] UO 2 2 + , [5] Hg 2 + , [6] Cd 2 + , [7] trivalent lanthanides, [8] and other metals. [1c, 9] Among these, Pb 2 + hasp layed ap articularly important role in the growth of the field.…”