Peptide Nucleic Acids Methods and Protocols 1st Edition by Peter E Nielsen ISBN 1592592902 9781592592906

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ISBN 10: 1592592902 
ISBN 13: 9781592592906
Author: Peter E Nielsen

Peptide nucleic acids (PNAs) have now existed for slightly more than ten years, with the interest in and applications of this pseudopeptide DNA mimic steadily increasing during the entire period. PNAs have rapidly attracted the attention of scientists from a diversity of fields ranging from (bio)organic and biophysical chemistry to prebiotic evolution, and from molecular biology to genetic diagnostics and drug development. Many of the applications take advantage of the unique properties of PNA—an uncharged pseudopeptide—that distinguish this DNA mimic from more traditional DNA analogs. Rather than trying to create a comprehensive collection of all published methods and protocols involving PNA—many of which have not yet been validated— I have decided to concentrate on select protocols that are either very well established by several groups around the world, such as PCR-clamping and in situ hybridization, or on new methods that may have broader future impact. Basic methods for PNA oligomer synthesis and analyses have also been included. I am very grateful to those friends and colleagues who have enthusiastically contributed their work, discussions, and writing, and thereby made this book possible.

Peptide Nucleic Acids Methods and Protocols 1st Table of contents:

Part I: Introduction to PNA Technology

Chapter 1: PNA Technology: An Overview

• Introduction to Peptide Nucleic Acids (PNA)
• Chemical Structure and Properties of PNA
• Advantages and Disadvantages of PNA in Molecular Biology
• Applications of PNA: A Broad Perspective

Part II: PNA Chemistry and Synthesis

Chapter 2: Solid-Phase Synthesis of PNA Oligomers

• Materials and Reagents
• Step-by-Step Protocol for PNA Synthesis
• Purification and Characterization of PNA
• Troubleshooting and Optimization

Chapter 3: Synthesis of PNA-Peptide Conjugates

• Rationale for PNA-Peptide Conjugates
• Methods for Conjugation
• Purification and Analysis of Conjugates
• Specific Examples and Applications

Chapter 4: Parallel Synthesis of PNA-Peptide Conjugate Libraries

• High-Throughput Approaches to PNA Conjugate Synthesis
• Design and Screening of Libraries
• Applications in Drug Discovery and Diagnostics

Chapter 5: Thermodynamics of PNA Interactions with DNA and RNA

• Principles of PNA-Nucleic Acid Hybridization
• Experimental Methods for Measuring Binding Affinity
• Factors Influencing PNA Binding Specificity

Part III: PNA Technology Applications

Chapter 6: Measurement of PNA Binding to Double-Stranded DNA

• Techniques for Assessing PNA Invasion and Strand Displacement
• Quantitative Methods for Binding Analysis
• Applications in Gene Regulation Studies

Chapter 7: PNA-Mediated Immobilization of Supercoiled DNA

• Protocol for PNA-Directed DNA Immobilization
• Applications in DNA Structure Studies and Biosensors

Chapter 8: PNA Openers and Their Applications

• Design and Mechanism of PNA Openers
• Use in Nucleic Acid Amplification and Detection

Chapter 9: Colorimetric Detection of PNA-DNA Hybridization Using Cyanine Dyes

• Principles of Dye-Based Hybridization Detection
• Protocol for Colorimetric Assays
• Applications in Diagnostics

Part IV: Diagnostic Applications of PNA

Chapter 10: PNA-Mediated PCR Clamping: Applications and Methods

• Principles of PNA Clamping in PCR
• Protocol for Allele-Specific PCR with PNA
• Applications in Mutation Detection and Diagnostics

Chapter 11: PNA Clamping Techniques for the Determination of Oncogene Mutations

• Specific Protocols for Detecting Oncogene Mutations
• Clinical Relevance and Examples

Chapter 12: PNA Fluorescent In Situ Hybridization for Rapid Microbiology and Cytogenetic Analysis

• Principles of PNA FISH
• Protocols for Bacterial Identification and Chromosomal Analysis
• Advantages in Rapid Diagnostics

Chapter 13: Detection of Point Mutations Using PNA-Containing Electrophoresis Matrices

• Design of PNA-Modified Gels
• Electrophoretic Separation of Mutated DNA/RNA
• Applications in Genetic Screening

Part V: Antisense and Antigene Strategies with PNA

Chapter 14: Lipid-Mediated Introduction of Peptide Nucleic Acids into Cells

• Methods for PNA Delivery into Cells
• Liposomal Formulations and Transfection Protocols
• Considerations for In Vitro and In Vivo Delivery

Chapter 15: Synthesis of Cell-Penetrating Peptide-PNA Constructs

• Design and Synthesis of CPP-PNA Conjugates
• Evaluation of Cell Uptake and Efficacy

Chapter 16: Antisense Inhibition of Bacterial Gene Expression and Cell Growth

• PNA as Antimicrobial Agents
• Protocols for Assaying Antisense Activity in Bacteria

Chapter 17: In Vitro Transcription from Peptide Nucleic Acid/DNA Strand Displacement Loops

• Mechanism of PNA-Mediated Transcription Modulation
• Protocols for In Vitro Transcription Assays

Part VI: Animal Studies with PNA

Chapter 18: In Vitro and In Vivo Studies on Pharmacokinetics and Metabolism of PNA Constructs in Rodents

• Methods for Assessing PNA Stability and Distribution
• Pharmacokinetic Profiling in Animal Models
• Considerations for Therapeutic Development

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Tags: Peter E Nielsen, Peptide, Nucleic