Plaxco Publications

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Pre-1996

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

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. USA, 86, 9841-9845

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.”  Biochemistry, 33, 3050-3054

1996

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. USA, 93, 10703-10706

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

1997

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. Biol. 270, 763-770

7.     Plaxco K.W. and Gross, M. (1997) “The importance of being unfolded.” Nature, 386, 657-659

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. NMR, 10, 221-230

9.     Gross, M. and Plaxco, K.W. (1997) “Protein engineering: reading, writing and re-designing.” Nature, 367, 419-420

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

1998

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.”  Biochemistry, 37, 2529-2537

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

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

14.  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

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

16.  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

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


1999

18.  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

19.  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

2000

20.  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

21.  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

22.  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

2001

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

2002

24.  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

25.  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

26.  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

27.  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

28.  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

29.  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

30.  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

2003

31.  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

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

33.  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

34.  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

35.  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.

36.  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

37.  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

38.  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

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

2004

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

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

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

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

2005

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

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

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

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

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

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

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

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

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.” Biochemistry, 44, 12160 -12167

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

2006

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, 036101

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

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.” Langmiur, 22, 1932-1936

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. USA, 103, 4017-4021

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, reagentless detection of cocaine in adulterated samples and biological fluids.” J. Am. Chem. Soc. 128, 3138-3139

59.  Xu, J., Plaxco, K.W. and Allen, S.J. (2006) “Probing the collective vibrational dynamics of a protein in liquid water by terahertz absorption spectroscopy.”  Prot. Sci, 15, 1175-1181

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

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

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

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

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

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 and nanoparticle functionalized electrodes.” Adv. Funct. Mat., 16, 2387–2392

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, 10796-10800

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  

2007

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

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, 031908

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 – 263

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

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

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

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

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

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

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

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

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

2008

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

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)

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

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

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.” Langmuir, 24, 10513–10518

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

2009

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

106. 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

107. 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

108. 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

109. 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

2010

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

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

112. 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

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

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

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

116. 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

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

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

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

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

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

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

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

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

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

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

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

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

129. Plaxco, K.W. and Soh, H.T. (2010) “Switch based biosensors: a new approach towards real-time, in vivo molecular detection.Trends Biotech., In press.

130. 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., In press.

Books:

1.     Plaxco, K.W. and Gross, M. (2006) Astrobiology; A Brief Introduction Johns Hopkins University Press. 

2.     Plaxco, K.W. and Gross, M. (2011) Astrobiology; A Brief Introduction 2nd Ed., Johns Hopkins University Press, In press.

Patents:

1.     Plaxco, K.W. and Kayyem, J.F. “Biosensors utilizing ligand-induced conformation changes.” Patent 6432723 Awarded 8/13/03

2.     Xiao, Y., Lubin, A., Plaxco, K.W. “A signal-on architecture for electronic, oligonucleotide-based detectors.” Patent 7803542 Awarded 9/28/10

3.     Fan, F., Heeger, A.J. and Plaxco, K.W. “Reagentless, reusable, bioelectronic detectors.” Submitted 6/03