List of Publications by Year

 

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2017

183. Kang, D., Sun, Sheng, Kurnik, M., Morales, D., Dahlquist, F.W. and Plaxco, K.W. (2017) “A new architecture for reagentless, protein-based electrochemical biosensors.” J. Am. Chem. Soc., 139, 12113-12116

182. Li, H., Dauphin-Ducharme, P., Ortega, G. and Plaxco, K.W. (2017) “Calibration-free electrochemical biosensors supporting accurate molecular measurements directly in undiluted whole blood.” J. Am. Chem. Soc., 139, 11207–11213

181. Dauphin-Ducharme, P., Arroyo-Currás, N., Kurnik, M., Ortega, G., Li, H., and Plaxco, K.W. (2017) “A simulation-based approach to determining electron transfer rates using square-wave voltammetry.” Langmuir, 33, 4407-4413

180. Mariottini, D., Idili, A., Vallee-Belisle, A., Plaxco, K.W. and Ricci, F. (2017) “A DNA nanodevice that loads and releases a cargo with hemoglobin-like allosteric control and cooperativity.” Nano. Lett., 17, 3225-3230

179. Li, H., Dauphin-Ducharme, P., Arroyo-Currás, N., Tran, C., Vieira, P.A., Li, S., Shin, C., Somerson, J., Kippin, T.E. and Plaxco, K.W. (2017) “A biomimetic, phosphatidylcholine-terminated monolayer greatly improves the in-vivo performance of electrochemical aptamer-based sensors.” Angew. Chem. Int. Ed., 56, 7492-7495

178. Hauke, A., Selva Kumar, L.S., Kim, M.Y., Pegan, J., Khine, M., Li, H., Plaxco, K.W. and Heikenfeld, J. (2017) “Superwetting and aptamer functionalized shrink-induced high surface area electrochemical sensors.” Biosens. Bioelec., 94, 438-442

177. Simon, A.J., Walls-Smith, L.T., Freddi, M., Fong, F.Y., Gubala, V. and Plaxco, K.W. (2017) “Quantitative measurement of the molecular- and micron-scale dissolution kinetics of responsive DNA hydrogels.” ACS Nano, 11(1), 461-468

176. Arroyo-Currás, N., Somerson, J., Vieira, P., Ploense, K., Kippin, T. and Plaxco, K.W. (2017) “Real-time measurement of small molecules in awake, ambulatory animals.” Proc. Natl. Acad. Sci., 114(4), 645-650

2016

175. Li, H., Arroyo-Currás, N., Kang, D., Ricci, F. and Plaxco, K.W. (2016) “Dual-reporter drift correction to enhance the performance of electrochemical aptamer-based sensors in whole blood.” J. Am. Chem. Soc., 138, 15809-15812

174. Daupin-Ducharme, P. and Plaxco, K. W. (2016) “Maximizing the signal gain of electrochemical-DNA sensors.” Anal. Chem., 88, 11654-11662

173. Kang, D., Ricci, F., White, R.J. and Plaxco, K.W. (2016) “A survey of redox-active moieties for application in multiplexed electrochemical biosensors.” Anal. Chem., 88, 10452-10458

172. Ricci, F., Vallée-Bélisle, A., Simon, A.J., Porchetta, A. and Plaxco, K.W. (2016) “Using Nature’s ‘tricks’ to rationally tune the binding properties of biomolecular receptors.” Acc. Chem. Res., 49, 1884-1892

171. Mao, X., Simon, A.J., Shi, J., Li, J., Huang, Q., Plaxco, K.W. and Fan, C. (2016) “Activity modulation and allosteric control of a scaffolded DNAzyme using a dynamic DNA nanostructure.” Chem. Sci., 7, 1200-1204


2015

170. Ranallo, S., Vallée-Bélisle, A., Plaxco, K.W. and Ricci, F. (2015) “A modular, DNA-based ‘beacon’ for the single-step fluorescence measurement of antibodies and other proteins.” Angewandte Chemie Intern., 54, 13214–13218

169. Watkins, H.M., Simon, A.J., Sosnick, T.R., Lipman, E.A., Hjelm, and Plaxco, K.W. (2015) “Random coil negative control reproduces the discrepancy between scattering- and FRET measurements of denatured protein dimensions.” Proc. Natl. Acad. Sci. USA, In press.

168. Adornetto, G., Porchetta, A., Palleschi, G., Plaxco, K.W. and Ricci, F. (2015) “A general approach to the design of allosteric, transcription-factor-regulated DNAzymes.” Chem. Sci., In press.

167. Hsieh, K., Ferguson, B., Eisenstein, M., Plaxco, K.W. and Soh, H. (2015) “Integrated Electrochemical Microsystems for Genetic Detection of Pathogens at the Point of Care.” Acc. Chem. Res., 48, 911-920.

166. Vinh, N.Q., Sherwin, M.S., Allen, S.J., George, D.K., Rahmani, A.J. and Plaxco, K.W. (2015) “High-precision gigahertz-to-terahertz spectroscopy of aqueous salt solutions as a probe of the femtosecond-to-picosecond dynamics of liquid water.” J. Chem. Phys., 142, 164502.


2014

165. Simon, A.J., Vallée-Bélisle, A., Ricci, F., and Plaxco, K.W. (2014) “Intrinsic disorder as a generalizable strategy for the rational design of highly responsive, allosterically cooperative receptors” Proc. Natl. Acad. Sci. USA, 111, 15048-53.

164. Simon, A.J., Vallée-Bélisle, A., Ricci, F., Watkins, H.M. and Plaxco, K.W. (2014) “Using the Population-Shift Mechanism to Rationally Introduce “Hill-type” Cooperativity into a Normally Non-Cooperative Receptor” Angew. Chem. Int. Ed., 53, 9471-5.

163. Watkins, H.M., Simon, A.J., Ricci, F., and Plaxco, K.W. (2014) “Effects of Crowding on the Stability of a Surface-Tethered Biopolymer: An Experimental Study of Folding in a Highly Crowded Regime.” J. Am. Chem. Soc., 136, 8923-7.

162. Yang, A.H.J., Hsieh, K., Patterson, A.S., Ferguson, B.S., Eisenstein, M., Plaxco, K.W. and Soh, H.T. (2014) “Accurate zygote-specific SNP discrimination using microfluidic electrochemical DNA melt curves.” Angewandte, 53, 3163-7.

161. Lawrence, C., Vallée-Bélisle, A., Pfeil, S.H., de Mornay, D., Lipman, E.A. and Plaxco, K.W. (2014) “A comparison of the folding kinetics of a small, artificially selected DNA aptamer with those of equivalently simple naturally occurring proteins.” Prot. Sci., 23, 56-66.


2013

160. Idilli, A., Vallée-Bélisle, A., Plaxco, K.W. and Ricci, F. (2013) “Thermodynamic basis for engineering high-affinity, high-specificity binding-induced DNA clamp nanoswitches.” J. Am Chem. Soc., 7, 10863-10869.

159. Ferguson, B.S., Hoggarth, D.A., Maliniak, D., Ploense, K., White, R.J., Woodward, N., Hsieh, K., Bonham, A.J., Eisenstein, M., Kippin, T., Plaxco K.W. and Soh, H.T. (2013) “Real-Time, Aptamer-Based Tracking of Circulating Therapeutic Agents in Living Animals.” Science Trans. Med., 5, 213ra165.

158. Patterson, A.S., Hsieh, K., Soh, H. T. and Plaxco, K.W. (2013) “Electrochemical real-time nucleic acid amplification: towards the point-of-care quantification of pathogens.” Trends in Biotech., 31, 704-712.

157. Porchetta, A., Vallée-Bélisle, A., Plaxco, K.W. and Ricci, F. (2013) “Allosterically-tunable, DNA-based switches triggered by heavy metals.” J. Am. Chem. Soc., 135, 13238-13241.

156. Bonham, A.J., Paden, N.G., Ricci, F. and Plaxco, K.W. (2013) “An E-DNA scaffold sensor for the electrochemical detection of a non-antibody protein marker in undiluted blood serum.” The Analyst, 138, 5580-5583.

155. Fernández de Ávila, B.E., Watkins, H.M., Pingarrón, J.M., Plaxco, K.W., Palleschi, G. and Ricci, F. (2013) “Determinants of the detection limit and specificity of surface-based biosensors.” Anal. Chem., 85, 6593-6597.

154. Uzawa, T., Isoshima, T., Ito, Y., Ishimori, K., Makarov, D.E. and Plaxco, K.W. (2013) “Sequence and Temperature Dependence of the End-to-End Collision Dynamics of Single-Stranded DNA.” Biophys. J., 104, 2485-2492.

153. Patterson, A.S., Heihoff, D.M., Ferguson, B.S., Soh, H.T., Mahan, M.J. and Plaxco, K.W. (2013) “Microfluidic chip-based detection and discrimination of Salmonella serovars in whole blood using multiplexed isothermal amplification and sequence-specific electrochemical detection.” Appl. Envir. Micro., 79, 2302-2011.


2012
152. Porchetta, A., Vallée-Bélisle, A., Plaxco, K.W. and Ricci, F. (2012) “Using distal site mutations and allosteric inhibition to tune, extend and narrow the useful dynamic range of aptamer-based sensors.” J. Am. Chem. Soc., 134, 20601-20604.

151. Ricci, F., Vallée-Bélisle, A., Porchetta, A., and Plaxco, K.W. (2012) “The rational design of allosteric inhibitors and activators using the population-shift model: in vitro validation and application to an artificial biosensor.” J. Am. Chem. Soc., 134, 15177-15180.

150. Vallée-Bélisle, A., Ricci, F., Uzawa, T., Xia, F. and Plaxco, K.W. (2012) “Bio-electrochemical switches for the quantitative detection of antibodies directly in whole blood.” J. Am. Chem. Soc., 134, 15197-15200.

149. Kang, D., Vallée-Bélisle, A., Porchetta, A., Plaxco, K.W. and Ricci, F. (2012) “Re-engineering electrochemical biosensors to narrow or extend their useful dynamic range.” Angewandte, 51, 6717-6721.

148. Hsieh, K., Patterson, A.S., Ferguson, B.S., Plaxco, K.W. and Soh, T.H. (2012) “Rapid, sensitive, and quantitative detection of pathogenic DNA at the point of care via microfluidic electrochemical quantitative loop-mediated isothermal amplification (MEQ-LAMP).” Angewandte, 20, 4896-4900.

147. Yoo, T.Y., Meisberger, S., Hinshaw, J., Pollack, L., Haran, G., Sosnick, T.R. and Plaxco, K.W. (2012) “Small-angle x-ray scattering and single-molecule FRET spectroscopy produce highly divergent views of the low-denaturant unfolded state.” J. Mol. Biol., 418, 226–236.

146. Bonham, A.J., Hsieh, K., Ferguson, B.S., Vallée-Bélisle, A., Soh, H. T., Ricci, F. and Plaxco, K.W. (2012) “Quantification of transcription factor binding in cell extracts using an electrochemical, structure-switching biosensor.” J. Am. Chem. Soc., 134, 3346-3348.

145. Vallée-Bélisle, A., Ricci, F. and Plaxco, K.W. (2012) “Engineering biosensors with extended, narrowed, or arbitrarily edited dynamic range.”J. Am. Chem. Soc., 134, 2876–2879.

144. Watkins, H.M., Vallée-Bélisle, A., Ricci, F., Makarov, D.E. and Plaxco, K.W. (2012) “Entropic and Electrostatic Effects on the Folding Free Energy of a Surface-Attached Biomolecule: An Experimental and Theoretical Study.”J. Am. Chem. Soc., 134, 2120–2126.

143. Kang D., Xia, F., Zuo, X., White, R., Vallée-Bélisle, A. and Plaxco, K.W. (2012) “DNA-based, biomolecular-electronic encoder and decoder devices constructed by multiplex biochip.” NPG Asia Mat., 4, e1.

142. Perez Rafael, S., Vallée-Bélisle, A., Fabregas, E., Plaxco, K., Palleschi, G. and Ricci, F. (2012) “Employing the metabolic ‘branch point effect’ to generate an all-or-none, digital-like response in enzymatic outputs and enzyme-based sensors.” Anal. Chem., 84, 1076–1082.

141. White, R.J., Kallewaard, H.M., Hsieh, W., Patterson, A.S., Kasehagen, J.B., Cash, K.J., Uzawa, T., Soh, H.T. and Plaxco, K.W. (2011) “Wash-free, Electrochemical Platform for the Quantitative, Multiplexed Detection of Specific Antibodies.” Anal. Chem., 841098-1103.

140. Biagiotti, V., Porchetta, A., Desiderati, S., Plaxco, K.W., Palleschi, G., Ricci, F. (2012) “Probe accessibility effects on the performance of electrochemical biosensors employing DNA monolayers.” Anal. Bioanal. Chem., 402, 413-21.


2011
139. Zuo, X., Xia, F., Patterson, A., Soh, H.T., Xiao, Y. and Plaxco, K.W. (2011) “Two step, PCR-free telomerase detection by using exonuclease III aided target recycling.” ChemBioChem, 12(18), 2745-2747.

138. Rowe, A.A., Chuh, K.N., Lubin, A.A., Miller, E.A., Cook, B., Hollis, D. and Plaxco, K.W. (2011) “Electrochemical Biosensors Employing an Internal Electrode Attachment Site Achieving Reversible, High Gain Detection of Specific Nucleic Acid Sequences.” Anal. Chem., 83, 9462–9466.

137. Hsieh, K., White, R., Ferguson, B., Plaxco, K.W., Xiao, Y. and Soh, H. (2011) “Polarity-Switching Electrochemical Sensor for Specific Detection of Single-Nucleotide Mismatches.” Angewandte Chemie, Int. Ed., 50(47), 11176-11180.

136. Ricci, F., Vallée-Bélisle, A. and Plaxco, K.W. (2011) “High-Precision, In Vitro Validation of the Sequestration Mechanism for Generating Ultrasensitive Dose-Response Curves in Regulatory Networks.” PLoS Computational Biology, 7(10): e1002171.

135. Rowe, A.A., Bonham, A.J., White, R.J., Zimmer, M.P., Yadgar, R.J., Hobza, T.M., Honea, J., Ben-Yaacov, I. and Plaxco, K.W. (2011) “CheapStat: an open-source, “do-it-yourself” potentiostat for analytical and educational applications.” PLoS I, 6, e23783.

134. Vallée-Bélisle, A., Bonham, A.J., Reich, N.O., Ricci, F. and Plaxco, K.W. (2011) “Transcription Factor Beacons for the Quantitative Detection of DNA Binding Activity.” J. Am. Chem. Soc., 133, 13836-13839.

133. Vinh, N.Q., Allen, S.J. and Plaxco, K.W. (2011) “Dielectric spectroscopy of proteins as a quantitative experimental test of computational models of their low-frequency harmonic motions.” J. Am. Chem. Soc., 133, 8942-8947.

132. Rowe, A.A., White, R.J., Bonham, A.J. and Plaxco, K.W. (2011) “Fabrication of electrochemical-DNA biosensors for the reagentless detection of nucleic acids, proteins and small molecules.” J. Vis. Expts., 52, 2922.

131. Abelow, A.E., White, R.J., Plaxco, K.W. and Zharov, I. (2011) “Nanoporous Silica Colloidal Films with Molecular Transport Gated by Aptamers Responsive to Small Molecules.” Coll. Czech. Chem. Comm., 76, 683-694.

130. Plaxco, K.W. and Soh, H.T. (2011) “Switch based biosensors: a new approach towards real-time, in vivo molecular detection.” Trends Biotech., 29, 1-5.


2010

129. Cheng, R.R., Uzawa, T., Plaxco, K.W. and Makarov, D.E. (2010) “Universality in the timescales of internal loop formation in unfolded proteins and single-stranded oligonucleotides.” Biophys. J., 99, 3959-3968.

128. Plaxco, K.W. (2010) “The art of writing science.” Prot. Sci., 19, 2261–2266.

127. Uzawa, T., Cheng, R.R., White, R.J., Makarov, D.E and Plaxco, K.W. (2010) “A mechanistic study of electron transfer from the distal termini of electrode-bound, single-stranded DNAs.” J. Am. Chem. Soc., 132, 16120–16126.

126. Patterson, A., Caprio, F., Vallée-Bélisle, A., Moscone, D., Plaxco, K.W., Palleschi, G. and Ricci, F. (2010) “Using triplex forming oligonucleotide probes for the reagentless, electrochemical detection of double stranded DNA.” Anal. Chem., 82, 9109–9115.

125. Xiao, Y., Dane, K.Y., Uzawa, T., Csordas, A., Qian, J., Soh, H.T., Daugherty, P.S., Lagally, E.T., Heeger, A.J., and Plaxco, K.W. (2010) “Detection of telomerase activity in high concentration of cell lysates using primer-modified gold nanoparticles.” J. Am. Chem. Soc., 132, 15299-15307.

124. Xia, F., White, R., Zuo, X., Patterson, A., Xiao, Y., Kang, D., Gong, X., Plaxco, K.W. and Heeger, A.J. (2010) “An electrochemical super-sandwich assay for sensitive and selective DNA detection in serum.” J. Am. Chem. Soc., 132, 14346–14348.

123. Abelow, A.E., Schepelina, O., White, R.J., Vallée-Bélisle, A., Plaxco, K.W. and Zharov, I. (2010) “Biomimetic glass nanopores employing aptamer gates responsive to a small molecule.” Chem. Com., 46, 7984-7986.

122. Lawrence, C., Kuge, J., Ahmad, K. and Plaxco, K.W. (2010) “Investigation of an anomalously accelerating substitution in the folding of a prototypical two-state protein.” J. Mol. Bio., 403, 446-458.

121. Rowe, A.A., Miller, E. and Plaxco, K.W. (2010) “Rapid, reagentless measurement of aminoglycoside antibiotics in blood serum via an electrochemical, RNA aptamer-based biosensor.” Anal. Chem., 82, 7090–7095.

120. Vallée-Bélisle, A. and Plaxco, K.W. (2010) “Structure-switching biosensors: inspired by nature.” Curr. Op. Struc. Biol., 20, 518-526.

119. Xia, F., Zuo, X., Yang, R., Xioa, Y., Kang, D., Gong, X., White, R., Lubin, A.A., Vallée-Bélisle, A., Yuen, J.D., Hsu, Y.B.B. and Plaxco, K.W. (2010) “Label-free, dual-analyte electrochemical biosensors: a new class of molecular-electronic logic gates.” J. Am. Chem. Soc., 132, 8557–8559.

118. Xia, F., Zuo, X., Yang, R., Xiao, Y., Kang, D., Vallée-Bélisle, A., Gong, X., Yuen, J.D., Hsu, B.Y., Heeger, A.J. and Plaxco, K.W. (2010) “Colorimetric detection of DNA, small molecules, proteins, and ions using unmodified gold nanoparticles and conjugated polyelectrolytes.” Proc. Natl. Acad. Sci. USA, 107, 10837-10841.

117. Lubin, A.A. and Plaxco, K.W. (2010) “Folding-based electrochemical biosensors: the case for responsive nucleic acid architectures.” Acc. Chem. Res., 43, 496–505.

116. Xia, F., Zuo, X., Yang, R., Xiao, Y., Kang, D., Vallée-Bélisle, A., Gong, X., Heeger, A.J. and Plaxco, K.W. (2010) “On the binding of cationic, water-soluble conjugated polyelectrolytes to DNA: electrostatic and hydrophobic interactions.” J. Am. Chem. Soc., 132, 1252–1254.

115. Ricci, F., Adornetto, G., Moscone, D., Plaxco, K.W. and Palleschi, G. (2010) “Quantitative, reagentless, single-step electronic detection of anti-DNA antibodies directly in blood serum.” Chem. Comm., 46, 1742-1744.

114. Wickersham, C.E., Cash, K.J., Pfeil, S.H., Bruck, I., Kaplan, D.L., Plaxco, K.W. and Lipman, E.A. (2010) “Tracking a molecular motor with a nanoscale optical encoder.” Nano. Let., 10, 1022-1027.

113. White, R.J., Rowe, A.A., and Plaxco, K.W (2010) “Re-engineering aptamers to support reagentless, self-reporting electrochemical sensors.” The Analyst, 135, 589-594.

112. Zuo, X., Xia, F., Xiao, Y. and Plaxco, K.W. (2010) “A sensitive and selective, amplified fluorescent DNA detection based on exonuclease III aided target recycling.” J. Am. Chem. Soc, 132, 1816-1818.

111. Kahn, K. and Plaxco, K.W. (2010) “Principles of biomolecular recognition.” In: Recognition Receptors in Biosensors, M. Zourob, Ed., Springer, pp 3-45.

110. White, R.J. and Plaxco, K.W. (2010) “Exploiting binding-induced changes in probe flexibility for the optimization of electrochemical biosensors.” Anal. Chem., 82, 73-76.


2009

109. Xiao, Y., Lou, X.H., Uzawa, T., Plakos, K.J.I., Plaxco, K.W. and Soh, H.T. (2009) “An electrochemical sensor for single nucleotide polymorphism detection in serum based on a triple-stem DNA probe.” J. Am. Chem. Soc., 131, 15311-15316.

108. Kang, D., Zuo, X., Yang, R., Xia, F., Plaxco, K.W. and White, R.J. (2009) “Comparing the properties of electrochemical-based DNA sensors employing different redox tags.” Anal. Chem., 81, 9109-9113.

107. Cheng, R.R., Uzawa, T., Plaxco, K.W. and Makarov, D.E. (2009) “The rate of intramolecular loop formation in DNA and polypeptides: The absence of the diffusion-controlled limit and fractional power law viscosity dependence.” J. Chem. Phys. B, 113, 14026–14034.

106. Kohn, J.E., Gillespie, B. and Plaxco, K.W. (2009) “Non-sequence-specific interactions can account for the compaction of proteins unfolded under ‘native’ conditions.” J. Mol. Biol., 394, 343–350.

105. Cash, K.J., Ricci, F. and Plaxco, K.W. (2009) “A general electrochemical method for label-free screening of protein-small molecule interactions.” Chem. Comm., 6222 – 6224.

104. Makarov, D.E. and Plaxco, K.W. (2009) “Measuring distances within unfolded biopolymers using fluorescence resonance energy transfer: The effect of polymer chain dynamics on the observed fluorescence resonance energy transfer efficiency.” J. Chem. Phys., 131 Art. No. 085105.

103. Vallée-Bélisle, A., Ricci, F. and Plaxco, K.W. (2009) “Thermodynamic basis for the optimization of binding-induced biomolecular switches and structure-switching biosensors.” Proc. Natl. Acad. Sci. USA, 106, 13802-13807.

102. Ricci, F., Zari, N., Caprio, F., Recine, S., Amine, A., Moscone, D., Palleschi, G. and Plaxco, K.W. (2009) “Surface chemistry effects on the performance of an electrochemical DNA sensor.” Bioelectrochemistry, 76, 208-213.

101. Uzawa, T., Cheng, R.R., Cash, K.J., Makarov, D.E. and Plaxco, K.W. (2009) “Characterization of the length and viscosity dependence of the end-to-end collision dynamics of single-stranded DNA.” Biophys. J., 97, 205-210.

100. Xiao, Y., Plakos, J.J.I., Lou, X., Qian, J., White, R.J., Plaxco, K.W. and Soh, H.T. (2009) “Fluorescence detection of single-nucleotide polymorphisms with a single, self-complementary, triple-stem DNA probe.” Angewante, 48, 4354-4358.

99. Xiao, Y., Uzawa, T., White, R.J., DeMartini, D. and Plaxco, K.W. (2009) “On the signaling of electrochemical, aptamer-based sensors: collision- and folding-based mechanisms.” Electroanalysis, 21, 1267 – 1271.

98. Zuo, X., Xiao, Y. and Plaxco, K.W. (2009) “High specificity, electrochemical sandwich assays based on single aptamer sequences and suitable for the direct detection of small-molecule targets in blood and other complex matrices.” J. Am. Chem. Soc., 131, 6944-6945.

97. Cash, K.J., Ricci, F. and Plaxco, K.W. (2009) “An electrochemical sensor for the detection of protein-small molecule interactions directly in serum and other complex matrices.” J. Am. Chem. Soc., 131, 6955-6957.

96. White, R.J. and Plaxco, K.W. (2009) “Engineering new aptamer geometries for electrochemical aptamer-based sensors.” In: Proc. SPIE Bio-Inspired/Biomimetic Sensor Technologies and Applications, N.F. Fell and V.S. Swaminathan Eds., 7321, 5.1-5.9.

95. Swenson, J.S., Xiao, Y., Ferguson, B.S., Lai, R.Y., Heeger, A.J., Plaxco, K.W. and Soh, T. (2009) “Continuous, real-time monitoring of cocaine in undiluted, unmodified blood serum via a microfluidic, aptamer-based sensor.” J. Am. Chem. Soc., 131, 4262–4266.

94. Plaxco, K.W. (2009) “Breaking symmetry.” Chem. World, 6, 61.

93. Lubin, A.A., Vander Stoep Hunt, B. and Plaxco, K.W. (2009) “The effects of probe length, probe geometry and redox-tag placement on the performance of the electrochemical E-DNA sensor .” Anal. Chem., 81, 2150–2158.

92. Xiao, Y. and Plaxco, K.W. (2009) “Electrochemical aptamer sensors.” in: Functional nucleic acids for sensing and other analytical applications, Y. Lu and Y. Li, Eds. pp 179-198, Springer, New York.

91. Oh, K.J., Cash, K.J. and Plaxco, K.W. (2009) “Beyond Molecular Beacons: optical sensors based on the binding-induced folding of proteins and polypeptides.” Chem. Europ. J., 15, 2244-2251.

90. Ricci, F., Bonham, A.J., Reich, N.O. and Plaxco, K.W. (2009) “A reagentless, electrochemical approach for the specific detection of double- and single-stranded DNA binding proteins.” Anal. Chem., 81, 1608-1614.

89. Phares, N., White, R.J. and Plaxco, K.W. (2009) “Improving the stability and sensing of electrochemical biosensors by employing trithiol-anchoring groups in a six-carbon self-assembled monolayer.” Anal. Chem., 81, 1095-1100.

88. Cash, K.J., Heeger, A.J., Plaxco, K.W. and Xiao, Y. (2009) “Optimization of a reusable, DNA pseudoknot-based electrochemical sensor for sequence-specific DNA detection in blood serum.” Anal. Chem., 81, 656-661.

87. Plaxco, K.W. and Gross, M. (2009) “Protein complexes: The evolution of symmetry.” Curr. Biol.19, R25-26.

86. Ruczinski, I. and Plaxco, K.W. (2009) “Some recommendations for the practitioner to improve the precision of experimentally determined protein folding rates and f values.”Proteins, Struc. Func. Genet., 74, 461-474.


2008

85. Ricci, F. and Plaxco, K.W. (2008) “E-DNA: a convenient, label-free method for the electrochemical detection of hybridization.” Microchim. Acta, 163, 149-155.

84. White, R.J., Phares, N., Lubin, A.A. Xiao, Y. and Plaxco, K.W. (2008) “Optimization of electrochemical aptamer-based sensors by controlling surface probe densities and surface attachment chemistry.” Langmuir24, 10513–10518.

83. Pavel, I., McCarney, E., Elkhaled, A., Morrill, A., Plaxco, K. and Moskivits, M. (2008) “Label-free SERS detection of small proteins modified to act as bifunctional linkers.”J. Phys. Chem., 112, pp 4880 – 4883.

82. Pavlovic, E., Lai, R.Y., Wu, T.T., Ferguson, B.S., Sun, R., Plaxco, K.W. and Soh, H.T. (2008) “Specific, electrochemical detection of multiple DNA sequences in an integrated microfluidic system.” Anal. Chem., 24, 1102 – 1107.

81. Lubin, A.A., Fan, C., Schafer, M., Clelland, C.T., Bancroft, C., Heeger, A.J. and Plaxco, K.W. (2008) “Rapid, electronic detection of DNA and non-natural DNA analogs for molecular marking applications.” For. Sci. Comm., 10 (1).

80. Xu, J., Plaxco, K.W. and Allen, S.J. (2008) “THz spectroscopy of proteins in water: direct absorption and circular dichroism.” Int. J. High Speed Elec. Sys.17, 709-718.


2007

79. Oh, K. J., Cash, K.J., Lubin, A.A. and Plaxco, K.W. (2007) “Chimeric peptide beacons: a direct polypeptide analog of DNA molecular beacons.” Chem. Comm., 4869 – 4871.

78. Xiao, Y., Lai, R.Y., and Plaxco, K.W. (2007) “Preparation of electrode-immobilized, redox- modified oligonucleotides for electrochemical DNA and aptamer-based sensing.” Nature Prot., 2, 2875 – 2880.

77. Xiao, Y., Qu, X., Plaxco, K.W. and Heeger, A.J. (2007) “Label-free electrochemical detection of DNA in blood serum via target-induced resolution of an electrode-bound DNA pseudoknot.” J. Am. Chem. Soc., 129, 11896 – 11897.

76. Ricci, F., Lai, R.Y. and Plaxco, K.W. (2007) “Linear, redox modified DNA probes as electrochemical DNA sensors.” Chem. Comm., 3768-3770.

75. Wang, Z., Plaxco, K.W., and Makarov, D.E. (2007) “Influence of local, residual structure on the scaling behavior and dimensions of unfolded proteins.” Biophys. J.86, 321-328.

74. Ricci, F., Lai, R.Y., Heeger, A.J., Plaxco, K.W. and Sumner, J.J. (2007) “Effect of molecular crowding on the response of an electrochemical DNA sensor.” Langmuir, 23, 6827-6834.

73. Oh, K.J., Cash, K.J., Hugenberg, V. and Plaxco, K.W. (2007) “Peptide beacons: A new design for polypeptide-based optical biosensors.” Bioconj. Chem.18, 607-609.

72. Werner, J.H., McCarney, E.R., Keller, R.A., Plaxco, K.W. and Goodwin, P.M. (2007) “Increasing the resolution of single pair energy transfer measurements.” Anal. Chem.,79, 3509-3513.

71. Plaxco, K.W. (2007) “A biologist’s perspective on Astrobiology.” Guest essay in Universe, 8th Ed by Freedman, R.A and Kaufmann, W.J., W.H. Freeman & Company, New York, NY, pp. 28-17.

70. Xiao, Y., Rowe, A.A. and Plaxco, K.W. (2007) “Electrochemical detection of parts per billion lead via an electrode-bound DNAzyme assembly.” J. Am. Chem. Soc., 129, 262 – 26.

69. Xu, J., Plaxco, K.W., Allen, S.J., Bjarnason, J.E. and Brown, E.R. (2007) “0.15 – 3.72 terahertz absorption of aqueous salts and saline solutions.” J. Chem. Phys., 90, 03190.

68. Lai, R.Y., Plaxco, K.W. and Heeger, A.J. (2007) “Rapid, aptamer-based electrochemical detection of platelet-derived growth factor at picomolar concentrations directly in blood serum.” Anal. Chem., 79, 229-233.


2006

67. Xu, J., Plaxco, K.W. and Allen, S.J. (2006) “The collective dynamics of lysozyme in water: terahertz absorption spectroscopy and comparison with theory.” J. Phys. Chem,,110, 24255-24259.

66. Lai, R.Y, Seferos, D.S., Heeger, A.J., Bazan, G.C. and Plaxco, K.W. (2006) “Comparison of the signaling and stability of electrochemical DNA sensors fabricated from 6- or 11- carbon self-assembled monolayers.” Langmuir, 22, 10790-10800.

65. Seferos, D.S., Lai, R.Y., Plaxco, K.W. and Bazan, G.C. (2006) “a,w-Dithiol oligo(phenylenevinylene)s for the preparation of high-quality conjugated SAMs andnanoparticle functionalized electrodes.” Adv. Funct. Mat., 16, 2387–2392.

64. Oh, K.J, Cash, K.J. and Plaxco, K.W. (2006) “Excimer-based peptide beacons; a convenient experimental approach for monitoring polypeptide-protein and polypeptide-oligonucleotide interactions.” J. Am. Chem. Soc., 128, 14018-14019.

63. Xiao, Y, Lubin, A.A., Baker, B.R., Plaxco, K.W. and Heeger, A.J. (2006) “Single-step electronic detection of femtomolar DNA by target-induced strand displacement in an electrode-bound duplex.” Proc. Natl. Acad. Sci. USA, 103, 16677-16680.

62. Ruczinski, I., Sosnick, T.R. and Plaxco, K.W. (2006) “Methods for the accurate estimation of confidence intervals on experimental f values.” Prot. Sci.15, 2257-2264.

61. Lubin, A.A, Lai, R.Y., Heeger, A.J. and Plaxco, K.W. (2006) “On the sequence specificity, selectivity and reusability of E-DNA, a reagentless, electronic DNA sensor.”Anal. Chem., 78, 5671-5677.

60. Faisca, P.F.N. and Plaxco, K.W. (2006) “Cooperativity and the origins of rapid, single- exponential kinetics in protein folding.” Prot. Sci., 15, 1608-1618.

59. Xu, J., Plaxco, K.W. and Allen, S.J. (2006) “0.3 – 3.72 Terahertz absorption spectroscopy of a protein in liquid water.” Prot. Sci, 15, 1175-1181.

58. Baker, B.R., Lai, R.Y., Wood, M.S., Doctor, E.H., Heeger, A.J. and Plaxco, K.W. (2006) “An electronic, aptamer-based small molecule sensor for the rapid, reagentlessdetection of cocaine in adulterated samples and biological fluids.” J. Am. Chem. Soc. 128, 3138-3139.

57. Lai, R.Y., Lagally, E.T., Lee, S.-H., Soh, T.H., Plaxco, K.W. and Heeger, A.J. (2006) “Rapid, sequence-specific detection of unpurified PCR amplicons via a reusable, electrochemical sensor.” Proc. Natl. Acad. Sci. USA103, 4017-4021.

56. Lai, R.Y, Lee, S-H., Soh, H., Plaxco, K.W. and Heeger, A.J. (2006) “Differential labeling of closely-spaced biosensor electrodes via electrochemical lithography.”Langmiur22, 1932-1936.

55. de los Rios, M.A., Muralidhara, B.K., Wildes, D., Marqusee, S., Wittung-Stafshed, P., Plaxco, K.W. and Ruczinski, I. (2006) “On the precision of experimentally determined folding rates and f-values.” Prot. Sci., 15, 553-563.

54. Xu, J., Plaxco, K.W. and Allen, S.J. (2006) “Absorption spectra of liquid water and aqueous buffers between 0.3 – 3.72 terahertz.” J. Chem. Phys. 124, 03610.


2005

53. Xiao, Y., Piorek, B.D., Plaxco, K.W. and Heeger, A.J. (2005) “A reagentless, signal-on design for electronic aptamer-based sensors via target-induced strand displacement.” J. Am. Chem. Soc., 127, 17990-17991.

52. de los Rios, M.A., Danashi, M. and Plaxco, K.W. (2005) “Experimental investigation of the frequency and substitution dependence of negative f-values in two-state proteins.” Biochemistry44, 12160 -12167.

51. McCarney, E.R., Werner, J.H., Ruczinski, I., Makarov, Goodwin, P.M. and Plaxco, K.W. (2005) “Random coil dimensions in a highly denatured protein; A single molecule study.” J. Mol. Biol., 352, 672-682.

50. Xiao, Y., Lubin, A.A., Heeger, A.J. and Plaxco, K.W. (2005) “Label-free electronic detection of thrombin in blood serum using an aptamer based sensor.” Angw. Chem. Int. Ed., 44, 2-5.

49. McCarney, E.R., Kohn, J.E. and Plaxco, K.W. (2005) “Is there or isn’t there? The case for (and against) residual structure in chemically denatured proteins.” Crit. Rev.Bioch. Mol. Biol., 40, 181-189.

48. Kohn, J.E. and Plaxco, K.W. (2005) “Engineering of a signal-transduction mechanism for protein-based biosensors.” Proc. Natl. Acad. Sci. USA, 102, 10841-10845.

47. Fan, C., Plaxco, K.W. and Heeger, A.J. (2005) Ligand-modulated electron- or energy- transfer as a biosensor signaling mechanism.” Trends Biotech., 23,186-192.

46. Maxwell, K.L., Wildes, D., Zarrine-Afsar, A., de los Rios, M.A., Brown, A.G., Friel, C.T, Hedberg, L., Horng, J-C., Bona, D., Miller, E.J., Vallée-Bélisle, A., Main, E.R.G., Bemporad, F., Qiu, L., Teilum, K., Vu, N.-D., Edwards, A.M., Ruczinski, I., Poulsen, F.M., Kragelund, B.B., Michnick, S.W., Chiti, F., Bai, Y., Hagen, S.J., Serrano, L., Oliveberg, M., Raleigh, D.P., Wittung-Stafshede, P., Radford, S.E., Jackson, S.E., Sosnick, T.R., Marqusee, S., Davidson, A.R., Plaxco, K.W. (2005) “Protein folding: defining a ‘standard’ set of experimental conditions and a preliminary kinetic data set of two-state proteins.” Prot. Sci., 14, 602-616.

45. de los Rios, M.A. and Plaxco, K.W. (2005) “Apparent Debye-Huckel electrostatic effects in the folding of a simple, single domain protein.” Biochemistry, 44, 1243-1250.

44. Raleigh, D.S. and Plaxco, K.W. (2005) “Plasticity and heterogeneity in the folding nucleus; what are f-values really telling us?” Prot. Pep. Sci.12, 117-122.


2004

43. Xu, J., Ramian, G.J., Galan, J.F., Savvidis, P.G., Scopatz, A.M., Birge, R.R., Allen, S.J. and Plaxco, K. (2004) “Terahertz circular dichroism spectroscopy of biomolecules.” In: Chemical and Biological Standoff Detection. J.O. Jensen and J-M. Theriault, Eds. Proceedings of the SPIE, Vol. 5268, pp 19-26.

42. Gillespie, B. and Plaxco, K.W. (2004) “Can theory predict two-state protein folding rates? An experimental perspective.” In: Forces, Growth and Form in Soft Condensed Matter: At the Interface between Physics and Biology, Skjeltorp, A.T. and Velushkin, A.V., Eds, Kluwer Academic Publishers BV, Dordrecht, Netherlands,pp 93-111.

41. Kohn, J.E., Millett, I.S., Jacob, J., Zagrovic, B., Dillon, T., Cingel, N., Seifert, S., Thiyagarajan, P., Sosnick. T.R., Ruczinski, I., Hasan, M.Z., Pande, V.S. Doniach, S. and Plaxco, K.W (2004) “Do the dimensions of chemically unfolded proteins differ significantly from the expectations of a random-coil model?” Proc. Natl. Acad. Sci. USA,101, 12491-12496.

40. Gillespie, B. and Plaxco, K.W. (2004) “Using protein folding rates to test protein folding theories.” Ann. Rev. Biochem. Biophys., 73, 837-859.


2003

39. Xu, J., Ramian, G.J., Galan, J.F., Savvidis, P.G., Scopatz, A.M., Birge, R.R. Allen, S.J. and 38. Plaxco, K.W. (2003) “Terahertz circular dichroism spectroscopy: a potential approach to unbiased, in situ life detection.” Astrobiology, 3, 489-504.

37. Ivankov, D.N., Alm, E., Plaxco, K.W., Baker, D. and Finkelstein, A.V. (2003) “Contact order revisited: the influence of protein size on folding rates.” Prot. Sci., 12, 2057-2062.

36. Fan, C., Plaxco, K.W. and Heeger, A.J. (2003) “Electrochemical interrogation of conformational changes as a reagentless method for the sequence-specific detection of DNA.” Proc. Natl. Acad. Sci. USA, 100, 9134-9137.

35. Gillespie, B., Vu, D., Shah, P.S., Marshall, S., Dyer, R.B., Mayo, S.L., and Plaxco, K.W. (2003) “NMR and Temperature Jump measurements of de novo designed proteins demonstrate rapid folding in the absence of explicit selection for kinetics.” J. Mol. Bio., 330, 813-819.

34. Calloni, G., Taddei, N., Plaxco, K.W., Ramponi, G., Stefani, M. and Chiti, F. (2003) “Comparison of the folding processes of distantly related proteins. Importance of hydrophobic content in folding.” J. Mol. Bio., 330, 577-591.

33. Fan, C., Wang, S., Hong, J.M., Bazan, G.C., Plaxco, K.W. and Heeger, A.J. (2003) “Beyond superquenching: hyper-efficient energy transfer from conjugated polymers to gold nanoparticles.” Proc. Natl. Acad. Sci. USA, 100, 6297-6301.

32. Fan,C., Hirasa, T., Plaxco, K.W. and Heeger, A.J. (2003) “Photoluminescence quenching of water-soluble conjugated polymers by viologen derivatives: effect of hydrophobicity.” Langmiur, 19, 3554-3556.

31. Jewett, A., Pande, V.S. and Plaxco, K.W. (2003) “Cooperativity, smooth energy landscapes and the origins of topology-dependent protein folding rates.” J. MolBio., 326, 247-253.

30. Makarov, D.E. and Plaxco, K.W. (2003) “The topomer search model: a quantitative, first- principles description of two-state protein folding kinetics.” Prot. Sci., 12, 17-26.


2002

29. Fan, C., Gillespie, B., Wang, G., Heeger, A.J. and Plaxco, K.W. (2002) “Spectroscopy and electrochemistry of the pyridine-chytochrome c complex and the pyridine-induced ‘ alkaline-like’ conformation.” J. Phys. Chem. B, 106, 11375-11383.

28. Millett, I.S., Doniach, S. and Plaxco, K.W. (2002) “Towards a taxonomy of the denatured state: small angle scattering studies of unfolded proteins.” Adv. Prot. Chem.62, 241-262.

27. Thompson, J.B., Hansma, H.H., Hansma, P.K. and Plaxco, K.W. (2002) “The backbone conformational entropy of protein folding: experimental measures from atomic force microscopy.” J. Mol. Bio., 322, 645-652.

26. Fan, C., Plaxco, K.W. and Heeger, A.J. (2002) “High-efficiency fluorescence quenching of conjugated polymers by proteins.” J. Am. Chem. Soc., 124, 5642-5643.

25. Larson, S., Ruczinski, I., Davidson, A.R., Baker, D. and Plaxco, K.W. (2002) “Residues participating in the protein folding nucleus do not exhibit preferential evolutionary conservation.” J. Mol. Biol., 316, 225-233.

24. Makarov, D.E., Keller, C.A., Plaxco, K.W. and Metiu, H. (2002) “How the folding rate constant of simple-single domain proteins depends on number of native contacts.”Proc. Natl. Acad. Sci. USA, 99, 3535-3539.

23. Millet, I.S., Townsley, L., Chiti, F., Doniach, S. and Plaxco, K.W. (2002) “Equilibrium collapse and the kinetic ‘foldability’ of proteins.” Biochemistry, 41, 321-325.


2001

22. Plaxco, K.W. and Gross, M. (2001) “Unfolded, yes, but random? Never!” Nat. Struct. Biol., 8, 659-670.


2000

21. Gillespie, B. and Plaxco, K.W. (2000) “Non-glassy kinetics in the folding of a simple, single domain protein.” Proc. Natl. Acad. Sci. USA, 97, 12014-12019.

20. Plaxco, K.W., Simons, K.T., Ruczinski, I. and Baker, D. (2000) “Sequence, stability, topology and length; the determinants of two-state protein folding kinetics.”Biochemistry, 39, 11177–11183.

19. Plaxco, K.W., Larson, S., Ruczinski, I., Riddle, D.S., Thayer, E.C., Buchwitz, B., Davidson, A.R. and Baker, D. (2000) “Evolutionary conservation in protein folding kinetics.” J. Mol. Biol., 298, 303-312.


1999

18. Viani, M.B., Schaffer, T.E., Paloczi, G.T., Pietrasanta, L., Smith, B.L, Thompson, J.B., Reif, M., Gaub, H.E., Plaxco, K.W., Cleland, A., Hansma, H.G. and Hansma, P.K. (1999) “Fast imaging and fast force spectroscopy of single biopolymers with anew atomic force microscope designed for small cantilevers.” Rev. Sci. Inst., 70, 4300-4303.

17. Plaxco, K.W., Millett, I.S., Segel, D.J., Doniach, S. and Baker, D. (1999) “Polypeptide chain collapse can occur concomitantly with the rate limiting step in protein folding.”Nat. Struct. Biol., 6, 554-557.


1998

16. Plaxco, K.W. and Dobson, C.M. (1998) “Monitoring protein folding using time-resolved biophysical techniques.” in Protein Dynamics, Function and Design, O. Jardetzkyand J. Lefevre, eds., Plenum Press, New York, pp 331-332.

15. Plaxco, K.W. and Baker, D. (1998) “Limited internal friction in the rate limiting conformational change of a two-state protein folding reaction.” Proc. Natl. Acad. Sci. USA,95, 13591-13596.

14. Plaxco, K.W. (1998) “Protein chemistry comes of age. Again.” Trends in Biotech., 16, 278.

Plaxco, K.W., Simons, K.T. and Baker, D. (1998) “Contact order, transition state placement and the refolding rates of single domain proteins.” J. Mol. Biol., 277, 985-994.

13. Plaxco, K.W., Riddle, D.S., Grantcharova, V. and Baker, D. (1998) “Simplified proteins: Minimalist solutions of the ‘protein folding problem’.” Curr. Op. Struct. Biol, 8, 80-85.

12. Guijarro, J.I., Morton, C.J., Plaxco, K.W., Campbell, I.D. and Dobson, C.M. (1998) “Folding kinetics of the SH3 domain of PI3 by real-time NMR and optical techniques.”J. Mol. Biol., 275, 657-667.

11. Plaxco, K.W., Guijarro, J.I., Morton, C.J., Pitkeathly, M., Campbell, I.D. and Dobson, C.M. (1998) “The folding kinetics and thermodynamics of the FynSH3 domain.” Biochemistry37, 2529-2537.


1997

10. O’Brien, R., Wynn, R., Driscoll, P.C., Davis, B., Plaxco, K.W., Sturtevant, J.M. and Ladbury, J.E. (1997) “The adaptability of Escherichia coli thioredoxin to non-conservative amino acid substitutions.” Prot. Sci., 6, 1325-133.

9. Gross, M. and Plaxco, K.W. (1997) “Protein engineering: reading, writing and re-designing.” Nature367, 419-420.

8. Plaxco, K.W., Morton, C.J., Grimshaw, S., Jones, J.A., Pitkeathly, M., Campbell, I.D. and Dobson, C.M. (1997) “The effects of guanidine hydrochloride on the ‘random coil’ conformations and NMR chemical shifts of the peptide series GGXGG.” J. Biomolec. NMR10, 221-230.

7. Plaxco K.W. and Gross, M. (1997) “The importance of being unfolded.” Nature386, 657-659.

6. Plaxco, K.W., Spitzfaden, C., Campbell, I.D. and Dobson, C.M. (1997) “Comparison of the folding kinetics and thermodynamics of two homologous fibronectin type III modules.” J. Mol. Biol270, 763-770.


1996

5. Plaxco, K.W. and Dobson, C.M. (1996) “Time-resolved biophysical methods in the study of protein folding.” Curr. Opin. Struc. Biol., 6, 630-636.

4. Plaxco, K.W., Spitzfaden, C., Campbell, I.D. and Dobson, C.M. (1996) “Rapid folding of a proline rich, all beta-sheet fibronectin type III domain.” Proc. Natl. Acad. Sci. USA93, 10703-10706.


Pre-1996

3. Plaxco, K.W. and Goddard, W.A. III (1994) “Contributions of the thymine methyl group to the specific recognition of poly- and mono-nucleotides: An analysis of the relative free energy of solvation of thymine and uracil.” Biochemistry33, 3050-3054.

2. Plaxco, K.W., Mathiowetz, A.A. and Goddard, W.A. (1989) “Predictions of structural elements for the binding of hin recombinase with the hix site of DNA.” Proc. Nat. Acad. Sci. USA86, 9841-9845.

1. Mason, F.R., Leong, F-C., Plaxco, K.W. and Morton, T.H. (1985) “Two n covalent modification of proteins: Selective labeling of Schiff base forming sites and selective blockade of the sense of smell in vivo.” J. Am. Chem. Soc., 107, 6075-6084.